HEADER OXIDOREDUCTASE 04-JUL-01 1H79 TITLE STRUCTURAL BASIS FOR ALLOSTERIC SUBSTRATE SPECIFICITY REGULATION IN TITLE 2 CLASS III RIBONUCLEOTIDE REDUCTASES: NRDD IN COMPLEX WITH DTTP COMPND MOL_ID: 1; COMPND 2 MOLECULE: ANAEROBIC RIBONUCLEOTIDE-TRIPHOSPHATE REDUCTASE LARGE COMPND 3 CHAIN; COMPND 4 CHAIN: A; COMPND 5 FRAGMENT: ACTIVE SITE SUBUNIT RESIDUES 1-605; COMPND 6 SYNONYM: ANAEROBIC NTP REDUCTASE; COMPND 7 EC: 1.17.4.2; COMPND 8 ENGINEERED: YES; COMPND 9 MUTATION: YES; COMPND 10 OTHER_DETAILS: SEQUENCE DETERMINATION\: YOUNG, P., OHMAN, M., XU, COMPND 11 M.Q. SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACTERIOPHAGE T4; SOURCE 3 ORGANISM_TAXID: 10665; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: JM109(DE3); SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PET29T4NRDD(G580A) KEYWDS OXIDOREDUCTASE, REDUCTASE, ALLOSTERIC REGULATION, SUBSTRATE KEYWDS 2 SPECIFICITY EXPDTA X-RAY DIFFRACTION AUTHOR K.-M.LARSSON,J.ANDERSSON,B.-M.SJOEBERG,P.NORDLUND,D.T.LOGAN REVDAT 5 13-DEC-23 1H79 1 LINK REVDAT 4 24-OCT-18 1H79 1 SOURCE REVDAT 3 24-FEB-09 1H79 1 VERSN REVDAT 2 25-MAR-03 1H79 1 REMARK HET HETNAM FORMUL REVDAT 2 2 1 LINK TER HETATM CONECT REVDAT 1 28-MAR-02 1H79 0 JRNL AUTH K.-M.LARSSON,J.ANDERSSON,B.-M.SJOEBERG,P.NORDLUND,D.T.LOGAN JRNL TITL STRUCTURAL BASIS FOR ALLOSTERIC SUBSTRATE SPECIFICTY JRNL TITL 2 REGULATION IN ANAEROBIC RIBONUCLEOTIDE REDUCTASE JRNL REF STRUCTURE V. 9 739 2001 JRNL REFN ISSN 0969-2126 JRNL PMID 11587648 JRNL DOI 10.1016/S0969-2126(01)00627-X REMARK 2 REMARK 2 RESOLUTION. 2.90 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 : MLF REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.99 REMARK 3 DATA CUTOFF (SIGMA(F)) : 164005 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 0.000 REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 98.9 REMARK 3 NUMBER OF REFLECTIONS : 26786 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) : 0.221 REMARK 3 FREE R VALUE : 0.261 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 8.500 REMARK 3 FREE R VALUE TEST SET COUNT : 2271 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.005 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) : 2.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.08 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.30 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 4005 REMARK 3 BIN R VALUE (WORKING SET) : 0.3490 REMARK 3 BIN FREE R VALUE : 0.4090 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 8.50 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 370 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.021 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4395 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 60 REMARK 3 SOLVENT ATOMS : 24 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 80.10 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 53.50 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 4.85000 REMARK 3 B22 (A**2) : 4.85000 REMARK 3 B33 (A**2) : -9.71000 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) : 0.36 REMARK 3 ESD FROM SIGMAA (A) : 0.42 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) : 0.43 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.50 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : 1.600 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 22.80 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.070 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) : 2.610 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 4.390 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 4.000 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 5.960 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.35 REMARK 3 BSOL : 43.10 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 : DTTP_PRDRG.PARAM REMARK 3 PARAMETER FILE 3 : ION.PARAM REMARK 3 PARAMETER FILE 4 : WATER.PARAM REMARK 3 PARAMETER FILE 5 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : DTTP_PRDRG.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: THE REGION BETWEEN APPROX. RESIDUES 545 REMARK 3 AND 570 IS INCOMPLETELY REFINED REMARK 4 REMARK 4 1H79 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 04-JUL-01. REMARK 100 THE DEPOSITION ID IS D_1290008257. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 7.50 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-3 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.931 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD 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 : 26786 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.900 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : 0.05000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 21.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.97 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.4 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.21700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 5.800 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: 1B8B.PDB REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 71.37 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.30 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 400, MGCL2, HEPES, DTT, PH 7.50 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 121.51950 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 49.04950 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 49.04950 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 182.27925 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 49.04950 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 49.04950 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 60.75975 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 49.04950 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 49.04950 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 182.27925 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 49.04950 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 49.04950 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 60.75975 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 121.51950 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 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: PQS REMARK 350 TOTAL BURIED SURFACE AREA: 6850 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 50130 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -39.9 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 BIOMT1 2 0.000000 -1.000000 0.000000 98.09900 REMARK 350 BIOMT2 2 -1.000000 0.000000 0.000000 98.09900 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 121.51950 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 MET A 1 REMARK 465 THR A 2 REMARK 465 ILE A 3 REMARK 465 GLU A 4 REMARK 465 LYS A 5 REMARK 465 GLU A 6 REMARK 465 ILE A 7 REMARK 465 GLU A 8 REMARK 465 GLY A 9 REMARK 465 LEU A 10 REMARK 465 ILE A 11 REMARK 465 HIS A 12 REMARK 465 LYS A 13 REMARK 465 THR A 14 REMARK 465 ASN A 15 REMARK 465 LYS A 16 REMARK 465 ASP A 17 REMARK 465 LEU A 18 REMARK 465 LEU A 19 REMARK 465 ASN A 20 REMARK 465 GLU A 21 REMARK 465 ASN A 22 REMARK 465 ALA A 23 REMARK 465 ASN A 24 REMARK 465 LYS A 25 REMARK 465 ASP A 26 REMARK 465 ASN A 586 REMARK 465 GLU A 587 REMARK 465 ARG A 588 REMARK 465 GLY A 589 REMARK 465 PHE A 590 REMARK 465 ASN A 591 REMARK 465 LEU A 592 REMARK 465 GLY A 593 REMARK 465 LYS A 594 REMARK 465 ASN A 595 REMARK 465 LYS A 596 REMARK 465 GLU A 597 REMARK 465 ILE A 598 REMARK 465 MET A 599 REMARK 465 HIS A 600 REMARK 465 ARG A 601 REMARK 465 VAL A 602 REMARK 465 LYS A 603 REMARK 465 HIS A 604 REMARK 465 GLN A 605 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 CB CYS A 564 FE FE2 A 1588 2.10 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 ARG A 28 30.26 -86.04 REMARK 500 TYR A 70 -55.25 -126.06 REMARK 500 ASN A 78 -109.29 -92.96 REMARK 500 GLU A 152 40.03 -85.01 REMARK 500 LYS A 153 -29.74 -148.01 REMARK 500 ALA A 157 -86.25 -57.24 REMARK 500 LEU A 185 23.33 -66.21 REMARK 500 PHE A 186 55.37 -113.88 REMARK 500 ASN A 189 16.89 41.41 REMARK 500 GLN A 191 90.06 80.42 REMARK 500 THR A 192 121.44 -10.63 REMARK 500 THR A 201 22.28 -78.40 REMARK 500 VAL A 242 -53.95 -136.26 REMARK 500 ASN A 243 17.02 -162.14 REMARK 500 LYS A 246 -30.71 -33.89 REMARK 500 ASN A 250 30.75 -93.65 REMARK 500 MET A 265 -46.95 83.10 REMARK 500 ARG A 291 25.70 -157.79 REMARK 500 SER A 300 -19.41 -45.05 REMARK 500 LEU A 306 -65.26 -120.05 REMARK 500 ALA A 367 85.98 -163.30 REMARK 500 GLU A 373 -150.92 -89.84 REMARK 500 ALA A 375 -64.10 -27.20 REMARK 500 LYS A 391 172.93 -57.71 REMARK 500 THR A 443 121.66 -38.80 REMARK 500 ALA A 445 69.76 36.95 REMARK 500 ASP A 465 -24.69 77.88 REMARK 500 VAL A 466 -71.72 -92.79 REMARK 500 SER A 475 -109.97 32.09 REMARK 500 GLU A 482 126.51 -38.67 REMARK 500 ILE A 499 -60.01 -94.43 REMARK 500 ASN A 516 52.56 -97.96 REMARK 500 ASP A 532 -82.71 -89.22 REMARK 500 CYS A 564 -34.51 170.20 REMARK 500 CYS A 579 -102.18 -117.12 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 TYR A 139 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 FE2 A1588 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 543 SG REMARK 620 2 CYS A 546 SG 100.4 REMARK 620 3 CYS A 561 SG 116.4 108.2 REMARK 620 4 CYS A 564 SG 85.2 129.8 113.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A1587 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 TTP A1586 O1A REMARK 620 2 TTP A1586 O1G 98.3 REMARK 620 3 TTP A1586 O3B 75.2 55.3 REMARK 620 4 TTP A1586 O2B 112.3 86.4 53.2 REMARK 620 5 TTP A1586 O3A 61.0 106.9 51.8 53.4 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A1587 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FE2 A1588 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE TTP A1586 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE TTP A1589 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1H77 RELATED DB: PDB REMARK 900 STRUCTURAL BASIS FOR ALLOSTERIC SUBSTRATE SPECIFICITY REGULATION IN REMARK 900 CLASS III RIBONUCLEOTIDE REDUCTASES: NRDD IN COMPLEX WITH DGTP. REMARK 900 RELATED ID: 1H78 RELATED DB: PDB REMARK 900 STRUCTURAL BASIS FOR ALLOSTERIC SUBSTRATE SPECIFICITY REGULATION IN REMARK 900 CLASS III RIBONUCLEOTIDE REDUCTASES: NRDD IN COMPLEX WITH DCTP. REMARK 900 RELATED ID: 1H7A RELATED DB: PDB REMARK 900 STRUCTURAL BASIS FOR ALLOSTERIC SUBSTRATE SPECIFICITY REGULATION IN REMARK 900 CLASS III RIBONUCLEOTIDE REDUCTASES: NRDD IN COMPLEX WITH DATP. REMARK 900 RELATED ID: 1H7B RELATED DB: PDB REMARK 900 STRUCTURAL BASIS FOR ALLOSTERIC SUBSTRATE SPECIFICITY REGULATION IN REMARK 900 CLASS III RIBONUCLEOTIDE REDUCTASES: NATIVE NRDD DBREF 1H79 A 1 605 UNP Q9T0V5 Q9T0V5 1 605 SEQADV 1H79 ALA A 580 UNP Q9T0V5 GLY 580 ENGINEERED MUTATION SEQRES 1 A 605 MET THR ILE GLU LYS GLU ILE GLU GLY LEU ILE HIS LYS SEQRES 2 A 605 THR ASN LYS ASP LEU LEU ASN GLU ASN ALA ASN LYS ASP SEQRES 3 A 605 SER ARG VAL PHE PRO THR GLN ARG ASP LEU MET ALA GLY SEQRES 4 A 605 ILE VAL SER LYS HIS ILE ALA LYS ASN MET VAL PRO SER SEQRES 5 A 605 PHE ILE MET LYS ALA HIS GLU SER GLY ILE ILE HIS VAL SEQRES 6 A 605 HIS ASP ILE ASP TYR SER PRO ALA LEU PRO PHE THR ASN SEQRES 7 A 605 CYS CYS LEU VAL ASP LEU LYS GLY MET LEU GLU ASN GLY SEQRES 8 A 605 PHE LYS LEU GLY ASN ALA GLN ILE GLU THR PRO LYS SER SEQRES 9 A 605 ILE GLY VAL ALA THR ALA ILE MET ALA GLN ILE THR ALA SEQRES 10 A 605 GLN VAL ALA SER HIS GLN TYR GLY GLY THR THR PHE ALA SEQRES 11 A 605 ASN VAL ASP LYS VAL LEU SER PRO TYR VAL LYS ARG THR SEQRES 12 A 605 TYR ALA LYS HIS ILE GLU ASP ALA GLU LYS TRP GLN ILE SEQRES 13 A 605 ALA ASP ALA LEU ASN TYR ALA GLN SER LYS THR GLU LYS SEQRES 14 A 605 ASP VAL TYR ASP ALA PHE GLN ALA TYR GLU TYR GLU VAL SEQRES 15 A 605 ASN THR LEU PHE SER SER ASN GLY GLN THR PRO PHE VAL SEQRES 16 A 605 THR ILE THR PHE GLY THR GLY THR ASP TRP THR GLU ARG SEQRES 17 A 605 MET ILE GLN LYS ALA ILE LEU LYS ASN ARG ILE LYS GLY SEQRES 18 A 605 LEU GLY ARG ASP GLY ILE THR PRO ILE PHE PRO LYS LEU SEQRES 19 A 605 VAL MET PHE VAL GLU GLU GLY VAL ASN LEU TYR LYS ASP SEQRES 20 A 605 ASP PRO ASN TYR ASP ILE LYS GLN LEU ALA LEU GLU CYS SEQRES 21 A 605 ALA SER LYS ARG MET TYR PRO ASP ILE ILE SER ALA LYS SEQRES 22 A 605 ASN ASN LYS ALA ILE THR GLY SER SER VAL PRO VAL SER SEQRES 23 A 605 PRO MET GLY CYS ARG SER PHE LEU SER VAL TRP LYS ASP SEQRES 24 A 605 SER THR GLY ASN GLU ILE LEU ASP GLY ARG ASN ASN LEU SEQRES 25 A 605 GLY VAL VAL THR LEU ASN LEU PRO ARG ILE ALA LEU ASP SEQRES 26 A 605 SER TYR ILE GLY THR GLN PHE ASN GLU GLN LYS PHE VAL SEQRES 27 A 605 GLU LEU PHE ASN GLU ARG MET ASP LEU CYS PHE GLU ALA SEQRES 28 A 605 LEU MET CYS ARG ILE SER SER LEU LYS GLY VAL LYS ALA SEQRES 29 A 605 THR VAL ALA PRO ILE LEU TYR GLN GLU GLY ALA PHE GLY SEQRES 30 A 605 VAL ARG LEU LYS PRO ASP ASP ASP ILE ILE GLU LEU PHE SEQRES 31 A 605 LYS ASN GLY ARG SER SER VAL SER LEU GLY TYR ILE GLY SEQRES 32 A 605 ILE HIS GLU LEU ASN ILE LEU VAL GLY ARG ASP ILE GLY SEQRES 33 A 605 ARG GLU ILE LEU THR LYS MET ASN ALA HIS LEU LYS GLN SEQRES 34 A 605 TRP THR GLU ARG THR GLY PHE ALA PHE SER LEU TYR SER SEQRES 35 A 605 THR PRO ALA GLU ASN LEU CYS TYR ARG PHE CYS LYS LEU SEQRES 36 A 605 ASP THR GLU LYS TYR GLY SER VAL LYS ASP VAL THR ASP SEQRES 37 A 605 LYS GLY TRP TYR THR ASN SER PHE HIS VAL SER VAL GLU SEQRES 38 A 605 GLU ASN ILE THR PRO PHE GLU LYS ILE SER ARG GLU ALA SEQRES 39 A 605 PRO TYR HIS PHE ILE ALA THR GLY GLY HIS ILE SER TYR SEQRES 40 A 605 VAL GLU LEU PRO ASP MET LYS ASN ASN LEU LYS GLY LEU SEQRES 41 A 605 GLU ALA VAL TRP ASP TYR ALA ALA GLN HIS LEU ASP TYR SEQRES 42 A 605 PHE GLY VAL ASN MET PRO VAL ASP LYS CYS PHE THR CYS SEQRES 43 A 605 GLY SER THR HIS GLU MET THR PRO THR GLU ASN GLY PHE SEQRES 44 A 605 VAL CYS SER ILE CYS GLY GLU THR ASP PRO LYS LYS MET SEQRES 45 A 605 ASN THR ILE ARG ARG THR CYS ALA TYR LEU GLY ASN PRO SEQRES 46 A 605 ASN GLU ARG GLY PHE ASN LEU GLY LYS ASN LYS GLU ILE SEQRES 47 A 605 MET HIS ARG VAL LYS HIS GLN HET TTP A1586 29 HET MG A1587 1 HET FE2 A1588 1 HET TTP A1589 29 HETNAM TTP THYMIDINE-5'-TRIPHOSPHATE HETNAM MG MAGNESIUM ION HETNAM FE2 FE (II) ION FORMUL 2 TTP 2(C10 H17 N2 O14 P3) FORMUL 3 MG MG 2+ FORMUL 4 FE2 FE 2+ FORMUL 6 HOH *24(H2 O) HELIX 1 1 VAL A 29 LYS A 47 1 19 HELIX 2 2 PRO A 51 SER A 60 1 10 HELIX 3 3 ASP A 83 GLY A 91 1 9 HELIX 4 4 SER A 104 SER A 121 1 18 HELIX 5 5 ASN A 131 LEU A 136 1 6 HELIX 6 6 LEU A 136 ASP A 150 1 15 HELIX 7 7 ASP A 150 GLN A 155 1 6 HELIX 8 8 ASP A 158 LEU A 185 1 28 HELIX 9 9 ASP A 204 GLY A 221 1 18 HELIX 10 10 ASN A 250 MET A 265 1 16 HELIX 11 11 ALA A 272 GLY A 280 1 9 HELIX 12 12 LEU A 319 ASP A 325 1 7 HELIX 13 13 ASN A 333 SER A 357 1 25 HELIX 14 14 SER A 358 LYS A 360 5 3 HELIX 15 15 ALA A 364 VAL A 366 5 3 HELIX 16 16 ALA A 367 GLN A 372 1 6 HELIX 17 17 ILE A 386 PHE A 390 5 5 HELIX 18 18 GLY A 403 GLY A 412 1 10 HELIX 19 19 ILE A 415 GLY A 435 1 21 HELIX 20 20 ASN A 447 GLY A 461 1 15 HELIX 21 21 THR A 485 ALA A 494 1 10 HELIX 22 22 PRO A 495 ALA A 500 1 6 HELIX 23 23 ASN A 516 LEU A 531 1 16 HELIX 24 24 ASP A 568 LYS A 570 5 3 SHEET 1 AA 4 ILE A 63 VAL A 65 0 SHEET 2 AA 4 ASN A 311 ASN A 318 -1 O THR A 316 N HIS A 64 SHEET 3 AA 4 SER A 396 ILE A 402 1 O SER A 396 N LEU A 312 SHEET 4 AA 4 ALA A 437 TYR A 441 1 O ALA A 437 N VAL A 397 SHEET 1 AB 7 CYS A 80 LEU A 81 0 SHEET 2 AB 7 THR A 127 PHE A 129 1 N THR A 128 O CYS A 80 SHEET 3 AB 7 VAL A 195 PHE A 199 1 O THR A 196 N PHE A 129 SHEET 4 AB 7 LYS A 233 VAL A 238 1 O LYS A 233 N ILE A 197 SHEET 5 AB 7 ASP A 268 SER A 271 1 O ASP A 268 N MET A 236 SHEET 6 AB 7 TYR A 533 ASN A 537 -1 O PHE A 534 N ILE A 269 SHEET 7 AB 7 SER A 506 GLU A 509 1 O SER A 506 N GLY A 535 SHEET 1 AC 2 PHE A 92 LEU A 94 0 SHEET 2 AC 2 ALA A 97 ILE A 99 -1 O ALA A 97 N LEU A 94 SHEET 1 AD 2 TYR A 327 ILE A 328 0 SHEET 2 AD 2 GLN A 331 PHE A 332 -1 O GLN A 331 N ILE A 328 SHEET 1 AE 2 VAL A 540 CYS A 543 0 SHEET 2 AE 2 MET A 572 ILE A 575 -1 N ASN A 573 O LYS A 542 SHEET 1 AF 2 THR A 553 THR A 555 0 SHEET 2 AF 2 GLY A 558 VAL A 560 -1 O GLY A 558 N THR A 555 LINK SG CYS A 543 FE FE2 A1588 1555 1555 2.53 LINK SG CYS A 546 FE FE2 A1588 1555 1555 2.00 LINK SG CYS A 561 FE FE2 A1588 1555 1555 2.25 LINK SG CYS A 564 FE FE2 A1588 1555 1555 2.58 LINK O1A TTP A1586 MG MG A1587 1555 1555 1.99 LINK O1G TTP A1586 MG MG A1587 1555 1555 1.71 LINK O3B TTP A1586 MG MG A1587 1555 1555 3.05 LINK O2B TTP A1586 MG MG A1587 1555 1555 2.64 LINK O3A TTP A1586 MG MG A1587 1555 1555 2.85 CISPEP 1 SER A 71 PRO A 72 0 -0.87 CISPEP 2 PHE A 231 PRO A 232 0 0.13 CISPEP 3 TYR A 266 PRO A 267 0 0.83 SITE 1 AC1 1 TTP A1586 SITE 1 AC2 5 CYS A 543 CYS A 546 CYS A 561 ILE A 563 SITE 2 AC2 5 CYS A 564 SITE 1 AC3 11 ILE A 99 GLU A 100 LYS A 103 VAL A 107 SITE 2 AC3 11 ILE A 111 GLN A 114 LYS A 146 ASP A 173 SITE 3 AC3 11 GLN A 176 TYR A 180 MG A1587 SITE 1 AC4 10 HIS A 64 HIS A 66 ASP A 67 GLN A 191 SITE 2 AC4 10 THR A 443 ALA A 445 GLU A 446 ASN A 447 SITE 3 AC4 10 LEU A 448 ARG A 451 CRYST1 98.099 98.099 243.039 90.00 90.00 90.00 P 43 21 2 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 0.010194 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010194 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004114 0.00000