HEADER HYDROLASE/DNA 31-JAN-07 2OQ4 TITLE CRYSTAL STRUCTURE OF THE DNA REPAIR ENZYME ENDONUCLEASE- TITLE 2 VIII (NEI) FROM E. COLI (E2Q) IN COMPLEX WITH AP-SITE TITLE 3 CONTAINING DNA SUBSTRATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: ENDONUCLEASE VIII; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: DNA GLYCOSYLASE/AP LYASE NEI, DNA-APURINIC OR COMPND 5 APYRIMIDINIC SITE, LYASE NEI; COMPND 6 EC: 3.2.2.-, 4.2.99.18; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: 5'-D(*G*GP*CP*TP*TP*CP*AP*TP*CP*CP*TP*GP*G)-3'; COMPND 11 CHAIN: C, E; COMPND 12 ENGINEERED: YES; COMPND 13 MOL_ID: 3; COMPND 14 MOLECULE: 5'-D(*C*CP*AP*GP*GP*AP*(PED)P*GP*AP*AP*GP*CP*C)- COMPND 15 3'; COMPND 16 CHAIN: D, F; COMPND 17 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 GENE: NEI; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: B834(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET13A; SOURCE 10 MOL_ID: 2; SOURCE 11 SYNTHETIC: YES; SOURCE 12 MOL_ID: 3; SOURCE 13 SYNTHETIC: YES KEYWDS ENDONUCLEASE VIII, OXIDATIVE DAMAGE, DNA REPAIR, BASE KEYWDS 2 EXCISION, COVALENT INTERMEDIATE, CRYSTAL STRUCTURE, KEYWDS 3 REACTION MECHANISM, HYDROLASE/DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR G.GOLAN,D.O.ZHARKOV,A.P.GROLLMAN,G.SHOAHM REVDAT 2 24-FEB-09 2OQ4 1 VERSN REVDAT 1 26-FEB-08 2OQ4 0 JRNL AUTH G.GOLAN,D.O.ZHARKOV,A.P.GROLLMAN,G.SHOHAM JRNL TITL ACTIVE SITE PLASTICITY OF ENDONUCLEASE VIII: JRNL TITL 2 CONFORMATIONAL CHANGES COMPENSATING FOR DIFFERENT JRNL TITL 3 SUBSTRATES AND MUTATIONS OF CRITICAL RESIDUES JRNL REF TO BE PUBLISHED JRNL REFN REMARK 1 REMARK 2 REMARK 2 RESOLUTION. 2.60 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 16.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 1272101.920 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 29947 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) : 0.374 REMARK 3 FREE R VALUE : 0.432 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2998 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.008 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) : 2.60 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.76 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.70 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 4359 REMARK 3 BIN R VALUE (WORKING SET) : 0.3690 REMARK 3 BIN FREE R VALUE : 0.4570 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 10.50 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 511 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.020 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4014 REMARK 3 NUCLEIC ACID ATOMS : 850 REMARK 3 HETEROGEN ATOMS : 19 REMARK 3 SOLVENT ATOMS : 93 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 48.10 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 47.00 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 7.17000 REMARK 3 B22 (A**2) : 7.17000 REMARK 3 B33 (A**2) : -14.34000 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) : 0.56 REMARK 3 ESD FROM SIGMAA (A) : -0.26 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) : 0.75 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.27 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.195 REMARK 3 BOND ANGLES (DEGREES) : 2.50 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 24.10 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.02 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) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.35 REMARK 3 BSOL : 57.89 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 : DNA-RNA-PED.PARAM REMARK 3 PARAMETER FILE 3 : ION.PARAM REMARK 3 PARAMETER FILE 4 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 5 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : DNA-RNA-PED.TOP REMARK 3 TOPOLOGY FILE 3 : ION.TOP REMARK 3 TOPOLOGY FILE 4 : WATER.TOP REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: DATA PROCESSING INDICATED THAT THE REMARK 3 CRYSTAL WAS TWINNED BUT THE EXACT NATURE OF THE TWINING WAS REMARK 3 NOT CLEAR. TREATMENT OF THE DATA WITH THE TWINNING UTILITY OF REMARK 3 CNS INDICATED UNEQUAL (MAJOR AND MINOR) TWINNING FRACTIONS, REMARK 3 BUT A REFINEMENT OF THE INITIAL MODEL, IGNORING THE TWINNING REMARK 3 AND CONSIDERING ONLY THE MAJOR TWINNING FRACTION, GAVE BETTER REMARK 3 STRUCTURAL RESULTS, WITH RELATIVELY REASONABLE FINAL R AND REMARK 3 RFREE. REMARK 4 REMARK 4 2OQ4 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 08-FEB-07. REMARK 100 THE RCSB ID CODE IS RCSB041448. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 5ID-B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.102 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MAR CCD 165 MM REMARK 200 INTENSITY-INTEGRATION SOFTWARE : D*TREK REMARK 200 DATA SCALING SOFTWARE : D*TREK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 30010 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.600 REMARK 200 RESOLUTION RANGE LOW (A) : 16.730 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 6.400 REMARK 200 R MERGE (I) : 0.08300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.69 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.4 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.33800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 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: 2EA0 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 60.49 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.11 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.8M AMMONIUM SULFATE, 0.1M SODIUM REMARK 280 ACETATE PH 4.6-5.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 82.43000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 53.56500 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 53.56500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 123.64500 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 53.56500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 53.56500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 41.21500 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 53.56500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 53.56500 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 123.64500 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 53.56500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 53.56500 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 41.21500 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 82.43000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 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: TRIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, D, A 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TRIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: E, F, 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 DG C 401 REMARK 465 DG C 413 REMARK 465 DC D 421 REMARK 465 DG E 401 REMARK 465 DG E 402 REMARK 465 DC E 403 REMARK 465 DG E 413 REMARK 465 DC F 421 REMARK 465 DC F 433 REMARK 465 GLN A 214 REMARK 465 VAL A 215 REMARK 465 ASP A 216 REMARK 465 GLU A 217 REMARK 465 ASN A 218 REMARK 465 LYS A 219 REMARK 465 HIS A 220 REMARK 465 HIS A 221 REMARK 465 GLY A 222 REMARK 465 ALA A 223 REMARK 465 GLY B 213 REMARK 465 GLN B 214 REMARK 465 VAL B 215 REMARK 465 ASP B 216 REMARK 465 GLU B 217 REMARK 465 ASN B 218 REMARK 465 LYS B 219 REMARK 465 HIS B 220 REMARK 465 HIS B 221 REMARK 465 GLY B 222 REMARK 465 PRO B 258 REMARK 465 GLY B 259 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 DG C 402 P OP1 OP2 REMARK 470 DC D 422 P OP1 OP2 REMARK 470 PED D 427 O3P REMARK 470 DT E 404 P OP1 OP2 REMARK 470 DC F 422 P OP1 OP2 REMARK 470 PED F 427 O3P REMARK 470 THR A 86 OG1 CG2 REMARK 470 ARG A 149 CG CD NE CZ NH1 NH2 REMARK 470 ILE A 243 CG1 CG2 CD1 REMARK 470 ASP B 195 CB CG OD1 OD2 REMARK 470 LEU B 224 CG CD1 CD2 REMARK 470 TYR B 255 CB CG CD1 CD2 CE1 CE2 CZ REMARK 470 TYR B 255 OH REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O GLN B 2 O GLY B 165 2.17 REMARK 500 OG1 THR A 181 OD1 ASN A 183 2.19 REMARK 500 REMARK 500 REMARK: NULL 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 GLN A 36 -79.18 -58.06 REMARK 500 HIS A 46 143.10 -176.09 REMARK 500 ARG A 50 50.27 -158.76 REMARK 500 GLN A 69 -111.24 44.94 REMARK 500 THR A 85 167.07 178.06 REMARK 500 SER A 104 -61.60 66.00 REMARK 500 ALA A 105 140.14 -21.09 REMARK 500 GLU A 114 -49.43 137.86 REMARK 500 PRO A 127 156.59 -48.51 REMARK 500 ASN A 133 -11.30 -48.80 REMARK 500 SER A 145 157.00 -48.53 REMARK 500 LEU A 157 2.06 -65.81 REMARK 500 VAL A 229 -9.76 -156.25 REMARK 500 SER A 250 33.72 72.87 REMARK 500 GLN B 2 -13.41 -147.96 REMARK 500 GLN B 69 -111.03 37.37 REMARK 500 SER B 104 -37.07 50.85 REMARK 500 LEU B 116 -88.72 -62.79 REMARK 500 THR B 117 -51.03 -24.30 REMARK 500 PHE B 153 -6.22 -55.83 REMARK 500 ARG B 171 -78.74 -34.98 REMARK 500 THR B 181 -147.08 -95.38 REMARK 500 ALA B 186 12.48 -64.33 REMARK 500 LEU B 201 -8.58 -58.68 REMARK 500 PHE B 230 103.13 -48.58 REMARK 500 ARG B 239 -63.27 -106.95 REMARK 500 THR B 247 -172.64 163.55 REMARK 500 SER B 251 50.81 37.71 REMARK 500 PHE B 254 -83.44 -113.89 REMARK 500 TYR B 255 133.48 87.62 REMARK 500 TRP B 256 -170.15 175.60 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 DG D 428 0.08 SIDE_CHAIN REMARK 500 DT E 411 0.06 SIDE_CHAIN 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 ZN A 501 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 237 SG REMARK 620 2 CYS A 240 SG 110.4 REMARK 620 3 CYS A 257 SG 100.5 94.6 REMARK 620 4 CYS A 260 SG 112.2 109.8 127.7 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 501 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 237 SG REMARK 620 2 CYS B 240 SG 108.2 REMARK 620 3 CYS B 257 SG 112.6 85.2 REMARK 620 4 CYS B 260 SG 110.4 122.8 115.5 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PED D 427 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PED F 427 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 501 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 501 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 601 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 602 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 603 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2EA0 RELATED DB: PDB REMARK 900 RELATED ID: 2OPF RELATED DB: PDB REMARK 999 REMARK 999 SEQUENCE REMARK 999 SEQUENCING AND CRYSTALLOGRAPHY CONFIRM THE SEQUENCE AS THR A 34, REMARK 999 THR B 34, ARG A 112, ARG B 112. DBREF 2OQ4 A 1 262 UNP P50465 END8_ECOLI 2 263 DBREF 2OQ4 B 1 262 UNP P50465 END8_ECOLI 2 263 DBREF 2OQ4 C 401 413 PDB 2OQ4 2OQ4 401 413 DBREF 2OQ4 D 421 433 PDB 2OQ4 2OQ4 421 433 DBREF 2OQ4 E 401 413 PDB 2OQ4 2OQ4 401 413 DBREF 2OQ4 F 421 433 PDB 2OQ4 2OQ4 421 433 SEQADV 2OQ4 GLN A 2 UNP P50465 GLU 3 ENGINEERED SEQADV 2OQ4 THR A 34 UNP P50465 PRO 35 SEE REMARK 999 SEQADV 2OQ4 ARG A 112 UNP P50465 THR 113 SEE REMARK 999 SEQADV 2OQ4 GLN B 2 UNP P50465 GLU 3 ENGINEERED SEQADV 2OQ4 THR B 34 UNP P50465 PRO 35 SEE REMARK 999 SEQADV 2OQ4 ARG B 112 UNP P50465 THR 113 SEE REMARK 999 SEQRES 1 A 262 PRO GLN GLY PRO GLU ILE ARG ARG ALA ALA ASP ASN LEU SEQRES 2 A 262 GLU ALA ALA ILE LYS GLY LYS PRO LEU THR ASP VAL TRP SEQRES 3 A 262 PHE ALA PHE PRO GLN LEU LYS THR TYR GLN SER GLN LEU SEQRES 4 A 262 ILE GLY GLN HIS VAL THR HIS VAL GLU THR ARG GLY LYS SEQRES 5 A 262 ALA LEU LEU THR HIS PHE SER ASN ASP LEU THR LEU TYR SEQRES 6 A 262 SER HIS ASN GLN LEU TYR GLY VAL TRP ARG VAL VAL ASP SEQRES 7 A 262 THR GLY GLU GLU PRO GLN THR THR ARG VAL LEU ARG VAL SEQRES 8 A 262 LYS LEU GLN THR ALA ASP LYS THR ILE LEU LEU TYR SER SEQRES 9 A 262 ALA SER ASP ILE GLU MET LEU ARG PRO GLU GLN LEU THR SEQRES 10 A 262 THR HIS PRO PHE LEU GLN ARG VAL GLY PRO ASP VAL LEU SEQRES 11 A 262 ASP PRO ASN LEU THR PRO GLU VAL VAL LYS GLU ARG LEU SEQRES 12 A 262 LEU SER PRO ARG PHE ARG ASN ARG GLN PHE ALA GLY LEU SEQRES 13 A 262 LEU LEU ASP GLN ALA PHE LEU ALA GLY LEU GLY ASN TYR SEQRES 14 A 262 LEU ARG VAL GLU ILE LEU TRP GLN VAL GLY LEU THR GLY SEQRES 15 A 262 ASN HIS LYS ALA LYS ASP LEU ASN ALA ALA GLN LEU ASP SEQRES 16 A 262 ALA LEU ALA HIS ALA LEU LEU GLU ILE PRO ARG PHE SER SEQRES 17 A 262 TYR ALA THR ARG GLY GLN VAL ASP GLU ASN LYS HIS HIS SEQRES 18 A 262 GLY ALA LEU PHE ARG PHE LYS VAL PHE HIS ARG ASP GLY SEQRES 19 A 262 GLU PRO CYS GLU ARG CYS GLY SER ILE ILE GLU LYS THR SEQRES 20 A 262 THR LEU SER SER ARG PRO PHE TYR TRP CYS PRO GLY CYS SEQRES 21 A 262 GLN HIS SEQRES 1 B 262 PRO GLN GLY PRO GLU ILE ARG ARG ALA ALA ASP ASN LEU SEQRES 2 B 262 GLU ALA ALA ILE LYS GLY LYS PRO LEU THR ASP VAL TRP SEQRES 3 B 262 PHE ALA PHE PRO GLN LEU LYS THR TYR GLN SER GLN LEU SEQRES 4 B 262 ILE GLY GLN HIS VAL THR HIS VAL GLU THR ARG GLY LYS SEQRES 5 B 262 ALA LEU LEU THR HIS PHE SER ASN ASP LEU THR LEU TYR SEQRES 6 B 262 SER HIS ASN GLN LEU TYR GLY VAL TRP ARG VAL VAL ASP SEQRES 7 B 262 THR GLY GLU GLU PRO GLN THR THR ARG VAL LEU ARG VAL SEQRES 8 B 262 LYS LEU GLN THR ALA ASP LYS THR ILE LEU LEU TYR SER SEQRES 9 B 262 ALA SER ASP ILE GLU MET LEU ARG PRO GLU GLN LEU THR SEQRES 10 B 262 THR HIS PRO PHE LEU GLN ARG VAL GLY PRO ASP VAL LEU SEQRES 11 B 262 ASP PRO ASN LEU THR PRO GLU VAL VAL LYS GLU ARG LEU SEQRES 12 B 262 LEU SER PRO ARG PHE ARG ASN ARG GLN PHE ALA GLY LEU SEQRES 13 B 262 LEU LEU ASP GLN ALA PHE LEU ALA GLY LEU GLY ASN TYR SEQRES 14 B 262 LEU ARG VAL GLU ILE LEU TRP GLN VAL GLY LEU THR GLY SEQRES 15 B 262 ASN HIS LYS ALA LYS ASP LEU ASN ALA ALA GLN LEU ASP SEQRES 16 B 262 ALA LEU ALA HIS ALA LEU LEU GLU ILE PRO ARG PHE SER SEQRES 17 B 262 TYR ALA THR ARG GLY GLN VAL ASP GLU ASN LYS HIS HIS SEQRES 18 B 262 GLY ALA LEU PHE ARG PHE LYS VAL PHE HIS ARG ASP GLY SEQRES 19 B 262 GLU PRO CYS GLU ARG CYS GLY SER ILE ILE GLU LYS THR SEQRES 20 B 262 THR LEU SER SER ARG PRO PHE TYR TRP CYS PRO GLY CYS SEQRES 21 B 262 GLN HIS SEQRES 1 C 13 DG DG DC DT DT DC DA DT DC DC DT DG DG SEQRES 1 D 13 DC DC DA DG DG DA PED DG DA DA DG DC DC SEQRES 1 E 13 DG DG DC DT DT DC DA DT DC DC DT DG DG SEQRES 1 F 13 DC DC DA DG DG DA PED DG DA DA DG DC DC HET PED D 427 11 HET PED F 427 11 HET NA F 701 1 HET ZN A 501 1 HET SO4 A 601 5 HET ZN B 501 1 HET SO4 B 602 5 HET SO4 B 603 5 HET NA B 702 1 HETNAM PED PENTANE-3,4-DIOL-5-PHOSPHATE HETNAM NA SODIUM ION HETNAM ZN ZINC ION HETNAM SO4 SULFATE ION HETSYN PED OPEN FORM OF 1'-2'-DIDEOXYRIBOFURANOSE-5'-PHOSPHATE FORMUL 2 PED 2(C5 H13 O6 P) FORMUL 7 NA 2(NA 1+) FORMUL 8 ZN 2(ZN 2+) FORMUL 9 SO4 3(O4 S 2-) FORMUL 14 HOH *93(H2 O) HELIX 1 1 GLN A 2 LYS A 18 1 17 HELIX 2 2 PHE A 29 THR A 34 1 6 HELIX 3 3 TYR A 35 ILE A 40 1 6 HELIX 4 4 GLU A 114 THR A 118 5 5 HELIX 5 5 HIS A 119 VAL A 125 1 7 HELIX 6 6 THR A 135 SER A 145 1 11 HELIX 7 7 GLN A 152 LEU A 157 1 6 HELIX 8 8 GLY A 167 VAL A 178 1 12 HELIX 9 9 ASN A 190 ARG A 212 1 23 HELIX 10 10 GLY B 3 LYS B 18 1 16 HELIX 11 11 THR B 34 ILE B 40 1 7 HELIX 12 12 ARG B 112 THR B 117 1 6 HELIX 13 13 HIS B 119 VAL B 125 1 7 HELIX 14 14 THR B 135 SER B 145 1 11 HELIX 15 15 GLN B 152 LEU B 157 1 6 HELIX 16 16 GLY B 167 VAL B 178 1 12 HELIX 17 17 ASN B 190 ARG B 212 1 23 SHEET 1 A 4 ASP A 24 PHE A 27 0 SHEET 2 A 4 LEU A 89 GLN A 94 -1 O LYS A 92 N TRP A 26 SHEET 3 A 4 LYS A 98 TYR A 103 -1 O LEU A 102 N ARG A 90 SHEET 4 A 4 VAL A 73 ASP A 78 -1 N ARG A 75 O LEU A 101 SHEET 1 B 4 VAL A 44 THR A 49 0 SHEET 2 B 4 ALA A 53 PHE A 58 -1 O LEU A 55 N GLU A 48 SHEET 3 B 4 THR A 63 HIS A 67 -1 O LEU A 64 N THR A 56 SHEET 4 B 4 ASP A 107 LEU A 111 -1 O GLU A 109 N TYR A 65 SHEET 1 C 2 GLU A 245 THR A 248 0 SHEET 2 C 2 PRO A 253 TRP A 256 -1 O PHE A 254 N THR A 247 SHEET 1 D 4 LEU B 22 PHE B 27 0 SHEET 2 D 4 LEU B 89 THR B 95 -1 O GLN B 94 N ASP B 24 SHEET 3 D 4 THR B 99 TYR B 103 -1 O LEU B 102 N VAL B 91 SHEET 4 D 4 VAL B 73 ARG B 75 -1 N VAL B 73 O TYR B 103 SHEET 1 E 4 HIS B 46 ARG B 50 0 SHEET 2 E 4 ALA B 53 HIS B 57 -1 O LEU B 55 N GLU B 48 SHEET 3 E 4 THR B 63 HIS B 67 -1 O SER B 66 N LEU B 54 SHEET 4 E 4 ASP B 107 LEU B 111 -1 O LEU B 111 N THR B 63 LINK C1' PED D 427 N PRO A 1 1555 1555 1.45 LINK C1' PED F 427 N PRO B 1 1555 1555 1.44 LINK ZN ZN A 501 SG CYS A 237 1555 1555 2.10 LINK ZN ZN A 501 SG CYS A 240 1555 1555 2.55 LINK ZN ZN A 501 SG CYS A 257 1555 1555 2.09 LINK ZN ZN A 501 SG CYS A 260 1555 1555 2.77 LINK ZN ZN B 501 SG CYS B 237 1555 1555 2.32 LINK ZN ZN B 501 SG CYS B 240 1555 1555 2.76 LINK ZN ZN B 501 SG CYS B 257 1555 1555 2.38 LINK ZN ZN B 501 SG CYS B 260 1555 1555 2.01 LINK O3' DA D 426 P PED D 427 1555 1555 1.61 LINK O3' PED D 427 P DG D 428 1555 1555 1.60 LINK O3' DA F 426 P PED F 427 1555 1555 1.60 LINK O3' PED F 427 P DG F 428 1555 1555 1.61 SITE 1 AC1 9 PRO A 1 GLN A 2 LEU A 70 ASN A 168 SITE 2 AC1 9 PHE A 230 PRO A 253 DA D 426 DG D 428 SITE 3 AC1 9 HOH D1053 SITE 1 AC2 6 PRO B 1 GLN B 2 ASN B 168 ARG B 252 SITE 2 AC2 6 DA F 426 DG F 428 SITE 1 AC3 4 CYS A 237 CYS A 240 CYS A 257 CYS A 260 SITE 1 AC4 4 CYS B 237 CYS B 240 CYS B 257 CYS B 260 SITE 1 AC5 4 PRO A 1 GLU A 5 ARG A 212 HOH D1053 SITE 1 AC6 4 GLU B 81 GLU B 82 PRO B 83 HOH B1085 SITE 1 AC7 2 ARG B 8 ASN B 12 CRYST1 107.130 107.130 164.860 90.00 90.00 90.00 P 43 21 2 16 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 0.009334 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009334 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006066 0.00000 MASTER 434 0 9 17 18 0 10 6 0 0 0 46 END