10 20 30 40 50 60 70 80 2CVV - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER OXIDOREDUCTASE 14-JUN-05 2CVV
TITLE STRUCTURES OF YEAST RIBONUCLEOTIDE REDUCTASE I
COMPND MOL_ID: 1; COMPND 2 MOLECULE: RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE LARGE CHAIN COMPND 3 1; COMPND 4 CHAIN: A; COMPND 5 SYNONYM: RIBONUCLEOTIDE REDUCTASE I; 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: BAKER'S YEAST; SOURCE 4 ORGANISM_TAXID: 4932; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PWJ751-3
KEYWDS EUKARYOTIC, RIBONUCLEOTIDE REDUCTASE, DNTP REGULATION, KEYWDS 2 OXIDOREDUCTASE
EXPDTA X-RAY DIFFRACTION
AUTHOR H.XU,C.FABER,T.UCHIKI,J.W.FAIRMAN,J.RACCA,C.DEALWIS
REVDAT 3 24-FEB-09 2CVV 1 VERSN REVDAT 2 04-APR-06 2CVV 1 JRNL REVDAT 1 07-MAR-06 2CVV 0
JRNL AUTH H.XU,C.FABER,T.UCHIKI,J.W.FAIRMAN,J.RACCA,C.DEALWIS JRNL TITL STRUCTURES OF EUKARYOTIC RIBONUCLEOTIDE REDUCTASE JRNL TITL 2 I PROVIDE INSIGHTS INTO DNTP REGULATION JRNL REF PROC.NATL.ACAD.SCI.USA V. 103 4022 2006 JRNL REFN ISSN 0027-8424 JRNL PMID 16537479 JRNL DOI 10.1073/PNAS.0600443103
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. 2.90 ANGSTROMS.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0007 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.0 REMARK 3 NUMBER OF REFLECTIONS : 16485 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) : 0.184 REMARK 3 R VALUE (WORKING SET) : 0.177 REMARK 3 FREE R VALUE : 0.245 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.200 REMARK 3 FREE R VALUE TEST SET COUNT : 1871 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) : 2.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.98 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1224 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.71 REMARK 3 BIN R VALUE (WORKING SET) : 0.2420 REMARK 3 BIN FREE R VALUE SET COUNT : 142 REMARK 3 BIN FREE R VALUE : 0.3710 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5208 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 57 REMARK 3 SOLVENT ATOMS : 138 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.20 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.96000 REMARK 3 B22 (A**2) : -1.98000 REMARK 3 B33 (A**2) : 2.94000 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): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.425 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.276 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 14.561 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.933 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.879 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5389 ; 0.013 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7308 ; 1.523 ; 1.955 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 649 ; 6.273 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 250 ;39.178 ;24.080 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 929 ;19.697 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 32 ;17.375 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 790 ; 0.104 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4071 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 2861 ; 0.233 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 3714 ; 0.317 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 286 ; 0.169 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 41 ; 0.204 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 3 ; 0.119 ; 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): 3303 ; 0.717 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 5236 ; 1.281 ; 2.000 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2375 ; 1.576 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2072 ; 2.544 ; 4.500 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 : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE REMARK 3 RIDING POSITIONS
REMARK 4 REMARK 4 2CVV COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 15-JUN-05. REMARK 100 THE RCSB ID CODE IS RCSB024681.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 31-MAR-05 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RUH3R REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18449 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.900 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.9 REMARK 200 DATA REDUNDANCY : 5.500 REMARK 200 R MERGE (I) : 0.12800 REMARK 200 R SYM (I) : 0.12800 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 13.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8 REMARK 200 DATA REDUNDANCY IN SHELL : 5.40 REMARK 200 R MERGE FOR SHELL (I) : 0.41400 REMARK 200 R SYM FOR SHELL (I) : 0.41400 REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.600 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: NATIVE STRUCTURE REMARK 200 REMARK 200 REMARK: NULL
REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 37.30 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.04 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 3350, SODIUM ACETATE, AMMONIUM REMARK 280 SULFATE, PH 6.5, EVAPORATION, 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 53.93300 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 58.79650 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 53.93300 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 58.79650 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 300 REMARK: THE SECOND PART OF THE ACTIVE BIOLOGICAL DIMER ASSEMBLY REMARK 300 IS GENERATED BY THE TWO FOLD AXIS: -X, -Y+1, Z.
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 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 117.59300 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000
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 ARG A 631 REMARK 465 ARG A 632 REMARK 465 VAL A 633 REMARK 465 LEU A 634 REMARK 465 SER A 635 REMARK 465 GLY A 636 REMARK 465 GLU A 637 REMARK 465 ALA A 747 REMARK 465 ALA A 748 REMARK 465 SER A 749 REMARK 465 ALA A 750 REMARK 465 ALA A 751 REMARK 465 ILE A 752 REMARK 465 GLN A 753 REMARK 465 PHE A 754 REMARK 465 THR A 755 REMARK 465 ILE A 756 REMARK 465 ASP A 757 REMARK 465 GLN A 758 REMARK 465 LYS A 759 REMARK 465 ILE A 760 REMARK 465 ALA A 761 REMARK 465 ASP A 762 REMARK 465 GLN A 763 REMARK 465 ALA A 764 REMARK 465 THR A 765 REMARK 465 GLU A 766 REMARK 465 ASN A 767 REMARK 465 VAL A 768 REMARK 465 ALA A 769 REMARK 465 ASP A 770 REMARK 465 ILE A 771 REMARK 465 SER A 772 REMARK 465 ASN A 773 REMARK 465 LEU A 774 REMARK 465 LYS A 775 REMARK 465 ARG A 776 REMARK 465 PRO A 777 REMARK 465 SER A 778 REMARK 465 TYR A 779 REMARK 465 MET A 780 REMARK 465 PRO A 781 REMARK 465 SER A 782 REMARK 465 SER A 783 REMARK 465 ALA A 784 REMARK 465 SER A 785 REMARK 465 TYR A 786 REMARK 465 ALA A 787 REMARK 465 ALA A 788 REMARK 465 SER A 789 REMARK 465 ASP A 790 REMARK 465 PHE A 791 REMARK 465 VAL A 792 REMARK 465 PRO A 793 REMARK 465 ALA A 794 REMARK 465 ALA A 795 REMARK 465 VAL A 796 REMARK 465 THR A 797 REMARK 465 ALA A 798 REMARK 465 ASN A 799 REMARK 465 ALA A 800 REMARK 465 THR A 801 REMARK 465 ILE A 802 REMARK 465 PRO A 803 REMARK 465 SER A 804 REMARK 465 LEU A 805 REMARK 465 ASP A 806 REMARK 465 SER A 807 REMARK 465 SER A 808 REMARK 465 SER A 809 REMARK 465 GLU A 810 REMARK 465 ALA A 811 REMARK 465 SER A 812 REMARK 465 ARG A 813 REMARK 465 GLU A 814 REMARK 465 ALA A 815 REMARK 465 SER A 816 REMARK 465 PRO A 817 REMARK 465 ALA A 818 REMARK 465 PRO A 819 REMARK 465 THR A 820 REMARK 465 GLY A 821 REMARK 465 SER A 822 REMARK 465 HIS A 823 REMARK 465 SER A 824 REMARK 465 LEU A 825 REMARK 465 THR A 826 REMARK 465 LYS A 827 REMARK 465 GLY A 828 REMARK 465 MET A 829 REMARK 465 ALA A 830 REMARK 465 GLU A 831 REMARK 465 LEU A 832 REMARK 465 ASN A 833 REMARK 465 VAL A 834 REMARK 465 GLN A 835 REMARK 465 GLU A 836 REMARK 465 SER A 837 REMARK 465 LYS A 838 REMARK 465 VAL A 839 REMARK 465 GLU A 840 REMARK 465 VAL A 841 REMARK 465 PRO A 842 REMARK 465 GLU A 843 REMARK 465 VAL A 844 REMARK 465 PRO A 845 REMARK 465 ALA A 846 REMARK 465 PRO A 847 REMARK 465 THR A 848 REMARK 465 LYS A 849 REMARK 465 ASN A 850 REMARK 465 GLU A 851 REMARK 465 GLU A 852 REMARK 465 LYS A 853 REMARK 465 ALA A 854 REMARK 465 ALA A 855 REMARK 465 PRO A 856 REMARK 465 ILE A 857 REMARK 465 VAL A 858 REMARK 465 ASP A 859 REMARK 465 ASP A 860 REMARK 465 GLU A 861 REMARK 465 GLU A 862 REMARK 465 THR A 863 REMARK 465 GLU A 864 REMARK 465 PHE A 865 REMARK 465 ASP A 866 REMARK 465 ILE A 867 REMARK 465 TYR A 868 REMARK 465 ASN A 869 REMARK 465 SER A 870 REMARK 465 LYS A 871 REMARK 465 VAL A 872 REMARK 465 ILE A 873 REMARK 465 ALA A 874 REMARK 465 CYS A 875 REMARK 465 ALA A 876 REMARK 465 ILE A 877 REMARK 465 ASP A 878 REMARK 465 ASN A 879 REMARK 465 PRO A 880 REMARK 465 GLU A 881 REMARK 465 ALA A 882 REMARK 465 CYS A 883 REMARK 465 GLU A 884 REMARK 465 MET A 885 REMARK 465 CYS A 886 REMARK 465 SER A 887 REMARK 465 GLY A 888
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 ASP A 100 CB - CG - OD2 ANGL. DEV. = 6.5 DEGREES REMARK 500 ASP A 182 CB - CG - OD2 ANGL. DEV. = 5.9 DEGREES REMARK 500 ASP A 233 CB - CG - OD2 ANGL. DEV. = 6.0 DEGREES REMARK 500 ASP A 310 CB - CG - OD2 ANGL. DEV. = 6.2 DEGREES REMARK 500 ASP A 682 CB - CG - OD2 ANGL. DEV. = 5.5 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 154 13.09 -147.06 REMARK 500 ASN A 160 74.36 48.46 REMARK 500 ASP A 182 78.37 -67.04 REMARK 500 LYS A 212 72.06 -112.48 REMARK 500 PRO A 213 87.55 -69.34 REMARK 500 ALA A 245 154.24 -47.81 REMARK 500 ARG A 256 124.72 -22.49 REMARK 500 ASN A 291 -142.09 -161.18 REMARK 500 ALA A 296 105.63 44.47 REMARK 500 HIS A 318 -143.64 -150.03 REMARK 500 LYS A 320 -139.91 -117.09 REMARK 500 GLU A 321 -38.71 -133.52 REMARK 500 SER A 425 -155.27 -98.61 REMARK 500 ASN A 426 -166.98 -117.52 REMARK 500 ALA A 452 -7.45 -57.84 REMARK 500 THR A 456 38.10 -78.44 REMARK 500 GLU A 458 -43.59 -148.40 REMARK 500 ASP A 459 -90.72 173.48 REMARK 500 LYS A 461 38.78 -155.82 REMARK 500 ARG A 503 58.55 35.56 REMARK 500 THR A 602 -30.68 -139.03 REMARK 500 ALA A 604 77.68 -153.21 REMARK 500 CYS A 620 -119.14 36.47 REMARK 500 TYR A 629 -110.08 19.20 REMARK 500 GLN A 639 103.74 53.92 REMARK 500 ASP A 656 -151.00 -148.38 REMARK 500 ASN A 667 67.40 36.08 REMARK 500 ASN A 675 51.92 -105.24 REMARK 500 ASP A 707 -49.68 -23.47 REMARK 500 GLN A 708 -122.50 -112.64 REMARK 500 TYR A 741 -119.08 -87.52 REMARK 500 THR A 745 -158.12 -137.72 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 A2001 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ANP A1001 O2A REMARK 620 2 ANP A1001 O2B 80.6 REMARK 620 3 ANP A1001 O2G 89.2 85.6 REMARK 620 N 1 2
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 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ANP A 1001 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE UDP A 1002
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1ZYZ RELATED DB: PDB REMARK 900 REDUCED APO STRUCTURE REMARK 900 RELATED ID: 2CVS RELATED DB: PDB REMARK 900 OXIDIZED NATIVE STRUCTURE REMARK 900 RELATED ID: 2CVT RELATED DB: PDB REMARK 900 COMPLEX STRUCTURE WITH EFFECTOR ATP ANOLOG AMPPNP REMARK 900 RELATED ID: 2CVU RELATED DB: PDB REMARK 900 COMPLEX STRUCTURE WITH EFFECTOR ATP ANOLOG AMPPNP AND REMARK 900 SUBSTRATE CDP REMARK 900 RELATED ID: 2CVW RELATED DB: PDB REMARK 900 COMPLEX STRUCTURE WITH EFFECTOR DTTP AND SUBSTRATE GDP REMARK 900 RELATED ID: 2CVX RELATED DB: PDB REMARK 900 COMPLEX STRUCTURE WITH EFFECTOR DGTP AND SUBSTRATE ADP REMARK 900 RELATED ID: 2CVY RELATED DB: PDB REMARK 900 COMPLEX STRUCTURE WITH YEAST RNR2 C-TERMINAL 9 MER PEPTIDE
DBREF 2CVV A 1 888 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 ANP A1001 31 HET UDP A1002 25
HETNAM MG MAGNESIUM ION HETNAM ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER HETNAM UDP URIDINE-5'-DIPHOSPHATE
FORMUL 2 MG MG 2+ FORMUL 3 ANP C10 H17 N6 O12 P3 FORMUL 4 UDP C9 H14 N2 O12 P2 FORMUL 5 HOH *138(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 307 ILE A 312 1 6 HELIX 12 12 PRO A 335 GLU A 344 1 10 HELIX 13 13 TYR A 363 GLU A 377 1 15 HELIX 14 14 ALA A 385 GLY A 400 1 16 HELIX 15 15 LYS A 407 LYS A 413 1 7 HELIX 16 16 GLN A 416 GLY A 420 5 5 HELIX 17 17 ASN A 466 ASN A 488 1 23 HELIX 18 18 VAL A 492 ARG A 503 1 12 HELIX 19 19 GLY A 511 LEU A 519 1 9 HELIX 20 20 SER A 525 GLY A 555 1 31 HELIX 21 21 PRO A 564 GLY A 568 5 5 HELIX 22 22 GLN A 571 ASP A 576 5 6 HELIX 23 23 ASP A 584 GLY A 596 1 13 HELIX 24 24 SER A 610 GLY A 616 1 7 HELIX 25 25 ASN A 642 LEU A 652 1 11 HELIX 26 26 ASP A 656 GLN A 666 1 11 HELIX 27 27 PRO A 677 TYR A 684 1 8 HELIX 28 28 THR A 686 ILE A 690 5 5 HELIX 29 29 SER A 691 VAL A 704 1 14 HELIX 30 30 THR A 720 LYS A 734 1 15
SHEET 1 A 2 ARG A 158 ILE A 159 0 SHEET 2 A 2 GLN A 162 VAL A 163 -1 O GLN A 162 N ILE A 159 SHEET 1 B 3 PHE A 198 HIS A 200 0 SHEET 2 B 3 LEU A 445 ALA A 449 -1 O SER A 447 N THR A 199 SHEET 3 B 3 ALA A 506 GLN A 510 1 O GLY A 508 N VAL A 448 SHEET 1 C 7 ALA A 441 CYS A 443 0 SHEET 2 C 7 CYS A 218 ALA A 222 -1 N LEU A 220 O ALA A 441 SHEET 3 C 7 GLY A 247 HIS A 251 1 O GLY A 249 N VAL A 221 SHEET 4 C 7 PHE A 297 LEU A 301 1 O ALA A 298 N LEU A 250 SHEET 5 C 7 LEU A 328 ILE A 334 1 O PHE A 329 N LEU A 299 SHEET 6 C 7 PHE A 403 TYR A 406 1 O PHE A 403 N LEU A 332 SHEET 7 C 7 THR A 738 MET A 740 -1 O MET A 740 N VAL A 404 SHEET 1 D 2 THR A 347 LEU A 350 0 SHEET 2 D 2 LYS A 381 LYS A 384 -1 O LYS A 381 N LEU A 350 SHEET 1 E 2 ILE A 454 GLU A 455 0 SHEET 2 E 2 THR A 464 TYR A 465 -1 O THR A 464 N GLU A 455 SHEET 1 F 2 LEU A 714 PHE A 715 0 SHEET 2 F 2 LEU A 743 ARG A 744 1 O ARG A 744 N LEU A 714
LINK O2A ANP A1001 MG MG A2001 1555 1555 2.03 LINK MG MG A2001 O2B ANP A1001 1555 1555 2.47 LINK MG MG A2001 O2G ANP A1001 1555 1555 2.08
CISPEP 1 THR A 401 PRO A 402 0 0.87
SITE 1 AC1 1 ANP A1001 SITE 1 AC2 14 ASP A 226 SER A 227 ILE A 228 ILE A 231 SITE 2 AC2 14 LYS A 243 ARG A 256 ILE A 262 ALA A 263 SITE 3 AC2 14 TYR A 285 ASP A 287 MG A2001 HOH A2016 SITE 4 AC2 14 HOH A2029 HOH A2031 SITE 1 AC3 18 ALA A 201 SER A 202 SER A 217 CYS A 218 SITE 2 AC3 18 GLY A 246 GLY A 247 GLN A 288 ASN A 426 SITE 3 AC3 18 CYS A 428 GLU A 430 MET A 606 PRO A 607 SITE 4 AC3 18 THR A 608 ALA A 609 THR A 611 HOH A2004 SITE 5 AC3 18 HOH A2064 HOH A2086
CRYST1 107.866 117.593 64.884 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 0.009271 0.000000 0.000000 0.00000
SCALE2 0.000000 0.008504 0.000000 0.00000
SCALE3 0.000000 0.000000 0.015412 0.00000