PDB Short entry for 1HK8 HEADER OXIDOREDUCTASE 06-MAR-03 1HK8 TITLE STRUCTURAL BASIS FOR ALLOSTERIC SUBSTRATE SPECIFICITY REGULATION IN TITLE 2 CLASS III RIBONUCLEOTIDE REDUCTASES: NRDD IN COMPLEX WITH DGTP COMPND MOL_ID: 1; COMPND 2 MOLECULE: ANAEROBIC RIBONUCLEOTIDE-TRIPHOSPHATE REDUCTASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: ACTIVE SITE SUBUNIT, RESIDUES 1-605; COMPND 5 EC: 1.17.4.2; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES; COMPND 8 OTHER_DETAILS: SEQUENCE DETERMINATION\: P.YOUNG, M.OHMAN, M.Q.XU. 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 18-APR-18 1HK8 1 JRNL REVDAT 4 17-JAN-18 1HK8 1 REMARK REVDAT 3 24-FEB-09 1HK8 1 VERSN REVDAT 2 03-APR-03 1HK8 1 JRNL REVDAT 1 27-MAR-03 1HK8 0 SPRSDE 27-MAR-03 1HK8 1H77 JRNL AUTH D.T.LOGAN,E.MULLIEZ,K.-M.LARSSON,S.BODEVIN,M.ATTA, JRNL AUTH 2 P.E.GARNAUD,B.-M.SJOBERG,M.FONTECAVE JRNL TITL A METAL-BINDING SITE IN THE CATALYTIC SUBUNIT OF ANAEROBIC JRNL TITL 2 RIBONUCLEOTIDE REDUCTASE. JRNL REF PROC.NATL.ACAD.SCI.USA V. 100 3826 2003 JRNL REFN ISSN 0027-8424 JRNL PMID 12655046 JRNL DOI 10.1073/PNAS.0736456100 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH K.M.LARSSON,J.ANDERSSON,B.M.SJOBERG,P.NORDLUND,D.T.LOGAN REMARK 1 TITL STRUCTURAL BASIS FOR ALLOSTERIC SUBSTRATE SPECIFICITY REMARK 1 TITL 2 REGULATION IN ANAEROBIC RIBONUCLEOTIDE REDUCTASES. REMARK 1 REF STRUCTURE V. 9 739 2001 REMARK 1 REFN ISSN 0969-2126 REMARK 1 PMID 11587648 REMARK 2 REMARK 2 RESOLUTION. 2.45 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.1.24 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.45 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.08 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 95.7 REMARK 3 NUMBER OF REFLECTIONS : 39943 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) : NULL REMARK 3 R VALUE (WORKING SET) : 0.204 REMARK 3 FREE R VALUE : 0.246 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.200 REMARK 3 FREE R VALUE TEST SET COUNT : 1742 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) : 2.45 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.52 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2298 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2750 REMARK 3 BIN FREE R VALUE SET COUNT : 116 REMARK 3 BIN FREE R VALUE : 0.3100 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4411 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 64 REMARK 3 SOLVENT ATOMS : 228 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 41.49 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.04000 REMARK 3 B22 (A**2) : -0.04000 REMARK 3 B33 (A**2) : 0.09000 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 OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.244 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.213 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.148 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 6.546 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.934 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.901 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4575 ; 0.011 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 4047 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6209 ; 1.397 ; 1.964 REMARK 3 BOND ANGLES OTHERS (DEGREES): 9458 ; 0.818 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 560 ; 6.203 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 682 ; 0.077 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5050 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 915 ; 0.003 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 975 ; 0.186 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 4777 ; 0.219 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): 2652 ; 0.085 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 245 ; 0.196 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 2 ; 0.015 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 22 ; 0.258 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 84 ; 0.268 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 14 ; 0.216 ; 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): 2788 ; 1.983 ; 2.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4514 ; 3.173 ; 3.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1787 ; 2.048 ; 2.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1695 ; 3.136 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL 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 : NULL REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : NULL REMARK 3 ION PROBE RADIUS : NULL REMARK 3 SHRINKAGE RADIUS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 1HK8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 06-MAR-03. REMARK 100 THE DEPOSITION ID IS D_1290012304. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-MAY-99 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 : MAX II REMARK 200 BEAMLINE : I711 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.043 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : BENT MIRROR 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 : 44361 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.430 REMARK 200 RESOLUTION RANGE LOW (A) : 37.800 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.6 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : 0.09600 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 15.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.43 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.49 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.1 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.27400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.800 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 1B8B REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 72.40 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.50 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30% PEG 400, 02M MGCL2, 0.1M HEPES PH REMARK 280 7.5, 7MM 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 123.06550 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 49.08150 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 49.08150 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 184.59825 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 49.08150 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 49.08150 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 61.53275 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 49.08150 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 49.08150 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 184.59825 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 49.08150 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 49.08150 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 61.53275 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 123.06550 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 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 98.16300 REMARK 350 BIOMT2 2 -1.000000 0.000000 0.000000 98.16300 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 123.06550 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A2004 LIES ON A SPECIAL POSITION. REMARK 400 REMARK 400 COMPOUND REMARK 400 CATALYTIC ACTIVITY INVOLVES 2'-DEOXYRIBONUCLEOSIDE TRIPHOSPHATE REMARK 400 + OXIDIZED THIOREDOXIN + H(2)O = RIBONUCLEOSIDE TRIPHOSPHATE + REMARK 400 REDUCED THIOREDOXIN. REMARK 400 REMARK 400 ENGINEERED MUTATION GLY 580 ALA 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 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 O HOH A 2133 O HOH A 2136 2.11 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG A 218 NE - CZ - NH2 ANGL. DEV. = -3.0 DEGREES REMARK 500 ASP A 532 CB - CG - OD2 ANGL. DEV. = 6.0 DEGREES REMARK 500 ASP A 568 CB - CG - OD2 ANGL. DEV. = 6.0 DEGREES 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 SER A 27 -60.22 -177.98 REMARK 500 PRO A 75 47.32 -77.16 REMARK 500 ASN A 78 -95.78 -101.54 REMARK 500 VAL A 242 -60.84 -129.94 REMARK 500 ASN A 243 19.07 -151.34 REMARK 500 ARG A 264 11.88 -142.66 REMARK 500 MET A 265 -60.55 69.41 REMARK 500 ARG A 291 38.32 -161.48 REMARK 500 LEU A 306 -67.69 -123.65 REMARK 500 ALA A 367 75.43 -158.58 REMARK 500 VAL A 466 -74.05 -119.51 REMARK 500 SER A 475 -113.57 39.28 REMARK 500 PRO A 511 -169.92 -76.21 REMARK 500 ASN A 516 53.72 -140.32 REMARK 500 ASP A 532 -68.33 -93.21 REMARK 500 CYS A 579 -86.00 -126.61 REMARK 500 ALA A 580 -56.23 -125.44 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 A2037 DISTANCE = 6.97 ANGSTROMS REMARK 525 HOH A2039 DISTANCE = 7.77 ANGSTROMS 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 MN A1590 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DGT A1587 O1G REMARK 620 2 DGT A1587 O1A 90.8 REMARK 620 3 DGT A1587 O2B 92.3 109.5 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A1589 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 564 SG REMARK 620 2 CYS A 561 SG 97.3 REMARK 620 3 CYS A 546 SG 117.4 126.6 REMARK 620 4 CYS A 543 SG 99.7 112.6 100.6 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 ZN A1589 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A1590 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DGT A1587 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DGT A1588 REMARK 900 REMARK 900 RELATED ENTRIES 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: 1H79 RELATED DB: PDB REMARK 900 STRUCTURAL BASIS FOR ALLOSTERIC SUBSTRATE SPECIFICITY REGULATION IN REMARK 900 CLASS III RIBONUCLEOTIDE REDUCTASES: NRDD IN COMPLEX WITH DTTP 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 1HK8 A 1 605 UNP P07071 NRDD_BPT4 1 605 SEQADV 1HK8 ALA A 580 UNP P07071 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 DGT A1587 31 HET DGT A1588 31 HET ZN A1589 1 HET MN A1590 1 HETNAM DGT 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE HETNAM ZN ZINC ION HETNAM MN MANGANESE (II) ION FORMUL 2 DGT 2(C10 H16 N5 O13 P3) FORMUL 4 ZN ZN 2+ FORMUL 5 MN MN 2+ FORMUL 6 HOH *228(H2 O) HELIX 1 1 VAL A 29 VAL A 50 1 22 HELIX 2 2 PRO A 51 SER A 60 1 10 HELIX 3 3 ASP A 83 ASN A 90 1 8 HELIX 4 4 SER A 104 SER A 121 1 18 HELIX 5 5 ASN A 131 TRP A 154 1 24 HELIX 6 6 ASP A 158 LEU A 185 1 28 HELIX 7 7 ASP A 204 GLY A 221 1 18 HELIX 8 8 ASN A 250 MET A 265 1 16 HELIX 9 9 ALA A 272 GLY A 280 1 9 HELIX 10 10 LEU A 319 ASP A 325 1 7 HELIX 11 11 ASN A 333 LEU A 359 1 27 HELIX 12 12 ALA A 364 VAL A 366 5 3 HELIX 13 13 ALA A 367 GLN A 372 1 6 HELIX 14 14 ILE A 386 LYS A 391 1 6 HELIX 15 15 GLY A 403 GLY A 412 1 10 HELIX 16 16 ILE A 415 GLY A 435 1 21 HELIX 17 17 ASN A 447 GLY A 461 1 15 HELIX 18 18 THR A 485 PHE A 498 1 14 HELIX 19 19 ASN A 516 LEU A 531 1 16 HELIX 20 20 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 SER A 442 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 O ASN A 573 N LYS A 542 SHEET 1 AF 2 THR A 553 PRO A 554 0 SHEET 2 AF 2 PHE A 559 VAL A 560 -1 O VAL A 560 N THR A 553 LINK O1G DGT A1587 MN MN A1590 1555 1555 1.73 LINK O1A DGT A1587 MN MN A1590 1555 1555 1.72 LINK ZN ZN A1589 SG CYS A 564 1555 1555 2.60 LINK ZN ZN A1589 SG CYS A 561 1555 1555 2.19 LINK ZN ZN A1589 SG CYS A 546 1555 1555 2.09 LINK ZN ZN A1589 SG CYS A 543 1555 1555 2.51 LINK MN MN A1590 O2B DGT A1587 1555 1555 2.26 CISPEP 1 SER A 71 PRO A 72 0 8.15 CISPEP 2 PHE A 231 PRO A 232 0 -4.50 CISPEP 3 TYR A 266 PRO A 267 0 6.67 SITE 1 AC1 4 CYS A 543 CYS A 546 CYS A 561 CYS A 564 SITE 1 AC2 1 DGT A1587 SITE 1 AC3 18 GLU A 100 PRO A 102 LYS A 103 VAL A 107 SITE 2 AC3 18 ILE A 111 LYS A 146 LYS A 169 ASP A 173 SITE 3 AC3 18 GLN A 176 ALA A 177 TYR A 180 GLU A 181 SITE 4 AC3 18 MN A1590 HOH A2077 HOH A2220 HOH A2221 SITE 5 AC3 18 HOH A2222 HOH A2223 SITE 1 AC4 11 HIS A 64 HIS A 66 ASP A 67 GLU A 446 SITE 2 AC4 11 ASN A 447 LEU A 448 HOH A2014 HOH A2224 SITE 3 AC4 11 HOH A2226 HOH A2227 HOH A2228 CRYST1 98.163 98.163 246.131 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 0.010187 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010187 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004063 0.00000