HEADER OXIDOREDUCTASE 04-JUL-01 1H78 TITLE STRUCTURAL BASIS FOR ALLOSTERIC SUBSTRATE SPECIFICITY REGULATION IN TITLE 2 CLASS III RIBONUCLEOTIDE REDUCTASES: NRDD IN COMPLEX WITH DCTP. 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 1H78 1 LINK REVDAT 4 24-OCT-18 1H78 1 SOURCE REVDAT 3 17-JAN-18 1H78 1 REMARK ATOM REVDAT 2 24-FEB-09 1H78 1 VERSN REVDAT 1 04-JUL-02 1H78 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. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.0 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.96 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 97.9 REMARK 3 NUMBER OF REFLECTIONS : 40833 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 : 0.254 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 8.500 REMARK 3 FREE R VALUE TEST SET COUNT : 3453 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.004 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) : 2.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.66 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.70 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 6032 REMARK 3 BIN R VALUE (WORKING SET) : 0.3000 REMARK 3 BIN FREE R VALUE : 0.3640 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 8.80 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 579 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.015 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4218 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 57 REMARK 3 SOLVENT ATOMS : 96 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 52.60 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 58.50 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 4.12000 REMARK 3 B22 (A**2) : 4.12000 REMARK 3 B33 (A**2) : -8.25000 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) : 0.32 REMARK 3 ESD FROM SIGMAA (A) : 0.28 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) : 0.39 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.36 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.022 REMARK 3 BOND ANGLES (DEGREES) : 2.100 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.40 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.330 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) : 2.020 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 3.180 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 3.310 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 4.480 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.35 REMARK 3 BSOL : 45.18 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 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: MLF TARGET FUNCTION RESIDUES 544-571 REMARK 3 NOT MODELLED BUT HAVE WEAK DENSITY REMARK 4 REMARK 4 1H78 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_1290008255. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-OCT-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) : 1.0266 REMARK 200 MONOCHROMATOR : SILICON CRYSTAL REMARK 200 OPTICS : BENT MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MAR SCANNER 345 MM PLATE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 41517 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : 0.08100 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 21.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.53 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.3 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.49300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.300 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: 1B8B.PDB REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 71.21 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.27 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 121.25750 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 48.96750 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 48.96750 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 181.88625 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 48.96750 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 48.96750 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 60.62875 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 48.96750 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 48.96750 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 181.88625 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 48.96750 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 48.96750 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 60.62875 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 121.25750 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 97.93500 REMARK 350 BIOMT2 2 -1.000000 0.000000 0.000000 97.93500 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 121.25750 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 GLY A 190 REMARK 465 GLN A 191 REMARK 465 CYS A 546 REMARK 465 GLY A 547 REMARK 465 SER A 548 REMARK 465 THR A 549 REMARK 465 HIS A 550 REMARK 465 GLU A 551 REMARK 465 MET A 552 REMARK 465 THR A 553 REMARK 465 PRO A 554 REMARK 465 THR A 555 REMARK 465 GLU A 556 REMARK 465 ASN A 557 REMARK 465 GLY A 558 REMARK 465 PHE A 559 REMARK 465 VAL A 560 REMARK 465 CYS A 561 REMARK 465 SER A 562 REMARK 465 ILE A 563 REMARK 465 CYS A 564 REMARK 465 GLY A 565 REMARK 465 GLU A 566 REMARK 465 THR A 567 REMARK 465 ASP A 568 REMARK 465 PRO A 569 REMARK 465 LYS A 570 REMARK 465 LYS A 571 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 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 NE2 GLN A 176 O1B DCP A 1589 8665 2.15 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 CYS A 543 CB CYS A 543 SG 0.283 REMARK 500 CYS A 579 CB CYS A 579 SG 0.129 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 91 C - N - CA ANGL. DEV. = -16.6 DEGREES REMARK 500 PRO A 193 C - N - CA ANGL. DEV. = 11.2 DEGREES REMARK 500 ARG A 218 NE - CZ - NH1 ANGL. DEV. = 5.2 DEGREES REMARK 500 ARG A 218 NE - CZ - NH2 ANGL. DEV. = -5.7 DEGREES REMARK 500 ARG A 379 NE - CZ - NH1 ANGL. DEV. = 4.9 DEGREES REMARK 500 ARG A 379 NE - CZ - NH2 ANGL. DEV. = -3.4 DEGREES REMARK 500 ARG A 451 NE - CZ - NH2 ANGL. DEV. = -5.2 DEGREES REMARK 500 CYS A 543 CA - CB - SG ANGL. DEV. = 21.5 DEGREES REMARK 500 CYS A 543 N - CA - C ANGL. DEV. = -16.7 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 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 ASN A 78 -93.30 -98.62 REMARK 500 LYS A 153 -26.05 -39.74 REMARK 500 GLN A 155 71.00 45.99 REMARK 500 ASP A 158 35.41 -74.97 REMARK 500 ALA A 159 -54.14 -23.60 REMARK 500 PRO A 193 99.45 -47.13 REMARK 500 ASP A 204 161.71 -45.74 REMARK 500 ASN A 243 21.92 -157.83 REMARK 500 LYS A 246 -23.93 -34.05 REMARK 500 MET A 265 -49.17 71.15 REMARK 500 ARG A 291 30.55 -150.57 REMARK 500 LEU A 306 -63.37 -122.75 REMARK 500 ALA A 367 85.36 -158.13 REMARK 500 ASP A 465 -6.58 70.04 REMARK 500 VAL A 466 -80.18 -111.59 REMARK 500 SER A 475 -106.72 28.64 REMARK 500 SER A 479 156.22 -48.42 REMARK 500 VAL A 480 -134.44 -67.51 REMARK 500 GLU A 481 42.50 25.79 REMARK 500 ASN A 483 74.71 -59.68 REMARK 500 ASN A 516 50.62 -144.19 REMARK 500 PHE A 544 23.13 -76.47 REMARK 500 CYS A 579 -98.48 -116.02 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 0.11 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 MG A1590 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DCP A1589 O1A REMARK 620 2 DCP A1589 O1G 86.7 REMARK 620 3 DCP A1589 O2B 100.3 106.9 REMARK 620 4 HOH A2096 O 77.2 121.4 131.2 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 MG A1590 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DCP A1588 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DCP 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: 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 1H78 A 1 605 UNP Q9T0V5 Q9T0V5 1 605 SEQADV 1H78 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 DCP A1588 28 HET DCP A1589 28 HET MG A1590 1 HETNAM DCP 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE HETNAM MG MAGNESIUM ION FORMUL 2 DCP 2(C9 H16 N3 O13 P3) FORMUL 4 MG MG 2+ FORMUL 5 HOH *96(H2 O) HELIX 1 1 VAL A 29 ASN A 48 1 20 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 ASN A 189 1 32 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 5 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 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 LYS A 542 0 SHEET 2 AE 2 ASN A 573 ILE A 575 -1 N ASN A 573 O LYS A 542 LINK O1A DCP A1589 MG MG A1590 1555 1555 1.78 LINK O1G DCP A1589 MG MG A1590 1555 1555 1.83 LINK O2B DCP A1589 MG MG A1590 1555 1555 2.14 LINK MG MG A1590 O HOH A2096 1555 1555 2.24 CISPEP 1 SER A 71 PRO A 72 0 1.43 CISPEP 2 PHE A 231 PRO A 232 0 -0.03 CISPEP 3 TYR A 266 PRO A 267 0 0.57 SITE 1 AC1 2 DCP A1589 HOH A2096 SITE 1 AC2 12 HIS A 64 HIS A 66 ASP A 67 THR A 443 SITE 2 AC2 12 PRO A 444 ALA A 445 GLU A 446 ASN A 447 SITE 3 AC2 12 LEU A 448 ARG A 451 HOH A2093 HOH A2095 SITE 1 AC3 15 ILE A 99 GLU A 100 LYS A 103 VAL A 107 SITE 2 AC3 15 ILE A 111 GLN A 114 LYS A 146 ASP A 173 SITE 3 AC3 15 GLN A 176 ALA A 177 TYR A 180 MG A1590 SITE 4 AC3 15 HOH A2019 HOH A2029 HOH A2096 CRYST1 97.935 97.935 242.515 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 0.010211 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010211 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004123 0.00000