10 20 30 40 50 60 70 80 3GME - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER TRANSFERASE / PROTEIN BINDING 13-MAR-09 3GME
TITLE CRYSTAL STRUCTURE OF POLYNUCLEOTIDE PHOSPHORYLASE IN COMPLEX TITLE 2 WITH RNASE E AND MANGANESE
COMPND MOL_ID: 1; COMPND 2 MOLECULE: POLYRIBONUCLEOTIDE NUCLEOTIDYLTRANSFERASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: POLYNUCLEOTIDE PHOSPHORYLASE, RESIDUES 1-549; COMPND 5 SYNONYM: POLYNUCLEOTIDE PHOSPHORYLASE, PNPASE; COMPND 6 EC: 2.7.7.8; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: RIBONUCLEASE E; COMPND 9 CHAIN: D; COMPND 10 FRAGMENT: RNASE E RECOGNITION MICRODOMAIN, RESIDUES 1021- COMPND 11 1061; COMPND 12 EC: 3.1.4.-; COMPND 13 ENGINEERED: YES
SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI E24377A; SOURCE 3 ORGANISM_TAXID: 331111; SOURCE 4 STRAIN: BL21 DE3; SOURCE 5 MOL_ID: 2; SOURCE 6 SYNTHETIC: YES; SOURCE 7 ORGANISM_COMMON: ESCHERICHIA COLI; SOURCE 8 ORGANISM_TAXID: 562; SOURCE 9 OTHER_DETAILS: THIS SEQUENCE OCCURS NATURALLY IN E. COLI
KEYWDS PROTEIN-RNA COMPLEX, CYTOPLASM, NUCLEOTIDYLTRANSFERASE, RNA- KEYWDS 2 BINDING, TRANSFERASE, HYDROLASE, TRANSFERASE / PROTEIN KEYWDS 3 BINDING COMPLEX
EXPDTA X-RAY DIFFRACTION
AUTHOR S.NURMOHAMED,B.L.LUISI
REVDAT 1 09-JUN-09 3GME 0
JRNL AUTH S.NURMOHAMED,B.VAIDIALINGAM,A.J.CALLAGHAN,B.F.LUISI JRNL TITL CRYSTAL STRUCTURE OF ESCHERICHIA COLI JRNL TITL 2 POLYNUCLEOTIDE PHOSPHORYLASE CORE BOUND TO RNASE E, JRNL TITL 3 RNA AND MANGANESE: IMPLICATIONS FOR CATALYTIC JRNL TITL 4 MECHANISM AND RNA DEGRADOSOME ASSEMBLY. JRNL REF J.MOL.BIOL. V. 389 17 2009 JRNL REFN ISSN 0022-2836 JRNL PMID 19327365 JRNL DOI 10.1016/J.JMB.2009.03.051
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. 2.40 ANGSTROMS.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.91 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 27938 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 + TEST SET) : 0.286 REMARK 3 R VALUE (WORKING SET) : 0.286 REMARK 3 FREE R VALUE : 0.298 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1490 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.40 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.46 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1976 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.82 REMARK 3 BIN R VALUE (WORKING SET) : 0.3630 REMARK 3 BIN FREE R VALUE SET COUNT : 117 REMARK 3 BIN FREE R VALUE : 0.3760 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3694 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 2 REMARK 3 SOLVENT ATOMS : 158 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 50.59 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.01000 REMARK 3 B22 (A**2) : -0.01000 REMARK 3 B33 (A**2) : 0.02000 REMARK 3 B12 (A**2) : -0.01000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.390 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.271 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): NULL REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.903 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.892 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3757 ; 0.005 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5103 ; 0.765 ; 1.965 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 497 ; 3.575 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 151 ;35.144 ;24.702 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 596 ;12.752 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 22 ;12.138 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 597 ; 0.045 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2838 ; 0.001 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1632 ; 0.136 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2565 ; 0.284 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 132 ; 0.096 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 81 ; 0.118 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 11 ; 0.106 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 2490 ; 1.533 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3980 ; 2.700 ; 2.000 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1267 ; 3.819 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1123 ; 5.980 ; 4.500 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE REMARK 3 RIDING POSITIONS
REMARK 4 REMARK 4 3GME COMPLIES WITH FORMAT V. 3.20, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 25-MAR-09. REMARK 100 THE RCSB ID CODE IS RCSB052041.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-AUG-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I02 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.07 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 27938 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 25.910 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.7 REMARK 200 DATA REDUNDANCY : 2.900 REMARK 200 R MERGE (I) : 0.12500 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) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.48 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.7 REMARK 200 DATA REDUNDANCY IN SHELL : 2.80 REMARK 200 R MERGE FOR SHELL (I) : 0.43200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL
REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 58.32 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.95 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2.5 M NACL, 9 % W/V PEG 6000, 20 MM REMARK 280 NA- CITRATE, 20 MM MANGANESE ACETATE , VAPOR DIFFUSION
REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z REMARK 290 6555 -X,-X+Y,-Z REMARK 290 7555 X+2/3,Y+1/3,Z+1/3 REMARK 290 8555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 9555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 10555 Y+2/3,X+1/3,-Z+1/3 REMARK 290 11555 X-Y+2/3,-Y+1/3,-Z+1/3 REMARK 290 12555 -X+2/3,-X+Y+1/3,-Z+1/3 REMARK 290 13555 X+1/3,Y+2/3,Z+2/3 REMARK 290 14555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 15555 -X+Y+1/3,-X+2/3,Z+2/3 REMARK 290 16555 Y+1/3,X+2/3,-Z+2/3 REMARK 290 17555 X-Y+1/3,-Y+2/3,-Z+2/3 REMARK 290 18555 -X+1/3,-X+Y+2/3,-Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 79.28700 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 45.77637 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 52.03933 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 79.28700 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 45.77637 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 52.03933 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 79.28700 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 45.77637 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 52.03933 REMARK 290 SMTRY1 10 -0.500000 0.866025 0.000000 79.28700 REMARK 290 SMTRY2 10 0.866025 0.500000 0.000000 45.77637 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 52.03933 REMARK 290 SMTRY1 11 1.000000 0.000000 0.000000 79.28700 REMARK 290 SMTRY2 11 0.000000 -1.000000 0.000000 45.77637 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 52.03933 REMARK 290 SMTRY1 12 -0.500000 -0.866025 0.000000 79.28700 REMARK 290 SMTRY2 12 -0.866025 0.500000 0.000000 45.77637 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 52.03933 REMARK 290 SMTRY1 13 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 91.55274 REMARK 290 SMTRY3 13 0.000000 0.000000 1.000000 104.07867 REMARK 290 SMTRY1 14 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 14 0.866025 -0.500000 0.000000 91.55274 REMARK 290 SMTRY3 14 0.000000 0.000000 1.000000 104.07867 REMARK 290 SMTRY1 15 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 15 -0.866025 -0.500000 0.000000 91.55274 REMARK 290 SMTRY3 15 0.000000 0.000000 1.000000 104.07867 REMARK 290 SMTRY1 16 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 16 0.866025 0.500000 0.000000 91.55274 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 104.07867 REMARK 290 SMTRY1 17 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 17 0.000000 -1.000000 0.000000 91.55274 REMARK 290 SMTRY3 17 0.000000 0.000000 -1.000000 104.07867 REMARK 290 SMTRY1 18 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 18 -0.866025 0.500000 0.000000 91.55274 REMARK 290 SMTRY3 18 0.000000 0.000000 -1.000000 104.07867 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: ONE RNASE E RECOGNITION MICRODOMAIN BINDS TO ONE MONOMER REMARK 300 OF PNPASE
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: HEXAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: HEXAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 15840 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 59420 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -100.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, D 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 BIOMT1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 3 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 PHE A 78 REMARK 465 ARG A 79 REMARK 465 ARG A 80 REMARK 465 GLU A 81 REMARK 465 GLY A 82 REMARK 465 ALA A 247 REMARK 465 ALA A 248 REMARK 465 LEU A 249 REMARK 465 ALA A 250 REMARK 465 GLU A 251 REMARK 465 ALA A 252 REMARK 465 ARG A 253 REMARK 465 LEU A 254 REMARK 465 SER A 255 REMARK 465 ASP A 256 REMARK 465 ALA A 257 REMARK 465 TYR A 258 REMARK 465 ARG A 259 REMARK 465 ILE A 260 REMARK 465 ALA A 268 REMARK 465 GLN A 269 REMARK 465 VAL A 270 REMARK 465 ASP A 271 REMARK 465 VAL A 272 REMARK 465 ILE A 273 REMARK 465 LYS A 274 REMARK 465 SER A 275 REMARK 465 GLU A 276 REMARK 465 THR A 277 REMARK 465 ILE A 278 REMARK 465 ALA A 279 REMARK 465 THR A 280 REMARK 465 LEU A 281 REMARK 465 LEU A 282 REMARK 465 ALA A 283 REMARK 465 GLU A 284 REMARK 465 ASP A 285 REMARK 465 GLU A 286 REMARK 465 THR A 287 REMARK 465 LEU A 288 REMARK 465 ASP A 289 REMARK 465 GLU A 290 REMARK 465 ASN A 291 REMARK 465 GLU A 292 REMARK 465 LEU A 293 REMARK 465 GLY A 294 REMARK 465 GLU A 295 REMARK 465 ILE A 296 REMARK 465 ALA A 359 REMARK 465 ARG A 360 REMARK 465 ASP A 361 REMARK 465 ALA A 362 REMARK 465 GLN A 363 REMARK 465 VAL A 364 REMARK 465 LEU A 365 REMARK 465 ASP A 366 REMARK 465 GLU A 367 REMARK 465 LEU A 368 REMARK 465 MET A 369 REMARK 465 GLY A 370 REMARK 465 GLU A 371 REMARK 465 ARG A 372 REMARK 465 THR A 373 REMARK 465 GLY A 546 REMARK 465 ASP A 547 REMARK 465 ILE A 548 REMARK 465 SER A 549 REMARK 465 GLU D 1021 REMARK 465 ALA D 1022 REMARK 465 PRO D 1023 REMARK 465 ARG D 1024 REMARK 465 HIS D 1025 REMARK 465 SER D 1026 REMARK 465 ASP D 1027 REMARK 465 TRP D 1028 REMARK 465 GLN D 1029 REMARK 465 ARG D 1030 REMARK 465 PRO D 1031 REMARK 465 THR D 1032 REMARK 465 PHE D 1033 REMARK 465 ALA D 1034 REMARK 465 PHE D 1035 REMARK 465 GLU D 1036 REMARK 465 GLY D 1037 REMARK 465 LYS D 1038 REMARK 465 VAL D 1060 REMARK 465 GLU D 1061
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 LYS A 51 CD CE NZ REMARK 470 PHE A 77 CG CD1 CD2 CE1 CE2 CZ REMARK 470 ARG A 83 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 174 CD CE NZ REMARK 470 ARG A 230 CD NE CZ NH1 NH2 REMARK 470 GLU A 240 CG CD OE1 OE2 REMARK 470 ARG A 245 CG CD NE CZ NH1 NH2 REMARK 470 VAL A 246 CG1 CG2 REMARK 470 THR A 261 OG1 CG2 REMARK 470 ASP A 262 CG OD1 OD2 REMARK 470 LYS A 263 CG CD CE NZ REMARK 470 GLN A 264 CG CD OE1 NE2 REMARK 470 GLU A 265 CG CD OE1 OE2 REMARK 470 ARG A 266 CG CD NE CZ NH1 NH2 REMARK 470 TYR A 267 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 LEU A 297 CG CD1 CD2 REMARK 470 ILE A 300 CG1 CG2 CD1 REMARK 470 GLU A 301 CG CD OE1 OE2 REMARK 470 LYS A 302 CG CD CE NZ REMARK 470 LYS A 397 CG CD CE NZ REMARK 470 ARG A 398 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 399 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 471 CG CD OE1 OE2 REMARK 470 ARG A 545 CG CD NE CZ NH1 NH2 REMARK 470 GLN D1058 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 MET A 22 -54.95 -139.10 REMARK 500 ALA A 30 119.30 -161.25 REMARK 500 ASP A 36 -116.96 56.13 REMARK 500 PRO A 52 -71.02 -46.93 REMARK 500 PRO A 144 109.17 -52.09 REMARK 500 ASN A 146 44.42 -81.18 REMARK 500 HIS A 298 50.97 -93.41 REMARK 500 PRO A 396 90.81 -63.85 REMARK 500 LYS A 397 78.60 -66.49 REMARK 500 ARG A 399 -65.13 -144.14 REMARK 500 ASN A 435 49.30 -156.85 REMARK 500 SER A 437 74.40 58.81 REMARK 500 ASP A 480 72.51 50.35 REMARK 500 REMARK 500 REMARK: NULL
REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 591 DISTANCE = 7.46 ANGSTROMS
REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A 550 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A 551
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3GCM RELATED DB: PDB REMARK 900 POLYNUCLEOTIDE PHOSPHORYLASE IN COMPLEX WITH RNASE E AND RNA REMARK 900 RELATED ID: 3GLL RELATED DB: PDB REMARK 900 POLYNUCLEOTIDE PHOSPHORYLASE
DBREF 3GME A 1 549 UNP A7ZS61 PNP_ECO24 1 549 DBREF 3GME D 1021 1061 UNP A7ZKI9 A7ZKI9_ECO24 1021 1061
SEQRES 1 A 549 MET LEU ASN PRO ILE VAL ARG LYS PHE GLN TYR GLY GLN SEQRES 2 A 549 HIS THR VAL THR LEU GLU THR GLY MET MET ALA ARG GLN SEQRES 3 A 549 ALA THR ALA ALA VAL MET VAL SER MET ASP ASP THR ALA SEQRES 4 A 549 VAL PHE VAL THR VAL VAL GLY GLN LYS LYS ALA LYS PRO SEQRES 5 A 549 GLY GLN ASP PHE PHE PRO LEU THR VAL ASN TYR GLN GLU SEQRES 6 A 549 ARG THR TYR ALA ALA GLY ARG ILE PRO GLY SER PHE PHE SEQRES 7 A 549 ARG ARG GLU GLY ARG PRO SER GLU GLY GLU THR LEU ILE SEQRES 8 A 549 ALA ARG LEU ILE ASP ARG PRO ILE ARG PRO LEU PHE PRO SEQRES 9 A 549 GLU GLY PHE VAL ASN GLU VAL GLN VAL ILE ALA THR VAL SEQRES 10 A 549 VAL SER VAL ASN PRO GLN VAL ASN PRO ASP ILE VAL ALA SEQRES 11 A 549 MET ILE GLY ALA SER ALA ALA LEU SER LEU SER GLY ILE SEQRES 12 A 549 PRO PHE ASN GLY PRO ILE GLY ALA ALA ARG VAL GLY TYR SEQRES 13 A 549 ILE ASN ASP GLN TYR VAL LEU ASN PRO THR GLN ASP GLU SEQRES 14 A 549 LEU LYS GLU SER LYS LEU ASP LEU VAL VAL ALA GLY THR SEQRES 15 A 549 GLU ALA ALA VAL LEU MET VAL GLU SER GLU ALA GLU LEU SEQRES 16 A 549 LEU SER GLU ASP GLN MET LEU GLY ALA VAL VAL PHE GLY SEQRES 17 A 549 HIS GLU GLN GLN GLN VAL VAL ILE GLN ASN ILE ASN GLU SEQRES 18 A 549 LEU VAL LYS GLU ALA GLY LYS PRO ARG TRP ASP TRP GLN SEQRES 19 A 549 PRO GLU PRO VAL ASN GLU ALA LEU ASN ALA ARG VAL ALA SEQRES 20 A 549 ALA LEU ALA GLU ALA ARG LEU SER ASP ALA TYR ARG ILE SEQRES 21 A 549 THR ASP LYS GLN GLU ARG TYR ALA GLN VAL ASP VAL ILE SEQRES 22 A 549 LYS SER GLU THR ILE ALA THR LEU LEU ALA GLU ASP GLU SEQRES 23 A 549 THR LEU ASP GLU ASN GLU LEU GLY GLU ILE LEU HIS ALA SEQRES 24 A 549 ILE GLU LYS ASN VAL VAL ARG SER ARG VAL LEU ALA GLY SEQRES 25 A 549 GLU PRO ARG ILE ASP GLY ARG GLU LYS ASP MET ILE ARG SEQRES 26 A 549 GLY LEU ASP VAL ARG THR GLY VAL LEU PRO ARG THR HIS SEQRES 27 A 549 GLY SER ALA LEU PHE THR ARG GLY GLU THR GLN ALA LEU SEQRES 28 A 549 VAL THR ALA THR LEU GLY THR ALA ARG ASP ALA GLN VAL SEQRES 29 A 549 LEU ASP GLU LEU MET GLY GLU ARG THR ASP THR PHE LEU SEQRES 30 A 549 PHE HIS TYR ASN PHE PRO PRO TYR SER VAL GLY GLU THR SEQRES 31 A 549 GLY MET VAL GLY SER PRO LYS ARG ARG GLU ILE GLY HIS SEQRES 32 A 549 GLY ARG LEU ALA LYS ARG GLY VAL LEU ALA VAL MET PRO SEQRES 33 A 549 ASP MET ASP LYS PHE PRO TYR THR VAL ARG VAL VAL SER SEQRES 34 A 549 GLU ILE THR GLU SER ASN GLY SER SER SER MET ALA SER SEQRES 35 A 549 VAL CYS GLY ALA SER LEU ALA LEU MET ASP ALA GLY VAL SEQRES 36 A 549 PRO ILE LYS ALA ALA VAL ALA GLY ILE ALA MET GLY LEU SEQRES 37 A 549 VAL LYS GLU GLY ASP ASN TYR VAL VAL LEU SER ASP ILE SEQRES 38 A 549 LEU GLY ASP GLU ASP HIS LEU GLY ASP MET ASP PHE LYS SEQRES 39 A 549 VAL ALA GLY SER ARG ASP GLY ILE SER ALA LEU GLN MET SEQRES 40 A 549 ASP ILE LYS ILE GLU GLY ILE THR LYS GLU ILE MET GLN SEQRES 41 A 549 VAL ALA LEU ASN GLN ALA LYS GLY ALA ARG LEU HIS ILE SEQRES 42 A 549 LEU GLY VAL MET GLU GLN ALA ILE ASN ALA PRO ARG GLY SEQRES 43 A 549 ASP ILE SER SEQRES 1 D 41 GLU ALA PRO ARG HIS SER ASP TRP GLN ARG PRO THR PHE SEQRES 2 D 41 ALA PHE GLU GLY LYS GLY ALA ALA GLY GLY HIS THR ALA SEQRES 3 D 41 THR HIS HIS ALA SER ALA ALA PRO ALA ARG PRO GLN PRO SEQRES 4 D 41 VAL GLU
HET MN A 550 1 HET MN A 551 1
HETNAM MN MANGANESE (II) ION
FORMUL 3 MN 2(MN 2+) FORMUL 5 HOH *158(H2 O)
HELIX 1 1 THR A 67 ALA A 70 5 4 HELIX 2 2 SER A 85 ARG A 100 1 16 HELIX 3 3 PRO A 101 PHE A 103 5 3 HELIX 4 4 ASN A 125 GLY A 142 1 18 HELIX 5 5 SER A 197 GLN A 212 1 16 HELIX 6 6 GLN A 212 GLY A 227 1 16 HELIX 7 7 ASN A 239 ALA A 244 1 6 HELIX 8 8 ASP A 262 TYR A 267 1 6 HELIX 9 9 HIS A 298 GLY A 312 1 15 HELIX 10 10 PRO A 383 VAL A 387 5 5 HELIX 11 11 ARG A 399 LEU A 412 1 14 HELIX 12 12 SER A 437 GLY A 454 1 18 HELIX 13 13 LEU A 482 GLY A 489 1 8 HELIX 14 14 THR A 515 ILE A 541 1 27
SHEET 1 A 6 ILE A 5 TYR A 11 0 SHEET 2 A 6 HIS A 14 THR A 20 -1 O HIS A 14 N TYR A 11 SHEET 3 A 6 ALA A 29 MET A 35 -1 O SER A 34 N THR A 17 SHEET 4 A 6 THR A 38 GLY A 46 -1 O VAL A 42 N VAL A 31 SHEET 5 A 6 VAL A 111 SER A 119 -1 O THR A 116 N PHE A 41 SHEET 6 A 6 LEU A 59 GLU A 65 1 N ASN A 62 O VAL A 113 SHEET 1 B 8 GLN A 160 LEU A 163 0 SHEET 2 B 8 GLY A 150 ILE A 157 -1 N GLY A 155 O VAL A 162 SHEET 3 B 8 LEU A 177 GLY A 181 -1 O LEU A 177 N VAL A 154 SHEET 4 B 8 VAL A 186 LEU A 196 -1 O GLU A 190 N VAL A 178 SHEET 5 B 8 ILE A 502 ILE A 509 -1 O SER A 503 N ALA A 193 SHEET 6 B 8 MET A 491 GLY A 497 -1 N ALA A 496 O ALA A 504 SHEET 7 B 8 ALA A 462 GLU A 471 -1 N MET A 466 O PHE A 493 SHEET 8 B 8 ASN A 474 SER A 479 -1 O LEU A 478 N GLY A 467 SHEET 1 C 6 PHE A 376 ASN A 381 0 SHEET 2 C 6 THR A 424 GLU A 433 1 O VAL A 427 N HIS A 379 SHEET 3 C 6 THR A 348 GLY A 357 -1 N LEU A 351 O GLU A 430 SHEET 4 C 6 GLY A 339 ARG A 345 -1 N ARG A 345 O THR A 348 SHEET 5 C 6 LEU A 327 THR A 331 -1 N ASP A 328 O THR A 344 SHEET 6 C 6 HIS D1048 ALA D1052 -1 O ALA D1050 N VAL A 329
LINK O PHE A 41 MN MN A 551 1555 1555 2.26
CISPEP 1 GLY A 147 PRO A 148 0 -2.51
SITE 1 AC1 2 ASP A 486 ASP A 492 SITE 1 AC2 5 PHE A 41 VAL A 42 THR A 43 ILE A 114 SITE 2 AC2 5 THR A 116
CRYST1 158.574 158.574 156.118 90.00 90.00 120.00 H 3 2 18
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 0.006306 0.003641 0.000000 0.00000
SCALE2 0.000000 0.007282 0.000000 0.00000
SCALE3 0.000000 0.000000 0.006405 0.00000