10 20 30 40 50 60 70 80 1PJ1 - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER OXIDOREDUCTASE 30-MAY-03 1PJ1
TITLE RIBONUCLEOTIDE REDUCTASE R2-D84E/W48F SOAKED WITH FERROUS TITLE 2 IONS AT PH 5
COMPND MOL_ID: 1; COMPND 2 MOLECULE: RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE 1 BETA COMPND 3 CHAIN; COMPND 4 CHAIN: A, B; COMPND 5 SYNONYM: RIBONUCLEOTIDE REDUCTASE 1, B2 PROTEIN, R2 COMPND 6 PROTEIN; COMPND 7 EC: 1.17.4.1; COMPND 8 ENGINEERED: YES; COMPND 9 MUTATION: YES
SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 GENE: RIR2; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562
KEYWDS FOUR HELIX BUNDLE, DIFERROUS CLUSTER, OXIDOREDUCTASE
EXPDTA X-RAY DIFFRACTION
AUTHOR W.C.VOEGTLI,M.SOMMERHALTER,L.SALEH,J.BALDWIN,J.M.BOLLINGER AUTHOR 2 JR.,A.C.ROSENZWEIG
REVDAT 2 24-FEB-09 1PJ1 1 VERSN REVDAT 1 13-JAN-04 1PJ1 0
JRNL AUTH W.C.VOEGTLI,M.SOMMERHALTER,L.SALEH,J.BALDWIN, JRNL AUTH 2 J.M.BOLLINGER JR.,A.C.ROSENZWEIG JRNL TITL VARIABLE COORDINATION GEOMETRIES AT THE DIIRON(II) JRNL TITL 2 ACTIVE SITE OF RIBONUCLEOTIDE REDUCTASE R2. JRNL REF J.AM.CHEM.SOC. V. 125 15822 2003 JRNL REFN ISSN 0002-7863 JRNL PMID 14677973 JRNL DOI 10.1021/JA0370387
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. 1.95 ANGSTROMS.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.0 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES, PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.95 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 713916.890 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 97.2 REMARK 3 NUMBER OF REFLECTIONS : 51480 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.192 REMARK 3 FREE R VALUE : 0.221 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2580 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.004 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.95 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.07 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 93.70 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 7719 REMARK 3 BIN R VALUE (WORKING SET) : 0.2170 REMARK 3 BIN FREE R VALUE : 0.2560 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.30 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 428 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.012 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5564 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 19 REMARK 3 SOLVENT ATOMS : 305 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 16.80 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.20 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -3.61000 REMARK 3 B22 (A**2) : 1.39000 REMARK 3 B33 (A**2) : 2.22000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.21 REMARK 3 ESD FROM SIGMAA (A) : 0.12 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.24 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.15 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : 1.10 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 18.60 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.77 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.400 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.170 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.410 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.740 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.39 REMARK 3 BSOL : 47.25 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : TOPPER_ION.PARAM REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : TOPPER_ION.TOP REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4 REMARK 4 1PJ1 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 05-JUN-03. REMARK 100 THE RCSB ID CODE IS RCSB019348.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-MAY-00 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL9-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 51480 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.950 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.2 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.95 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.07 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.7 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: PDB ENTRY 1PIU REMARK 200 REMARK 200 REMARK: NULL
REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.32 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.06 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG 4000, 200MM NACL, 50MM MES, REMARK 280 0.3% DIOXANE, PH 6.0, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 310K
REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 37.05000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 57.35000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 42.10000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 57.35000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 37.05000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 42.10000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL
REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 300 REMARK: TETRAMER OF TWO ALPHA AND TWO BETA SUBUNITS
REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 7880 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 24150 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -387.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000
REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 SER A 341 REMARK 465 ASP A 342 REMARK 465 ASN A 343 REMARK 465 VAL A 344 REMARK 465 GLN A 345 REMARK 465 VAL A 346 REMARK 465 ALA A 347 REMARK 465 PRO A 348 REMARK 465 GLN A 349 REMARK 465 GLU A 350 REMARK 465 VAL A 351 REMARK 465 GLU A 352 REMARK 465 VAL A 353 REMARK 465 SER A 354 REMARK 465 SER A 355 REMARK 465 TYR A 356 REMARK 465 LEU A 357 REMARK 465 VAL A 358 REMARK 465 GLY A 359 REMARK 465 GLN A 360 REMARK 465 ILE A 361 REMARK 465 ASP A 362 REMARK 465 SER A 363 REMARK 465 GLU A 364 REMARK 465 VAL A 365 REMARK 465 ASP A 366 REMARK 465 THR A 367 REMARK 465 ASP A 368 REMARK 465 ASP A 369 REMARK 465 LEU A 370 REMARK 465 SER A 371 REMARK 465 ASN A 372 REMARK 465 PHE A 373 REMARK 465 GLN A 374 REMARK 465 LEU A 375 REMARK 465 SER B 341 REMARK 465 ASP B 342 REMARK 465 ASN B 343 REMARK 465 VAL B 344 REMARK 465 GLN B 345 REMARK 465 VAL B 346 REMARK 465 ALA B 347 REMARK 465 PRO B 348 REMARK 465 GLN B 349 REMARK 465 GLU B 350 REMARK 465 VAL B 351 REMARK 465 GLU B 352 REMARK 465 VAL B 353 REMARK 465 SER B 354 REMARK 465 SER B 355 REMARK 465 TYR B 356 REMARK 465 LEU B 357 REMARK 465 VAL B 358 REMARK 465 GLY B 359 REMARK 465 GLN B 360 REMARK 465 ILE B 361 REMARK 465 ASP B 362 REMARK 465 SER B 363 REMARK 465 GLU B 364 REMARK 465 VAL B 365 REMARK 465 ASP B 366 REMARK 465 THR B 367 REMARK 465 ASP B 368 REMARK 465 ASP B 369 REMARK 465 LEU B 370 REMARK 465 SER B 371 REMARK 465 ASN B 372 REMARK 465 PHE B 373 REMARK 465 GLN B 374 REMARK 465 LEU B 375
REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS(M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 GLN A 7 CG CD OE1 NE2 REMARK 470 GLN B 7 CG CD OE1 NE2
REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 PHE A 5 88.76 -159.13 REMARK 500 ASN A 24 -78.76 -97.63 REMARK 500 ASN A 143 107.17 -52.88 REMARK 500 ASP A 257 -126.06 -98.56 REMARK 500 SER A 295 -167.76 -117.45 REMARK 500 ASN B 24 -80.28 -97.96 REMARK 500 LYS B 148 40.08 -80.93 REMARK 500 ARG B 149 -50.02 -155.96 REMARK 500 ILE B 206 -52.04 -120.68 REMARK 500 SER B 295 -164.66 -105.77 REMARK 500 REMARK 500 REMARK: NULL
REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 FE A 407 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 115 OE2 REMARK 620 2 GLU A 238 OE1 136.8 REMARK 620 3 GLU A 204 OE1 121.3 82.2 REMARK 620 4 HIS A 241 ND1 102.5 98.8 113.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 FE A 406 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 238 OE2 REMARK 620 2 GLU A 115 OE1 101.9 REMARK 620 3 HIS A 118 ND1 96.9 89.2 REMARK 620 4 GLU A 84 OE2 105.1 149.9 100.3 REMARK 620 5 GLU A 84 OE1 147.8 90.8 113.0 59.2 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 FE B 409 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU B 238 OE2 REMARK 620 2 GLU B 204 OE1 89.5 REMARK 620 3 GLU B 115 OE2 133.1 122.8 REMARK 620 4 HIS B 241 ND1 94.2 113.5 101.0 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 FE B 408 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU B 238 OE1 REMARK 620 2 HIS B 118 ND1 99.8 REMARK 620 3 GLU B 115 OE1 107.5 90.0 REMARK 620 4 GLU B 84 OE2 100.2 100.1 148.3 REMARK 620 5 GLU B 84 OE1 144.8 111.5 88.7 59.7 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HG A 408 HG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 272 SG REMARK 620 2 TYR A 194 OH 96.1 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HG A 409 HG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 196 O REMARK 620 2 CYS A 196 SG 77.0 REMARK 620 3 HG A 413 HG 63.5 43.3 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HG A 410 HG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 214 SG REMARK 620 2 CYS A 214 N 69.1 REMARK 620 3 VAL A 210 O 93.7 69.5 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HG A 413 HG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 196 O REMARK 620 2 CYS A 196 SG 74.0 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HG A 414 HG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 268 SG REMARK 620 2 CYS A 268 O 82.1 REMARK 620 3 CYS A 272 SG 154.3 96.3 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HG B 410 HG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HG B 417 HG REMARK 620 2 CYS B 196 SG 47.5 REMARK 620 3 CYS B 196 O 65.8 83.5 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HG B 411 HG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 268 O REMARK 620 2 CYS B 268 SG 83.8 REMARK 620 3 CYS B 272 SG 107.2 168.7 REMARK 620 4 HOH B 512 O 80.2 98.9 80.7 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HG B 412 HG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 214 SG REMARK 620 2 VAL B 210 O 79.7 REMARK 620 3 CYS B 214 N 64.7 66.2 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HG B 417 HG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 196 SG REMARK 620 2 CYS B 196 O 75.6 REMARK 620 N 1
REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FE A 406 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FE A 407 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FE B 408 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FE B 409 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HG A 408 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HG A 409 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HG A 410 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HG B 410 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HG B 411 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HG B 412 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HG A 411 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HG B 413 REMARK 800 SITE_IDENTIFIER: BC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HG A 412 REMARK 800 SITE_IDENTIFIER: BC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HG B 414 REMARK 800 SITE_IDENTIFIER: BC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HG B 415 REMARK 800 SITE_IDENTIFIER: BC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HG B 416 REMARK 800 SITE_IDENTIFIER: BC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HG B 417 REMARK 800 SITE_IDENTIFIER: BC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HG A 413 REMARK 800 SITE_IDENTIFIER: CC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HG A 414
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1PIM RELATED DB: PDB REMARK 900 DITHIONITE REDUCED E. COLI RIBONUCLEOTIDE REDUCTASE R2 REMARK 900 SUBUNIT, D84E MUTANT REMARK 900 RELATED ID: 1PIU RELATED DB: PDB REMARK 900 OXIDIZED RIBONUCLEOTIDE REDUCTASE R2-D84E MUTANT CONTAINING REMARK 900 OXO-BRIDGED DIFERRIC CLUSTER REMARK 900 RELATED ID: 1PIY RELATED DB: PDB REMARK 900 RIBONUCLEOTIDE REDUCTASE R2 SOAKED WITH FERROUS IONS AT REMARK 900 NEUTRAL PH REMARK 900 RELATED ID: 1PIZ RELATED DB: PDB REMARK 900 RIBONUCLEOTIDE REDUCTASE R2-D84E MUTANT SOAKED WITH FERROUS REMARK 900 IONS AT NEUTRAL PH REMARK 900 RELATED ID: 1PJ0 RELATED DB: PDB REMARK 900 RIBONUCLEOTIDE REDUCTASE R2-D84E/W48F DOUBLE MUTANT SOAKED REMARK 900 WITH FERROUS IONS AT NEUTRAL PH
REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE CONFLICTS ARE DUE TO A MODELLING ERROR REMARK 999 IN THE INITIAL MODEL.
DBREF 1PJ1 A 1 375 UNP P69924 RIR2_ECOLI 1 375 DBREF 1PJ1 B 1 375 UNP P69924 RIR2_ECOLI 1 375
SEQADV 1PJ1 PHE A 48 UNP P69924 TRP 48 ENGINEERED SEQADV 1PJ1 GLU A 84 UNP P69924 ASP 84 ENGINEERED SEQADV 1PJ1 ASN A 326 UNP P69924 GLN 326 SEE REMARK 999 SEQADV 1PJ1 PHE B 48 UNP P69924 TRP 48 ENGINEERED SEQADV 1PJ1 GLU B 84 UNP P69924 ASP 84 ENGINEERED SEQADV 1PJ1 ASN B 326 UNP P69924 GLN 326 SEE REMARK 999
SEQRES 1 A 375 ALA TYR THR THR PHE SER GLN THR LYS ASN ASP GLN LEU SEQRES 2 A 375 LYS GLU PRO MET PHE PHE GLY GLN PRO VAL ASN VAL ALA SEQRES 3 A 375 ARG TYR ASP GLN GLN LYS TYR ASP ILE PHE GLU LYS LEU SEQRES 4 A 375 ILE GLU LYS GLN LEU SER PHE PHE PHE ARG PRO GLU GLU SEQRES 5 A 375 VAL ASP VAL SER ARG ASP ARG ILE ASP TYR GLN ALA LEU SEQRES 6 A 375 PRO GLU HIS GLU LYS HIS ILE PHE ILE SER ASN LEU LYS SEQRES 7 A 375 TYR GLN THR LEU LEU GLU SER ILE GLN GLY ARG SER PRO SEQRES 8 A 375 ASN VAL ALA LEU LEU PRO LEU ILE SER ILE PRO GLU LEU SEQRES 9 A 375 GLU THR TRP VAL GLU THR TRP ALA PHE SER GLU THR ILE SEQRES 10 A 375 HIS SER ARG SER TYR THR HIS ILE ILE ARG ASN ILE VAL SEQRES 11 A 375 ASN ASP PRO SER VAL VAL PHE ASP ASP ILE VAL THR ASN SEQRES 12 A 375 GLU GLN ILE GLN LYS ARG ALA GLU GLY ILE SER SER TYR SEQRES 13 A 375 TYR ASP GLU LEU ILE GLU MET THR SER TYR TRP HIS LEU SEQRES 14 A 375 LEU GLY GLU GLY THR HIS THR VAL ASN GLY LYS THR VAL SEQRES 15 A 375 THR VAL SER LEU ARG GLU LEU LYS LYS LYS LEU TYR LEU SEQRES 16 A 375 CYS LEU MET SER VAL ASN ALA LEU GLU ALA ILE ARG PHE SEQRES 17 A 375 TYR VAL SER PHE ALA CYS SER PHE ALA PHE ALA GLU ARG SEQRES 18 A 375 GLU LEU MET GLU GLY ASN ALA LYS ILE ILE ARG LEU ILE SEQRES 19 A 375 ALA ARG ASP GLU ALA LEU HIS LEU THR GLY THR GLN HIS SEQRES 20 A 375 MET LEU ASN LEU LEU ARG SER GLY ALA ASP ASP PRO GLU SEQRES 21 A 375 MET ALA GLU ILE ALA GLU GLU CYS LYS GLN GLU CYS TYR SEQRES 22 A 375 ASP LEU PHE VAL GLN ALA ALA GLN GLN GLU LYS ASP TRP SEQRES 23 A 375 ALA ASP TYR LEU PHE ARG ASP GLY SER MET ILE GLY LEU SEQRES 24 A 375 ASN LYS ASP ILE LEU CYS GLN TYR VAL GLU TYR ILE THR SEQRES 25 A 375 ASN ILE ARG MET GLN ALA VAL GLY LEU ASP LEU PRO PHE SEQRES 26 A 375 ASN THR ARG SER ASN PRO ILE PRO TRP ILE ASN THR TRP SEQRES 27 A 375 LEU VAL SER ASP ASN VAL GLN VAL ALA PRO GLN GLU VAL SEQRES 28 A 375 GLU VAL SER SER TYR LEU VAL GLY GLN ILE ASP SER GLU SEQRES 29 A 375 VAL ASP THR ASP ASP LEU SER ASN PHE GLN LEU SEQRES 1 B 375 ALA TYR THR THR PHE SER GLN THR LYS ASN ASP GLN LEU SEQRES 2 B 375 LYS GLU PRO MET PHE PHE GLY GLN PRO VAL ASN VAL ALA SEQRES 3 B 375 ARG TYR ASP GLN GLN LYS TYR ASP ILE PHE GLU LYS LEU SEQRES 4 B 375 ILE GLU LYS GLN LEU SER PHE PHE PHE ARG PRO GLU GLU SEQRES 5 B 375 VAL ASP VAL SER ARG ASP ARG ILE ASP TYR GLN ALA LEU SEQRES 6 B 375 PRO GLU HIS GLU LYS HIS ILE PHE ILE SER ASN LEU LYS SEQRES 7 B 375 TYR GLN THR LEU LEU GLU SER ILE GLN GLY ARG SER PRO SEQRES 8 B 375 ASN VAL ALA LEU LEU PRO LEU ILE SER ILE PRO GLU LEU SEQRES 9 B 375 GLU THR TRP VAL GLU THR TRP ALA PHE SER GLU THR ILE SEQRES 10 B 375 HIS SER ARG SER TYR THR HIS ILE ILE ARG ASN ILE VAL SEQRES 11 B 375 ASN ASP PRO SER VAL VAL PHE ASP ASP ILE VAL THR ASN SEQRES 12 B 375 GLU GLN ILE GLN LYS ARG ALA GLU GLY ILE SER SER TYR SEQRES 13 B 375 TYR ASP GLU LEU ILE GLU MET THR SER TYR TRP HIS LEU SEQRES 14 B 375 LEU GLY GLU GLY THR HIS THR VAL ASN GLY LYS THR VAL SEQRES 15 B 375 THR VAL SER LEU ARG GLU LEU LYS LYS LYS LEU TYR LEU SEQRES 16 B 375 CYS LEU MET SER VAL ASN ALA LEU GLU ALA ILE ARG PHE SEQRES 17 B 375 TYR VAL SER PHE ALA CYS SER PHE ALA PHE ALA GLU ARG SEQRES 18 B 375 GLU LEU MET GLU GLY ASN ALA LYS ILE ILE ARG LEU ILE SEQRES 19 B 375 ALA ARG ASP GLU ALA LEU HIS LEU THR GLY THR GLN HIS SEQRES 20 B 375 MET LEU ASN LEU LEU ARG SER GLY ALA ASP ASP PRO GLU SEQRES 21 B 375 MET ALA GLU ILE ALA GLU GLU CYS LYS GLN GLU CYS TYR SEQRES 22 B 375 ASP LEU PHE VAL GLN ALA ALA GLN GLN GLU LYS ASP TRP SEQRES 23 B 375 ALA ASP TYR LEU PHE ARG ASP GLY SER MET ILE GLY LEU SEQRES 24 B 375 ASN LYS ASP ILE LEU CYS GLN TYR VAL GLU TYR ILE THR SEQRES 25 B 375 ASN ILE ARG MET GLN ALA VAL GLY LEU ASP LEU PRO PHE SEQRES 26 B 375 ASN THR ARG SER ASN PRO ILE PRO TRP ILE ASN THR TRP SEQRES 27 B 375 LEU VAL SER ASP ASN VAL GLN VAL ALA PRO GLN GLU VAL SEQRES 28 B 375 GLU VAL SER SER TYR LEU VAL GLY GLN ILE ASP SER GLU SEQRES 29 B 375 VAL ASP THR ASP ASP LEU SER ASN PHE GLN LEU
HET FE A 406 1 HET FE A 407 1 HET FE B 408 1 HET FE B 409 1 HET HG A 408 1 HET HG A 409 1 HET HG A 410 1 HET HG B 410 1 HET HG B 411 1 HET HG B 412 1 HET HG A 411 1 HET HG B 413 1 HET HG A 412 1 HET HG B 414 1 HET HG B 415 1 HET HG B 416 1 HET HG B 417 1 HET HG A 413 1 HET HG A 414 1
HETNAM FE FE (III) ION HETNAM HG MERCURY (II) ION
FORMUL 3 FE 4(FE 3+) FORMUL 7 HG 15(HG 2+) FORMUL 22 HOH *305(H2 O)
HELIX 1 1 TYR A 33 PHE A 46 1 14 HELIX 2 2 ARG A 49 VAL A 53 5 5 HELIX 3 3 VAL A 55 ALA A 64 1 10 HELIX 4 4 PRO A 66 LEU A 96 1 31 HELIX 5 5 PRO A 97 ILE A 99 5 3 HELIX 6 6 ILE A 101 VAL A 130 1 30 HELIX 7 7 ASP A 132 ASN A 143 1 12 HELIX 8 8 ASN A 143 GLU A 151 1 9 HELIX 9 9 GLY A 152 GLY A 171 1 20 HELIX 10 10 SER A 185 ILE A 206 1 22 HELIX 11 11 ILE A 206 GLU A 220 1 15 HELIX 12 12 MET A 224 GLY A 255 1 32 HELIX 13 13 ASP A 258 CYS A 268 1 11 HELIX 14 14 CYS A 268 PHE A 291 1 24 HELIX 15 15 ASN A 300 VAL A 319 1 20 HELIX 16 16 TRP A 334 LEU A 339 1 6 HELIX 17 17 TYR B 33 PHE B 46 1 14 HELIX 18 18 ARG B 49 VAL B 53 5 5 HELIX 19 19 ARG B 57 LEU B 65 1 9 HELIX 20 20 PRO B 66 LEU B 96 1 31 HELIX 21 21 ILE B 101 VAL B 130 1 30 HELIX 22 22 ASP B 132 ASN B 143 1 12 HELIX 23 23 ASN B 143 GLY B 171 1 29 HELIX 24 24 SER B 185 ILE B 206 1 22 HELIX 25 25 ILE B 206 ARG B 221 1 16 HELIX 26 26 MET B 224 GLY B 255 1 32 HELIX 27 27 ASP B 258 CYS B 268 1 11 HELIX 28 28 CYS B 268 PHE B 291 1 24 HELIX 29 29 ASN B 300 VAL B 319 1 20 HELIX 30 30 ILE B 332 TRP B 338 5 7
SHEET 1 A 2 GLY A 173 VAL A 177 0 SHEET 2 A 2 LYS A 180 VAL A 184 -1 O VAL A 182 N HIS A 175 SHEET 1 B 2 GLY B 173 VAL B 177 0 SHEET 2 B 2 LYS B 180 VAL B 184 -1 O LYS B 180 N VAL B 177
LINK OE2 GLU A 115 FE FE A 407 1555 1555 1.98 LINK OE1 GLU A 238 FE FE A 407 1555 1555 1.99 LINK OE1 GLU A 204 FE FE A 407 1555 1555 1.99 LINK OE2 GLU A 238 FE FE A 406 1555 1555 2.01 LINK ND1 HIS A 241 FE FE A 407 1555 1555 2.04 LINK OE1 GLU A 115 FE FE A 406 1555 1555 2.10 LINK ND1 HIS A 118 FE FE A 406 1555 1555 2.10 LINK OE2 GLU A 84 FE FE A 406 1555 1555 2.19 LINK OE2 GLU B 238 FE FE B 409 1555 1555 1.87 LINK OE1 GLU B 238 FE FE B 408 1555 1555 1.96 LINK OE1 GLU B 204 FE FE B 409 1555 1555 2.05 LINK OE2 GLU B 115 FE FE B 409 1555 1555 2.05 LINK ND1 HIS B 241 FE FE B 409 1555 1555 2.08 LINK ND1 HIS B 118 FE FE B 408 1555 1555 2.10 LINK OE1 GLU B 115 FE FE B 408 1555 1555 2.11 LINK OE2 GLU B 84 FE FE B 408 1555 1555 2.12 LINK FE FE A 406 OE1 GLU A 84 1555 1555 2.25 LINK HG HG A 408 SG CYS A 272 1555 1555 2.61 LINK HG HG A 408 OH TYR A 194 1555 1555 3.16 LINK HG HG A 409 O CYS A 196 1555 1555 3.13 LINK HG HG A 409 SG CYS A 196 1555 1555 2.21 LINK HG HG A 409 HG HG A 413 1555 1555 3.13 LINK HG HG A 410 SG CYS A 214 1555 1555 2.33 LINK HG HG A 410 N CYS A 214 1555 1555 3.33 LINK HG HG A 410 O VAL A 210 1555 1555 2.90 LINK HG HG A 411 OE2 GLU A 309 1555 1555 3.32 LINK HG HG A 412 SG CYS A 268 1555 1555 3.37 LINK HG HG A 413 O CYS A 196 1555 1555 3.30 LINK HG HG A 413 SG CYS A 196 1555 1555 2.15 LINK HG HG A 414 SG CYS A 268 1555 1555 2.47 LINK HG HG A 414 O CYS A 268 1555 1555 2.73 LINK HG HG A 414 SG CYS A 272 1555 1555 2.21 LINK FE FE B 408 OE1 GLU B 84 1555 1555 2.29 LINK HG HG B 410 HG HG B 417 1555 1555 3.02 LINK HG HG B 410 SG CYS B 196 1555 1555 2.09 LINK HG HG B 410 O CYS B 196 1555 1555 3.02 LINK HG HG B 411 O CYS B 268 1555 1555 2.72 LINK HG HG B 411 SG CYS B 268 1555 1555 2.32 LINK HG HG B 411 SG CYS B 272 1555 1555 2.31 LINK HG HG B 411 O HOH B 512 1555 1555 2.99 LINK HG HG B 412 SG CYS B 214 1555 1555 2.64 LINK HG HG B 412 O VAL B 210 1555 1555 2.81 LINK HG HG B 412 N CYS B 214 1555 1555 3.47 LINK HG HG B 413 O CYS B 272 1555 1555 2.38 LINK HG HG B 414 O CYS B 305 1555 1555 3.08 LINK HG HG B 415 O CYS B 214 1555 1555 2.80 LINK HG HG B 416 OE2 GLU B 309 1555 1555 3.13 LINK HG HG B 417 SG CYS B 196 1555 1555 2.22 LINK HG HG B 417 O CYS B 196 1555 1555 3.28
SITE 1 AC1 4 GLU A 84 GLU A 115 HIS A 118 GLU A 238 SITE 1 AC2 5 TRP A 111 GLU A 115 GLU A 204 GLU A 238 SITE 2 AC2 5 HIS A 241 SITE 1 AC3 4 GLU B 84 GLU B 115 HIS B 118 GLU B 238 SITE 1 AC4 5 GLU B 115 GLU B 204 PHE B 208 GLU B 238 SITE 2 AC4 5 HIS B 241 SITE 1 AC5 3 TYR A 194 ALA A 265 CYS A 272 SITE 1 AC6 3 TYR A 157 CYS A 196 HG A 413 SITE 1 AC7 2 VAL A 210 CYS A 214 SITE 1 AC8 5 TYR B 156 TYR B 157 CYS B 196 VAL B 200 SITE 2 AC8 5 HG B 417 SITE 1 AC9 5 TYR B 194 LEU B 195 CYS B 268 CYS B 272 SITE 2 AC9 5 HOH B 512 SITE 1 BC1 4 VAL B 210 ALA B 213 CYS B 214 LEU B 304 SITE 1 BC2 2 CYS A 305 GLU A 309 SITE 1 BC3 4 MET B 198 CYS B 272 LEU B 275 PHE B 276 SITE 1 BC4 2 LYS A 191 CYS A 268 SITE 1 BC5 4 LYS B 284 CYS B 305 GLU B 309 HG B 416 SITE 1 BC6 5 ILE B 72 CYS B 214 PHE B 218 MET B 296 SITE 2 BC6 5 LEU B 299 SITE 1 BC7 4 CYS B 305 GLN B 306 GLU B 309 HG B 414 SITE 1 BC8 4 TYR B 157 CYS B 196 VAL B 200 HG B 410 SITE 1 BC9 3 TYR A 157 CYS A 196 HG A 409 SITE 1 CC1 4 TYR A 194 LEU A 195 CYS A 268 CYS A 272
CRYST1 74.100 84.200 114.700 90.00 90.00 90.00 P 21 21 21 8
ORIGX1 1.000000 0.000000 0.000000 0.00000
ORIGX2 0.000000 1.000000 0.000000 0.00000
ORIGX3 0.000000 0.000000 1.000000 0.00000
SCALE1 0.013495 0.000000 0.000000 0.00000
SCALE2 0.000000 0.011876 0.000000 0.00000
SCALE3 0.000000 0.000000 0.008718 0.00000