PDB Short entry for 1H7A HEADER OXIDOREDUCTASE 04-JUL-01 1H7A TITLE STRUCTURAL BASIS FOR ALLOSTERIC SUBSTRATE SPECIFICITY TITLE 2 REGULATION IN CLASS III RIBONUCLEOTIDE REDUCTASES: NRDD IN TITLE 3 COMPLEX WITH DATP COMPND MOL_ID: 1; COMPND 2 MOLECULE: ANAEROBIC RIBONUCLEOTIDE-TRIPHOSPHATE REDUCTASE COMPND 3 LARGE 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, COMPND 11 M., XU, 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 3 24-FEB-09 1H7A 1 VERSN REVDAT 2 25-MAR-03 1H7A 1 REMARK HET HETNAM FORMUL REVDAT 2 2 LINK SITE TER HETATM REVDAT 2 3 CONECT REVDAT 1 28-MAR-02 1H7A 0 SPRSDE 28-MAR-02 1H7A 1B8B JRNL AUTH K.-M.LARSSON,J.ANDERSSON,B.-M.SJOEBERG,P.NORDLUND, JRNL AUTH 2 D.T.LOGAN JRNL TITL STRUCTURAL BASIS FOR ALLOSTERIC SUBSTRATE JRNL TITL 2 SPECIFICTY REGULATION IN ANAEROBIC RIBONUCLEOTIDE JRNL TITL 3 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. 2.75 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 : MAXIMUM LIKELIHOOD FUNCTION ON F REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.75 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.87 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 2332481.25 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 92.6 REMARK 3 NUMBER OF REFLECTIONS : 29676 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) : 0.215 REMARK 3 FREE R VALUE : 0.258 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 8.5 REMARK 3 FREE R VALUE TEST SET COUNT : 2512 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) : 2.75 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.92 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 72.90 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 3482 REMARK 3 BIN R VALUE (WORKING SET) : 0.324 REMARK 3 BIN FREE R VALUE : 0.369 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 8.20 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 313 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 : 4428 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 32 REMARK 3 SOLVENT ATOMS : 58 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 61.1 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 50.2 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 3.44 REMARK 3 B22 (A**2) : 3.44 REMARK 3 B33 (A**2) : -6.89 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) : 0.39 REMARK 3 LOW RESOLUTION CUTOFF (A) : 30.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.45 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.47 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.013 REMARK 3 BOND ANGLES (DEGREES) : 1.8 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.2 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.98 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.78 ; 1.50 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.88 ; 2.00 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.88 ; 2.00 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 4.31 ; 2.50 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.318931 REMARK 3 BSOL : 40.2851 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 : DATP.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 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE REGIONS BETWEEN RESIDUES 590 AND REMARK 3 605 ARE NOT SEEN IN THE ELECTRON DENSITY REMARK 4 REMARK 4 1H7A COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 05-JUL-01. REMARK 100 THE PDBE ID CODE IS EBI-8259. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-JUL-98 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 : NSLS REMARK 200 BEAMLINE : X12B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0714 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : BENT MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 29688 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.750 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.0 REMARK 200 DATA REDUNDANCY : 2.600 REMARK 200 R MERGE (I) : 0.09000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 8.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.75 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.81 REMARK 200 COMPLETENESS FOR SHELL (%) : 70.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.35800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: OTHER REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: 1B8B.PDB REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): NULL REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): NULL REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30% PEG 400, 0.2M MGCL2, REMARK 280 0.1M HEPES PH 7.5, 5MM DTT 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 122.06000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 49.18000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 49.18000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 183.09000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 49.18000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 49.18000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 61.03000 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 49.18000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 49.18000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 183.09000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 49.18000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 49.18000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 61.03000 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 122.06000 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 GENERATING THE BIOMOLECULE 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 98.36000 REMARK 350 BIOMT2 2 -1.000000 0.000000 0.000000 98.36000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 122.06000 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 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 NH2 ARG A 218 - O PRO A 232 2.12 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 REMARK 500 OH TYR A 162 OH TYR A 162 8665 2.18 REMARK 500 O HOH A 2002 O HOH A 2002 8665 1.33 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 GLY A 374 N - CA - C ANGL. DEV. = 17.7 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 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 TYR A 70 -60.45 -130.72 REMARK 500 ASN A 78 -92.21 -92.06 REMARK 500 CYS A 80 168.77 176.81 REMARK 500 GLU A 89 -70.67 -61.47 REMARK 500 ASN A 131 60.64 60.11 REMARK 500 ALA A 157 -83.10 -44.67 REMARK 500 ALA A 159 -87.21 -69.67 REMARK 500 LEU A 160 -10.23 -46.58 REMARK 500 ASP A 204 152.57 -44.69 REMARK 500 VAL A 242 -56.01 -145.99 REMARK 500 LYS A 246 -36.43 -27.86 REMARK 500 ARG A 264 20.68 -147.66 REMARK 500 MET A 265 -63.98 71.80 REMARK 500 ARG A 291 34.93 -158.93 REMARK 500 ALA A 367 81.59 -168.09 REMARK 500 ALA A 375 -66.25 -27.68 REMARK 500 THR A 443 130.52 -36.20 REMARK 500 ASP A 465 -10.05 70.13 REMARK 500 VAL A 466 -89.58 -106.52 REMARK 500 SER A 475 -108.37 27.72 REMARK 500 GLU A 481 1.70 -59.23 REMARK 500 ALA A 494 -47.43 -29.83 REMARK 500 ASN A 516 25.76 -173.91 REMARK 500 LEU A 517 -19.21 -46.35 REMARK 500 ASP A 532 -76.17 -97.95 REMARK 500 THR A 549 42.29 -82.69 REMARK 500 THR A 567 -32.18 -133.48 REMARK 500 CYS A 579 -62.99 -137.09 REMARK 500 ALA A 580 -38.37 -141.53 REMARK 500 PRO A 585 4.33 -63.40 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CHIRAL CENTERS REMARK 500 REMARK 500 UNEXPECTED CONFIGURATION OF THE FOLLOWING CHIRAL REMARK 500 CENTER(S) USING IMPROPER CA--C--CB--N CHIRALITY REMARK 500 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,A1,6X,F5.1,6X,A1,10X,A1,3X,A16) REMARK 500 REMARK 500 M RES CSSEQI IMPROPER EXPECTED FOUND DETAILS REMARK 500 LEU A 244 23.4 L L OUTSIDE RANGE 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 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 A1591 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 543 SG REMARK 620 2 CYS A 546 SG 103.0 REMARK 620 3 CYS A 564 SG 121.5 113.7 REMARK 620 4 CYS A 561 SG 115.6 94.1 105.7 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A1592 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DTP A1590 O1A REMARK 620 2 HOH A2057 O 79.7 REMARK 620 3 DTP A1590 O2B 108.9 153.4 REMARK 620 4 DTP A1590 O1G 79.6 113.4 93.1 REMARK 620 5 DTP A1590 O3B 69.1 147.6 52.5 53.5 REMARK 620 6 DTP A1590 O3A 56.2 117.8 56.1 100.2 50.0 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FE2 A1591 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A1592 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DTP A1590 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1H77 RELATED DB: PDB REMARK 900 STRUCTURAL BASIS FOR ALLOSTERIC SUBSTRATE REMARK 900 SPECIFICITY REGULATION IN CLASS III REMARK 900 RIBONUCLEOTIDE REDUCTASES: NRDD IN COMPLEX REMARK 900 WITH DGTP. REMARK 900 RELATED ID: 1H78 RELATED DB: PDB REMARK 900 STRUCTURAL BASIS FOR ALLOSTERIC SUBSTRATE REMARK 900 SPECIFICITY REGULATION IN CLASS III REMARK 900 RIBONUCLEOTIDE REDUCTASES: NRDD IN COMPLEX REMARK 900 WITH DCTP. REMARK 900 RELATED ID: 1H79 RELATED DB: PDB REMARK 900 STRUCTURAL BASIS FOR ALLOSTERIC SUBSTRATE REMARK 900 SPECIFICITY REGULATION IN CLASS III REMARK 900 RIBONUCLEOTIDE REDUCTASES: NRDD IN COMPLEX REMARK 900 WITH DTTP REMARK 900 RELATED ID: 1H7B RELATED DB: PDB REMARK 900 STRUCTURAL BASIS FOR ALLOSTERIC SUBSTRATE REMARK 900 SPECIFICITY REGULATION IN CLASS III REMARK 900 RIBONUCLEOTIDE REDUCTASES: NATIVE NRDD DBREF 1H7A A 1 605 UNP Q9T0V5 Q9T0V5 1 605 SEQADV 1H7A 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 FE2 A1591 1 HET MG A1592 1 HET DTP A1590 30 HETNAM FE2 FE (II) ION HETNAM MG MAGNESIUM ION HETNAM DTP 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE FORMUL 2 FE2 FE 2+ FORMUL 3 MG MG 2+ FORMUL 4 DTP C10 H16 N5 O12 P3 FORMUL 5 HOH *58(H2 O1) 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 LEU A 136 1 6 HELIX 6 6 LEU A 136 GLU A 152 1 17 HELIX 7 7 ASP A 158 LEU A 185 1 28 HELIX 8 8 ASP A 204 GLY A 221 1 18 HELIX 9 9 ASN A 250 MET A 265 1 16 HELIX 10 10 ALA A 272 GLY A 280 1 9 HELIX 11 11 LEU A 319 SER A 326 1 8 HELIX 12 12 ASN A 333 LEU A 359 1 27 HELIX 13 13 ALA A 364 VAL A 366 5 3 HELIX 14 14 ALA A 367 GLN A 372 1 6 HELIX 15 15 ILE A 386 LYS A 391 1 6 HELIX 16 16 GLY A 403 GLY A 412 1 10 HELIX 17 17 ILE A 415 GLY A 435 1 21 HELIX 18 18 ASN A 447 GLY A 461 1 15 HELIX 19 19 THR A 485 PHE A 498 1 14 HELIX 20 20 ASN A 516 LEU A 531 1 16 HELIX 21 21 CYS A 561 GLY A 565 5 5 HELIX 22 22 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 O ASN A 573 N 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 FE FE2 A1591 SG CYS A 543 1555 1555 2.04 LINK FE FE2 A1591 SG CYS A 546 1555 1555 1.77 LINK FE FE2 A1591 SG CYS A 564 1555 1555 1.44 LINK FE FE2 A1591 SG CYS A 561 1555 1555 2.16 LINK MG MG A1592 O2B DTP A1590 1555 1555 2.56 LINK MG MG A1592 O HOH A2057 1555 1555 2.71 LINK MG MG A1592 O1G DTP A1590 1555 1555 2.09 LINK MG MG A1592 O3B DTP A1590 1555 1555 3.05 LINK MG MG A1592 O3A DTP A1590 1555 1555 2.85 LINK MG MG A1592 O1A DTP A1590 1555 1555 2.21 CISPEP 1 SER A 71 PRO A 72 0 1.40 CISPEP 2 PHE A 231 PRO A 232 0 -0.08 CISPEP 3 TYR A 266 PRO A 267 0 0.00 SITE 1 AC1 5 CYS A 543 CYS A 546 CYS A 561 CYS A 564 SITE 2 AC1 5 GLU A 566 SITE 1 AC2 2 DTP A1590 HOH A2057 SITE 1 AC3 16 ILE A 99 GLU A 100 LYS A 103 VAL A 107 SITE 2 AC3 16 GLN A 114 LYS A 146 LYS A 169 ASP A 173 SITE 3 AC3 16 GLN A 176 ALA A 177 TYR A 180 GLU A 181 SITE 4 AC3 16 MG A1592 HOH A2013 HOH A2056 HOH A2058 CRYST1 98.360 98.360 244.120 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 0.010167 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010167 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004096 0.00000