HEADER OXIDOREDUCTASE 02-MAY-11 3RSR TITLE CRYSTAL STRUCTURE OF 5-NITP INHIBITION OF YEAST RIBONUCLEOTIDE TITLE 2 REDUCTASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE LARGE CHAIN 1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: RIBONUCLEOTIDE REDUCTASE R1 SUBUNIT 1, RIBONUCLEOTIDE COMPND 5 REDUCTASE LARGE SUBUNIT 1; COMPND 6 EC: 1.17.4.1; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 3 ORGANISM_COMMON: YEAST; SOURCE 4 ORGANISM_TAXID: 4932; SOURCE 5 GENE: RNR1, CRT7, RIR1, SDS12, YER070W; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS 10-STRANDED ALPHA/BETA BARREL, NUCLEOTIDE REDUCTION, OXIDIZED, KEYWDS 2 OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR Q.WAN,F.MOHAMMED,S.JHA,E.MOTEA,A.BERDIS,C.G.DEALWIS REVDAT 1 14-NOV-12 3RSR 0 JRNL AUTH M.F.AHMAD,Q.WAN,S.JHA,E.MOTEA,A.BERDIS,C.DEALWIS JRNL TITL EVALUATING THE THERAPEUTIC POTENTIAL OF A NON-NATURAL JRNL TITL 2 NUCLEOTIDE THAT INHIBITS HUMAN RIBONUCLEOTIDE REDUCTASE. JRNL REF MOL.CANCER THER. V. 11 2077 2012 JRNL REFN ISSN 1535-7163 JRNL PMID 22933704 JRNL DOI 10.1158/1535-7163.MCT-12-0199 REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.7_650) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VICENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE- REMARK 3 : KUNSTLEVE,LI-WEI HUNG,ROBERT IMMORMINO, REMARK 3 : TOM IOERGER,AIRLIE MCCOY,ERIK MCKEE,NIGEL REMARK 3 : MORIARTY,REETAL PAI,RANDY READ,JANE REMARK 3 : RICHARDSON,DAVID RICHARDSON,TOD ROMO,JIM REMARK 3 : SACCHETTINI,NICHOLAS SAUTER,JACOB SMITH, REMARK 3 : LAURENT STORONI,TOM TERWILLIGER,PETER REMARK 3 : ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.97 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 37089 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.188 REMARK 3 R VALUE (WORKING SET) : 0.188 REMARK 3 FREE R VALUE : 0.233 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.010 REMARK 3 FREE R VALUE TEST SET COUNT : 1860 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 19.9693 - 5.3757 1.00 2878 148 0.2034 0.2242 REMARK 3 2 5.3757 - 4.2807 1.00 2774 159 0.1647 0.2045 REMARK 3 3 4.2807 - 3.7436 1.00 2743 132 0.1684 0.2047 REMARK 3 4 3.7436 - 3.4032 1.00 2714 148 0.1765 0.2068 REMARK 3 5 3.4032 - 3.1603 1.00 2758 109 0.1922 0.2505 REMARK 3 6 3.1603 - 2.9746 1.00 2689 148 0.2013 0.2770 REMARK 3 7 2.9746 - 2.8260 1.00 2716 128 0.2030 0.2739 REMARK 3 8 2.8260 - 2.7033 1.00 2690 138 0.1925 0.2302 REMARK 3 9 2.7033 - 2.5995 1.00 2667 152 0.1974 0.2508 REMARK 3 10 2.5995 - 2.5100 1.00 2676 157 0.2004 0.2549 REMARK 3 11 2.5100 - 2.4316 1.00 2647 150 0.2107 0.3045 REMARK 3 12 2.4316 - 2.3622 1.00 2660 135 0.2082 0.2754 REMARK 3 13 2.3622 - 2.3001 1.00 2661 156 0.2119 0.2793 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 REMARK 3 SHRINKAGE RADIUS : 0.83 REMARK 3 K_SOL : 0.37 REMARK 3 B_SOL : 61.75 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.270 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.780 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -2.50610 REMARK 3 B22 (A**2) : -12.00050 REMARK 3 B33 (A**2) : 14.50660 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 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.008 4938 REMARK 3 ANGLE : 1.303 6706 REMARK 3 CHIRALITY : 0.093 743 REMARK 3 PLANARITY : 0.006 852 REMARK 3 DIHEDRAL : 16.676 1788 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3RSR COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-MAY-11. REMARK 100 THE RCSB ID CODE IS RCSB065330. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-APR-10 REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 23-BM-B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 37089 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 3.500 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : 99.0 REMARK 200 DATA REDUNDANCY IN SHELL : 5.70 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.49600 REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.10 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.05 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10 MG/ML PROTEIN, 0.1 M SODIUM ACETATE REMARK 280 AT PH 6.5, 25% PEG 3350, 0.2 M AMMONIUM SULFATE , VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X+1/2,Y+1/2,-Z REMARK 290 4555 X+1/2,-Y+1/2,-Z 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 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 54.17650 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 59.10400 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 54.17650 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 59.10400 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4410 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 43930 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -41.0 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 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 118.20800 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 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 A 899 LIES ON A SPECIAL POSITION. 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 TYR A 2 REMARK 465 VAL A 3 REMARK 465 TYR A 4 REMARK 465 LYS A 5 REMARK 465 ARG A 6 REMARK 465 ASP A 7 REMARK 465 GLY A 8 REMARK 465 ARG A 9 REMARK 465 LYS A 10 REMARK 465 GLU A 11 REMARK 465 PRO A 12 REMARK 465 VAL A 13 REMARK 465 GLN A 14 REMARK 465 PHE A 15 REMARK 465 ASP A 16 REMARK 465 LYS A 17 REMARK 465 ILE A 18 REMARK 465 THR A 19 REMARK 465 ALA A 20 REMARK 465 ARG A 21 REMARK 465 ILE A 22 REMARK 465 SER A 23 REMARK 465 ARG A 24 REMARK 465 LEU A 25 REMARK 465 CYS A 26 REMARK 465 TYR A 27 REMARK 465 GLY A 28 REMARK 465 LEU A 29 REMARK 465 ASP A 30 REMARK 465 PRO A 31 REMARK 465 LYS A 32 REMARK 465 HIS A 33 REMARK 465 ILE A 34 REMARK 465 ASP A 35 REMARK 465 ALA A 36 REMARK 465 VAL A 37 REMARK 465 LYS A 38 REMARK 465 VAL A 39 REMARK 465 THR A 40 REMARK 465 GLN A 41 REMARK 465 ARG A 42 REMARK 465 ILE A 43 REMARK 465 ILE A 44 REMARK 465 SER A 45 REMARK 465 GLY A 46 REMARK 465 VAL A 47 REMARK 465 TYR A 48 REMARK 465 GLU A 49 REMARK 465 GLY A 50 REMARK 465 VAL A 51 REMARK 465 THR A 52 REMARK 465 THR A 53 REMARK 465 ILE A 54 REMARK 465 GLU A 55 REMARK 465 LEU A 56 REMARK 465 ASP A 57 REMARK 465 ASN A 58 REMARK 465 LEU A 59 REMARK 465 ALA A 60 REMARK 465 ALA A 61 REMARK 465 GLU A 62 REMARK 465 THR A 63 REMARK 465 CYS A 64 REMARK 465 ALA A 65 REMARK 465 TYR A 66 REMARK 465 MET A 67 REMARK 465 THR A 68 REMARK 465 THR A 69 REMARK 465 VAL A 70 REMARK 465 HIS A 71 REMARK 465 PRO A 72 REMARK 465 ASP A 73 REMARK 465 TYR A 74 REMARK 465 ALA A 75 REMARK 465 THR A 76 REMARK 465 LEU A 77 REMARK 465 ALA A 78 REMARK 465 ALA A 79 REMARK 465 ARG A 80 REMARK 465 ILE A 81 REMARK 465 ALA A 82 REMARK 465 ILE A 83 REMARK 465 SER A 84 REMARK 465 ASN A 85 REMARK 465 LEU A 86 REMARK 465 HIS A 87 REMARK 465 LYS A 88 REMARK 465 ASP A 286A REMARK 465 GLN A 286B REMARK 465 GLY A 286C REMARK 465 GLY A 286D REMARK 465 ASN A 286E REMARK 465 LYS A 286F REMARK 465 ARG A 286G REMARK 465 PRO A 286H REMARK 465 GLY A 286I REMARK 465 ALA A 286J REMARK 465 ASN A 306A REMARK 465 HIS A 306B REMARK 465 GLY A 306C REMARK 465 LYS A 306D REMARK 465 GLU A 306E REMARK 465 GLU A 306F REMARK 465 ILE A 306G REMARK 465 ARG A 306H REMARK 465 ALA A 306I REMARK 465 ARG A 306J REMARK 465 GLU A 437A REMARK 465 ASP A 437B REMARK 465 GLY A 437C REMARK 465 ALA A 585A REMARK 465 SER A 585B REMARK 465 VAL A 598A REMARK 465 THR A 598B REMARK 465 SER A 598C REMARK 465 ASN A 598D REMARK 465 MET A 598E REMARK 465 TYR A 598F REMARK 465 SER A 598G REMARK 465 ARG A 598H REMARK 465 ARG A 598I REMARK 465 VAL A 598J REMARK 465 LEU A 598K REMARK 465 SER A 598L REMARK 465 GLY A 598M REMARK 465 GLU A 598N REMARK 465 PHE A 598O REMARK 465 GLN A 598P REMARK 465 VAL A 598Q REMARK 465 VAL A 598R REMARK 465 ASP A 612A REMARK 465 GLU A 612B REMARK 465 GLY A 612C REMARK 465 MET A 612D REMARK 465 LYS A 612E REMARK 465 ALA A 699 REMARK 465 ALA A 700 REMARK 465 SER A 701 REMARK 465 ALA A 702 REMARK 465 ALA A 703 REMARK 465 ILE A 704 REMARK 465 GLN A 705 REMARK 465 PHE A 706 REMARK 465 THR A 707 REMARK 465 ILE A 708 REMARK 465 ASP A 709 REMARK 465 GLN A 710 REMARK 465 LYS A 711 REMARK 465 ILE A 712 REMARK 465 ALA A 713 REMARK 465 ASP A 714 REMARK 465 GLN A 715 REMARK 465 ALA A 716 REMARK 465 THR A 717 REMARK 465 GLU A 718 REMARK 465 ASN A 719 REMARK 465 VAL A 720 REMARK 465 ALA A 721 REMARK 465 ASP A 722 REMARK 465 ILE A 723 REMARK 465 SER A 724 REMARK 465 ASN A 725 REMARK 465 LEU A 726 REMARK 465 LYS A 727 REMARK 465 ARG A 728 REMARK 465 PRO A 729 REMARK 465 SER A 730 REMARK 465 TYR A 731 REMARK 465 MET A 732 REMARK 465 PRO A 733 REMARK 465 SER A 734 REMARK 465 SER A 735 REMARK 465 ALA A 736 REMARK 465 SER A 737 REMARK 465 TYR A 738 REMARK 465 ALA A 739 REMARK 465 ALA A 740 REMARK 465 SER A 741 REMARK 465 ASP A 742 REMARK 465 PHE A 743 REMARK 465 VAL A 744 REMARK 465 PRO A 745 REMARK 465 ALA A 746 REMARK 465 ALA A 747 REMARK 465 VAL A 748 REMARK 465 THR A 749 REMARK 465 ALA A 750 REMARK 465 ASN A 751 REMARK 465 ALA A 752 REMARK 465 THR A 753 REMARK 465 ILE A 754 REMARK 465 PRO A 755 REMARK 465 SER A 756 REMARK 465 LEU A 757 REMARK 465 ASP A 758 REMARK 465 SER A 759 REMARK 465 SER A 760 REMARK 465 SER A 761 REMARK 465 GLU A 762 REMARK 465 ALA A 763 REMARK 465 SER A 764 REMARK 465 ARG A 765 REMARK 465 GLU A 766 REMARK 465 ALA A 767 REMARK 465 SER A 768 REMARK 465 PRO A 769 REMARK 465 ALA A 770 REMARK 465 PRO A 771 REMARK 465 THR A 772 REMARK 465 GLY A 773 REMARK 465 SER A 774 REMARK 465 HIS A 775 REMARK 465 SER A 776 REMARK 465 LEU A 777 REMARK 465 THR A 778 REMARK 465 LYS A 779 REMARK 465 GLY A 780 REMARK 465 MET A 781 REMARK 465 ALA A 782 REMARK 465 GLU A 783 REMARK 465 LEU A 784 REMARK 465 ASN A 785 REMARK 465 VAL A 786 REMARK 465 GLN A 787 REMARK 465 GLU A 788 REMARK 465 SER A 789 REMARK 465 LYS A 790 REMARK 465 VAL A 791 REMARK 465 GLU A 792 REMARK 465 VAL A 793 REMARK 465 PRO A 794 REMARK 465 GLU A 795 REMARK 465 VAL A 796 REMARK 465 PRO A 797 REMARK 465 ALA A 798 REMARK 465 PRO A 799 REMARK 465 THR A 800 REMARK 465 LYS A 801 REMARK 465 ASN A 802 REMARK 465 GLU A 803 REMARK 465 GLU A 804 REMARK 465 LYS A 805 REMARK 465 ALA A 806 REMARK 465 ALA A 807 REMARK 465 PRO A 808 REMARK 465 ILE A 809 REMARK 465 VAL A 810 REMARK 465 ASP A 811 REMARK 465 ASP A 812 REMARK 465 GLU A 813 REMARK 465 GLU A 814 REMARK 465 THR A 815 REMARK 465 GLU A 816 REMARK 465 PHE A 817 REMARK 465 ASP A 818 REMARK 465 ILE A 819 REMARK 465 TYR A 820 REMARK 465 ASN A 821 REMARK 465 SER A 822 REMARK 465 LYS A 823 REMARK 465 VAL A 824 REMARK 465 ILE A 825 REMARK 465 ALA A 826 REMARK 465 CYS A 827 REMARK 465 ALA A 828 REMARK 465 ILE A 829 REMARK 465 ASP A 830 REMARK 465 ASN A 831 REMARK 465 PRO A 832 REMARK 465 GLU A 833 REMARK 465 ALA A 834 REMARK 465 CYS A 835 REMARK 465 GLU A 836 REMARK 465 MET A 837 REMARK 465 CYS A 838 REMARK 465 SER A 839 REMARK 465 GLY A 840 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 GLN A 89 CG CD OE1 NE2 REMARK 470 ASP A 138 CG OD1 OD2 REMARK 470 PHE A 146 CG CD1 CD2 CE1 CE2 CZ REMARK 470 ARG A 153 CG CD NE CZ NH1 NH2 REMARK 470 GLN A 162 CG CD OE1 NE2 REMARK 470 GLU A 184 CG CD OE1 OE2 REMARK 470 LYS A 212 CG CD CE NZ REMARK 470 ARG A 277 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 306 CG CD CE NZ REMARK 470 LYS A 356 CG CD CE NZ REMARK 470 SER A 437 OG REMARK 470 LYS A 438 CG CD CE NZ REMARK 470 LYS A 445 CG CD CE NZ REMARK 470 LYS A 555 CD CE NZ REMARK 470 MET A 583 CG SD CE REMARK 470 GLU A 594 CG CD OE1 OE2 REMARK 470 ARG A 604 CG CD NE CZ NH1 NH2 REMARK 470 ILE A 611 CG1 CG2 CD1 REMARK 470 TRP A 612 CG CD1 CD2 NE1 CE2 CE3 CZ2 REMARK 470 TRP A 612 CZ3 CH2 REMARK 470 GLN A 613 CG CD OE1 NE2 REMARK 470 ILE A 616 CG1 CG2 CD1 REMARK 470 GLU A 631 CG CD OE1 OE2 REMARK 470 ARG A 669 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 675 CG CD CE NZ 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 154 -58.49 -120.89 REMARK 500 SER A 405 -163.67 -118.95 REMARK 500 ARG A 480 51.59 36.50 REMARK 500 GLN A 660 -149.34 -97.14 REMARK 500 ALA A 670 78.87 -114.89 REMARK 500 TYR A 693 -87.57 -102.12 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 FOR AMINO ACIDS AND C1'--O4'--N1(N9)--C2' FOR REMARK 500 NUCLEIC ACIDS OR EQUIVALENT ANGLE 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 LYS A 393 24.7 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 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A1020 DISTANCE = 6.22 ANGSTROMS REMARK 525 HOH A1033 DISTANCE = 6.87 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 MG A2001 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 N5P A 841 O1G REMARK 620 2 HOH A1084 O 135.0 REMARK 620 3 HOH A1013 O 85.3 96.1 REMARK 620 4 N5P A 841 O1A 53.2 83.5 75.4 REMARK 620 5 HOH A1083 O 83.9 136.7 107.2 137.1 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 A 2001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE N5P A 841 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2CVV RELATED DB: PDB REMARK 900 THE SAME PROTEIN COMPLEXED WITH AMPPNP AND UDP REMARK 900 RELATED ID: 2CVU RELATED DB: PDB REMARK 900 THE SAMPLE PROTEIN COMPLEXED WITH EFFECTOR ATP ANOLOG REMARK 900 AMPPNP AND SUBSTRATE CDP REMARK 900 RELATED ID: 2CVW RELATED DB: PDB REMARK 900 THE SAME PROTEIN COMPLEXED WITH EFFECTOR DTTP AND SUBSTRATE REMARK 900 GDP REMARK 900 RELATED ID: 2CVX RELATED DB: PDB REMARK 900 THE SAME PROTEIN COMPLEXED WITH EFFECTOR DGTP AND SUBSTRATE REMARK 900 ADP REMARK 900 RELATED ID: 2CVY RELATED DB: PDB REMARK 900 THE SAME PROTEIN COMPLEXED WITH YEAST RNR2 C-TERMINAL 9 MER REMARK 900 PEPTIDE REMARK 900 RELATED ID: 2CVS RELATED DB: PDB REMARK 900 THE SAME PROTEIN IN THE OXIDIZED NATIVE STATE DBREF 3RSR A 1 840 UNP P21524 RIR1_YEAST 1 888 SEQRES 1 A 888 MET TYR VAL TYR LYS ARG ASP GLY ARG LYS GLU PRO VAL SEQRES 2 A 888 GLN PHE ASP LYS ILE THR ALA ARG ILE SER ARG LEU CYS SEQRES 3 A 888 TYR GLY LEU ASP PRO LYS HIS ILE ASP ALA VAL LYS VAL SEQRES 4 A 888 THR GLN ARG ILE ILE SER GLY VAL TYR GLU GLY VAL THR SEQRES 5 A 888 THR ILE GLU LEU ASP ASN LEU ALA ALA GLU THR CYS ALA SEQRES 6 A 888 TYR MET THR THR VAL HIS PRO ASP TYR ALA THR LEU ALA SEQRES 7 A 888 ALA ARG ILE ALA ILE SER ASN LEU HIS LYS GLN THR THR SEQRES 8 A 888 LYS GLN PHE SER LYS VAL VAL GLU ASP LEU TYR ARG TYR SEQRES 9 A 888 VAL ASN ALA ALA THR GLY LYS PRO ALA PRO MET ILE SER SEQRES 10 A 888 ASP ASP VAL TYR ASN ILE VAL MET GLU ASN LYS ASP LYS SEQRES 11 A 888 LEU ASN SER ALA ILE VAL TYR ASP ARG ASP PHE GLN TYR SEQRES 12 A 888 SER TYR PHE GLY PHE LYS THR LEU GLU ARG SER TYR LEU SEQRES 13 A 888 LEU ARG ILE ASN GLY GLN VAL ALA GLU ARG PRO GLN HIS SEQRES 14 A 888 LEU ILE MET ARG VAL ALA LEU GLY ILE HIS GLY ARG ASP SEQRES 15 A 888 ILE GLU ALA ALA LEU GLU THR TYR ASN LEU MET SER LEU SEQRES 16 A 888 LYS TYR PHE THR HIS ALA SER PRO THR LEU PHE ASN ALA SEQRES 17 A 888 GLY THR PRO LYS PRO GLN MET SER SER CYS PHE LEU VAL SEQRES 18 A 888 ALA MET LYS GLU ASP SER ILE GLU GLY ILE TYR ASP THR SEQRES 19 A 888 LEU LYS GLU CYS ALA LEU ILE SER LYS THR ALA GLY GLY SEQRES 20 A 888 ILE GLY LEU HIS ILE HIS ASN ILE ARG SER THR GLY SER SEQRES 21 A 888 TYR ILE ALA GLY THR ASN GLY THR SER ASN GLY LEU ILE SEQRES 22 A 888 PRO MET ILE ARG VAL PHE ASN ASN THR ALA ARG TYR VAL SEQRES 23 A 888 ASP GLN GLY GLY ASN LYS ARG PRO GLY ALA PHE ALA LEU SEQRES 24 A 888 TYR LEU GLU PRO TRP HIS ALA ASP ILE PHE ASP PHE ILE SEQRES 25 A 888 ASP ILE ARG LYS ASN HIS GLY LYS GLU GLU ILE ARG ALA SEQRES 26 A 888 ARG ASP LEU PHE PRO ALA LEU TRP ILE PRO ASP LEU PHE SEQRES 27 A 888 MET LYS ARG VAL GLU GLU ASN GLY THR TRP THR LEU PHE SEQRES 28 A 888 SER PRO THR SER ALA PRO GLY LEU SER ASP CYS TYR GLY SEQRES 29 A 888 ASP GLU PHE GLU ALA LEU TYR THR ARG TYR GLU LYS GLU SEQRES 30 A 888 GLY ARG GLY LYS THR ILE LYS ALA GLN LYS LEU TRP TYR SEQRES 31 A 888 SER ILE LEU GLU ALA GLN THR GLU THR GLY THR PRO PHE SEQRES 32 A 888 VAL VAL TYR LYS ASP ALA CYS ASN ARG LYS SER ASN GLN SEQRES 33 A 888 LYS ASN LEU GLY VAL ILE LYS SER SER ASN LEU CYS CYS SEQRES 34 A 888 GLU ILE VAL GLU TYR SER ALA PRO ASP GLU THR ALA VAL SEQRES 35 A 888 CYS ASN LEU ALA SER VAL ALA LEU PRO ALA PHE ILE GLU SEQRES 36 A 888 THR SER GLU ASP GLY LYS THR SER THR TYR ASN PHE LYS SEQRES 37 A 888 LYS LEU HIS GLU ILE ALA LYS VAL VAL THR ARG ASN LEU SEQRES 38 A 888 ASN ARG VAL ILE ASP ARG ASN TYR TYR PRO VAL GLU GLU SEQRES 39 A 888 ALA ARG LYS SER ASN MET ARG HIS ARG PRO ILE ALA LEU SEQRES 40 A 888 GLY VAL GLN GLY LEU ALA ASP THR PHE MET LEU LEU ARG SEQRES 41 A 888 LEU PRO PHE ASP SER GLU GLU ALA ARG LEU LEU ASN ILE SEQRES 42 A 888 GLN ILE PHE GLU THR ILE TYR HIS ALA SER MET GLU ALA SEQRES 43 A 888 SER CYS GLU LEU ALA GLN LYS ASP GLY PRO TYR GLU THR SEQRES 44 A 888 PHE GLN GLY SER PRO ALA SER GLN GLY ILE LEU GLN PHE SEQRES 45 A 888 ASP MET TRP ASP GLN LYS PRO TYR GLY MET TRP ASP TRP SEQRES 46 A 888 ASP THR LEU ARG LYS ASP ILE MET LYS HIS GLY VAL ARG SEQRES 47 A 888 ASN SER LEU THR MET ALA PRO MET PRO THR ALA SER THR SEQRES 48 A 888 SER GLN ILE LEU GLY TYR ASN GLU CYS PHE GLU PRO VAL SEQRES 49 A 888 THR SER ASN MET TYR SER ARG ARG VAL LEU SER GLY GLU SEQRES 50 A 888 PHE GLN VAL VAL ASN PRO TYR LEU LEU ARG ASP LEU VAL SEQRES 51 A 888 ASP LEU GLY ILE TRP ASP GLU GLY MET LYS GLN TYR LEU SEQRES 52 A 888 ILE THR GLN ASN GLY SER ILE GLN GLY LEU PRO ASN VAL SEQRES 53 A 888 PRO GLN GLU LEU LYS ASP LEU TYR LYS THR VAL TRP GLU SEQRES 54 A 888 ILE SER GLN LYS THR ILE ILE ASN MET ALA ALA ASP ARG SEQRES 55 A 888 SER VAL TYR ILE ASP GLN SER HIS SER LEU ASN LEU PHE SEQRES 56 A 888 LEU ARG ALA PRO THR MET GLY LYS LEU THR SER MET HIS SEQRES 57 A 888 PHE TYR GLY TRP LYS LYS GLY LEU LYS THR GLY MET TYR SEQRES 58 A 888 TYR LEU ARG THR GLN ALA ALA SER ALA ALA ILE GLN PHE SEQRES 59 A 888 THR ILE ASP GLN LYS ILE ALA ASP GLN ALA THR GLU ASN SEQRES 60 A 888 VAL ALA ASP ILE SER ASN LEU LYS ARG PRO SER TYR MET SEQRES 61 A 888 PRO SER SER ALA SER TYR ALA ALA SER ASP PHE VAL PRO SEQRES 62 A 888 ALA ALA VAL THR ALA ASN ALA THR ILE PRO SER LEU ASP SEQRES 63 A 888 SER SER SER GLU ALA SER ARG GLU ALA SER PRO ALA PRO SEQRES 64 A 888 THR GLY SER HIS SER LEU THR LYS GLY MET ALA GLU LEU SEQRES 65 A 888 ASN VAL GLN GLU SER LYS VAL GLU VAL PRO GLU VAL PRO SEQRES 66 A 888 ALA PRO THR LYS ASN GLU GLU LYS ALA ALA PRO ILE VAL SEQRES 67 A 888 ASP ASP GLU GLU THR GLU PHE ASP ILE TYR ASN SER LYS SEQRES 68 A 888 VAL ILE ALA CYS ALA ILE ASP ASN PRO GLU ALA CYS GLU SEQRES 69 A 888 MET CYS SER GLY HET MG A2001 1 HET N5P A 841 32 HETNAM MG MAGNESIUM ION HETNAM N5P 1-{2-DEOXY-5-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY) HETNAM 2 N5P PHOSPHORYL]OXY}PHOSPHORYL]-BETA-D-ERYTHRO- HETNAM 3 N5P PENTOFURANOSYL}-5-NITRO-1H-INDOLE HETSYN N5P 5-NITRO-1-INDOLYL-2'-DEOXYRIBOSIDE-5'-TRIPHOSPHATE FORMUL 2 MG MG 2+ FORMUL 3 N5P C13 H17 N2 O14 P3 FORMUL 4 HOH *243(H2 O) HELIX 1 1 GLN A 93 TYR A 104 1 12 HELIX 2 2 SER A 117 ASN A 127 1 11 HELIX 3 3 ASN A 127 ILE A 135 1 9 HELIX 4 4 VAL A 136 TYR A 143 5 8 HELIX 5 5 SER A 144 TYR A 155 1 12 HELIX 6 6 ARG A 166 GLY A 180 1 15 HELIX 7 7 ASP A 182 LEU A 195 1 14 HELIX 8 8 ALA A 201 ALA A 208 1 8 HELIX 9 9 SER A 227 LYS A 243 1 17 HELIX 10 10 GLY A 271 VAL A 286 1 16 HELIX 11 11 ASP A 297 ILE A 302 1 6 HELIX 12 12 PRO A 315 GLU A 324 1 10 HELIX 13 13 GLY A 338 CYS A 342 5 5 HELIX 14 14 TYR A 343 GLU A 357 1 15 HELIX 15 15 ALA A 365 GLY A 380 1 16 HELIX 16 16 LYS A 387 LYS A 393 1 7 HELIX 17 17 ASN A 443 ASN A 465 1 23 HELIX 18 18 VAL A 469 ARG A 480 1 12 HELIX 19 19 GLY A 488 LEU A 496 1 9 HELIX 20 20 SER A 502 GLY A 532 1 31 HELIX 21 21 SER A 540 GLY A 545 5 6 HELIX 22 22 LEU A 547 TRP A 552 1 6 HELIX 23 23 ASP A 561 GLY A 573 1 13 HELIX 24 24 ASN A 599 LEU A 609 1 11 HELIX 25 25 GLN A 613 ASN A 619 1 7 HELIX 26 26 PRO A 629 TYR A 636 1 8 HELIX 27 27 SER A 643 SER A 655 1 13 HELIX 28 28 VAL A 656 ILE A 658 5 3 HELIX 29 29 THR A 672 LYS A 686 1 15 SHEET 1 A 2 VAL A 105 ASN A 106 0 SHEET 2 A 2 LYS A 111 PRO A 112 -1 O LYS A 111 N ASN A 106 SHEET 1 B 2 ARG A 158 ILE A 159 0 SHEET 2 B 2 GLN A 162 VAL A 163 -1 O GLN A 162 N ILE A 159 SHEET 1 C 3 PHE A 198 HIS A 200 0 SHEET 2 C 3 LEU A 425 ALA A 429 -1 O SER A 427 N THR A 199 SHEET 3 C 3 ALA A 483 GLN A 487 1 O GLY A 485 N ALA A 426 SHEET 1 D 6 CYS A 218 ALA A 222 0 SHEET 2 D 6 GLY A 247 HIS A 251 1 O GLY A 249 N VAL A 221 SHEET 3 D 6 ALA A 288 LEU A 291 1 O ALA A 288 N ILE A 248 SHEET 4 D 6 PHE A 309 ILE A 314 1 O PHE A 309 N LEU A 289 SHEET 5 D 6 PHE A 383 TYR A 386 1 O PHE A 383 N LEU A 312 SHEET 6 D 6 THR A 690 MET A 692 -1 O MET A 692 N VAL A 384 SHEET 1 E 2 TYR A 261 ILE A 262 0 SHEET 2 E 2 GLY A 267 THR A 268 -1 O GLY A 267 N ILE A 262 SHEET 1 F 2 THR A 327 LEU A 330 0 SHEET 2 F 2 LYS A 361 LYS A 364 -1 O ILE A 363 N TRP A 328 SHEET 1 G 2 ILE A 434 THR A 436 0 SHEET 2 G 2 SER A 440 TYR A 442 -1 O THR A 441 N GLU A 435 SHEET 1 H 2 LEU A 666 LEU A 668 0 SHEET 2 H 2 LEU A 695 THR A 697 1 O ARG A 696 N LEU A 666 SSBOND 1 CYS A 218 CYS A 423 1555 1555 2.05 LINK MG MG A2001 O1G N5P A 841 1555 1555 2.18 LINK MG MG A2001 O HOH A1084 1555 1555 2.33 LINK MG MG A2001 O HOH A1013 1555 1555 2.40 LINK MG MG A2001 O1A N5P A 841 1555 1555 2.61 LINK MG MG A2001 O HOH A1083 1555 1555 2.63 CISPEP 1 THR A 381 PRO A 382 0 7.03 CISPEP 2 CYS A 595 PHE A 596 0 0.88 SITE 1 AC1 4 N5P A 841 HOH A1013 HOH A1083 HOH A1084 SITE 1 AC2 17 ASP A 226 SER A 227 ILE A 228 ILE A 231 SITE 2 AC2 17 LYS A 243 ARG A 256 ILE A 262 ALA A 263 SITE 3 AC2 17 GLY A 264 THR A 265 TYR A 285 VAL A 286 SITE 4 AC2 17 HOH A 884 HOH A 908 HOH A1013 HOH A1083 SITE 5 AC2 17 MG A2001 CRYST1 108.353 118.208 63.921 90.00 90.00 90.00 P 21 21 2 4 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 0.009229 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008460 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015644 0.00000