HEADER HYDROLASE 13-FEB-17 5X4K TITLE THE COMPLEX CRYSTAL STRUCTURE OF PYROCOCCUS FURIOSUS RECJ AND CMP COMPND MOL_ID: 1; COMPND 2 MOLECULE: UNCHARACTERIZED PROTEIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: RECJ; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PYROCOCCUS FURIOSUS; SOURCE 3 ORGANISM_TAXID: 186497; SOURCE 4 STRAIN: ATCC 43587 / DSM 3638 / JCM 8422 / VC1; SOURCE 5 GENE: PF2055; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS ARCHAEAL RECJ, CMG INTERACTION DOMAIN, NUCLEASE ACTIVITY, GINS, KEYWDS 2 INTERACTION, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR M.J.LI,G.S.YI,F.YU,H.ZHOU,J.N.CHEN,C.Y.XU,F.P.WANG,X.XIAO,J.H.HE, AUTHOR 2 X.P.LIU REVDAT 3 22-NOV-23 5X4K 1 LINK REVDAT 2 18-DEC-19 5X4K 1 JRNL REVDAT 1 14-FEB-18 5X4K 0 JRNL AUTH M.J.LI,G.S.YI,F.YU,H.ZHOU,J.N.CHEN,C.Y.XU,F.P.WANG,X.XIAO, JRNL AUTH 2 J.H.HE,X.P.LIU JRNL TITL THE CRYSTAL STRUCTURE OF PYROCOCCUS FURIOSUS RECJ IMPLICATES JRNL TITL 2 IT AS AN ANCESTOR OF EUKARYOTIC CDC45. JRNL REF NUCLEIC ACIDS RES. V. 45 12551 2017 JRNL REFN ESSN 1362-4962 JRNL PMID 30053256 JRNL DOI 10.1093/NAR/GKX887 REMARK 2 REMARK 2 RESOLUTION. 1.75 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.10.1_2155) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.75 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 49.11 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.470 REMARK 3 COMPLETENESS FOR RANGE (%) : 86.5 REMARK 3 NUMBER OF REFLECTIONS : 72646 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.164 REMARK 3 R VALUE (WORKING SET) : 0.163 REMARK 3 FREE R VALUE : 0.189 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.930 REMARK 3 FREE R VALUE TEST SET COUNT : 3584 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 49.1262 - 5.1787 0.99 3045 135 0.1735 0.1883 REMARK 3 2 5.1787 - 4.1112 0.99 3059 146 0.1281 0.1553 REMARK 3 3 4.1112 - 3.5917 0.99 3095 117 0.1371 0.1485 REMARK 3 4 3.5917 - 3.2633 0.99 3003 189 0.1507 0.1752 REMARK 3 5 3.2633 - 3.0295 0.99 3028 173 0.1681 0.1732 REMARK 3 6 3.0295 - 2.8509 0.99 3024 162 0.1672 0.2068 REMARK 3 7 2.8509 - 2.7081 0.99 3076 148 0.1701 0.2034 REMARK 3 8 2.7081 - 2.5902 0.99 2984 189 0.1610 0.2134 REMARK 3 9 2.5902 - 2.4905 0.99 3042 163 0.1715 0.2048 REMARK 3 10 2.4905 - 2.4046 0.98 2967 178 0.1757 0.2080 REMARK 3 11 2.4046 - 2.3294 0.98 2986 188 0.1680 0.1887 REMARK 3 12 2.3294 - 2.2628 0.97 3015 159 0.1620 0.2078 REMARK 3 13 2.2628 - 2.2033 0.97 2864 195 0.1696 0.1713 REMARK 3 14 2.2033 - 2.1495 0.95 2946 165 0.1657 0.2145 REMARK 3 15 2.1495 - 2.1006 0.93 2929 120 0.1614 0.1938 REMARK 3 16 2.1006 - 2.0559 0.92 2801 130 0.1748 0.1707 REMARK 3 17 2.0559 - 2.0148 0.89 2737 146 0.1827 0.1800 REMARK 3 18 2.0148 - 1.9768 0.86 2663 123 0.1736 0.2082 REMARK 3 19 1.9768 - 1.9415 0.83 2507 102 0.1714 0.1914 REMARK 3 20 1.9415 - 1.9086 0.78 2411 133 0.1699 0.1810 REMARK 3 21 1.9086 - 1.8778 0.73 2231 109 0.1746 0.2070 REMARK 3 22 1.8778 - 1.8489 0.67 2089 82 0.1796 0.2460 REMARK 3 23 1.8489 - 1.8217 0.61 1881 98 0.1951 0.2473 REMARK 3 24 1.8217 - 1.7960 0.56 1746 86 0.2165 0.2499 REMARK 3 25 1.7960 - 1.7718 0.52 1562 79 0.2437 0.2928 REMARK 3 26 1.7718 - 1.7488 0.44 1371 69 0.2805 0.2816 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.160 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.750 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) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL 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 : 0.003 3856 REMARK 3 ANGLE : 0.624 5208 REMARK 3 CHIRALITY : 0.043 578 REMARK 3 PLANARITY : 0.003 668 REMARK 3 DIHEDRAL : 14.876 2327 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID -1 THROUGH 135 ) REMARK 3 ORIGIN FOR THE GROUP (A): 80.6139 -4.6051 141.3022 REMARK 3 T TENSOR REMARK 3 T11: 0.1214 T22: 0.1791 REMARK 3 T33: 0.1093 T12: -0.0268 REMARK 3 T13: -0.0023 T23: -0.0112 REMARK 3 L TENSOR REMARK 3 L11: 2.2520 L22: 1.4141 REMARK 3 L33: 1.5115 L12: -0.4835 REMARK 3 L13: 0.7656 L23: 0.0071 REMARK 3 S TENSOR REMARK 3 S11: 0.0115 S12: -0.4877 S13: -0.0371 REMARK 3 S21: 0.1834 S22: 0.0439 S23: -0.0003 REMARK 3 S31: 0.0744 S32: -0.2322 S33: -0.0325 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 136 THROUGH 281 ) REMARK 3 ORIGIN FOR THE GROUP (A): 76.1385 -0.8801 111.6638 REMARK 3 T TENSOR REMARK 3 T11: 0.1115 T22: 0.0755 REMARK 3 T33: 0.1103 T12: -0.0072 REMARK 3 T13: 0.0179 T23: 0.0124 REMARK 3 L TENSOR REMARK 3 L11: 1.0679 L22: 0.4388 REMARK 3 L33: 2.1585 L12: 0.0551 REMARK 3 L13: 1.1107 L23: 0.1450 REMARK 3 S TENSOR REMARK 3 S11: -0.0186 S12: 0.0637 S13: 0.1212 REMARK 3 S21: -0.0785 S22: 0.0144 S23: -0.0037 REMARK 3 S31: -0.0267 S32: 0.0179 S33: 0.0148 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 282 THROUGH 469 ) REMARK 3 ORIGIN FOR THE GROUP (A): 64.3641 -11.3245 125.2771 REMARK 3 T TENSOR REMARK 3 T11: 0.1274 T22: 0.0757 REMARK 3 T33: 0.0801 T12: 0.0031 REMARK 3 T13: 0.0039 T23: -0.0092 REMARK 3 L TENSOR REMARK 3 L11: 2.3580 L22: 0.6752 REMARK 3 L33: 0.6639 L12: 0.1290 REMARK 3 L13: -0.3916 L23: 0.2773 REMARK 3 S TENSOR REMARK 3 S11: -0.0458 S12: 0.0497 S13: -0.0800 REMARK 3 S21: 0.0814 S22: -0.0044 S23: 0.0570 REMARK 3 S31: 0.0888 S32: -0.0674 S33: 0.0523 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE ENTRY CONTAINS FRIEDEL PAIRS IN REMARK 3 F_PLUS/MINUS COLUMNS AND I_PLUS/MINUS COLUMNS REMARK 4 REMARK 4 5X4K COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 15-FEB-17. REMARK 100 THE DEPOSITION ID IS D_1300002924. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-MAY-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL17U REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9793 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 72646 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.749 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.9 REMARK 200 DATA REDUNDANCY : 7.500 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 27.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.75 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.78 REMARK 200 COMPLETENESS FOR SHELL (%) : 90.3 REMARK 200 DATA REDUNDANCY IN SHELL : 7.20 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.600 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: 5X4J REMARK 200 REMARK 200 REMARK: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS REMARK 200 AND I_PLUS/MINUS COLUMNS REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 35.39 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.90 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 4.3% W/V PEG 2000 MME, 50 MM BICINE PH REMARK 280 8.8, 28.6% W/V PEG 600, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 33.08600 REMARK 290 SMTRY3 2 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: MONOMERIC 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 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 MSE A -22 REMARK 465 SER A -21 REMARK 465 TYR A -20 REMARK 465 TYR A -19 REMARK 465 HIS A -18 REMARK 465 HIS A -17 REMARK 465 HIS A -16 REMARK 465 HIS A -15 REMARK 465 HIS A -14 REMARK 465 HIS A -13 REMARK 465 LEU A -12 REMARK 465 GLU A -11 REMARK 465 SER A -10 REMARK 465 THR A -9 REMARK 465 SER A -8 REMARK 465 LEU A -7 REMARK 465 TYR A -6 REMARK 465 LYS A -5 REMARK 465 LYS A -4 REMARK 465 ALA A -3 REMARK 465 GLY A -2 REMARK 465 LYS A 470 REMARK 465 GLY A 471 REMARK 465 GLY A 472 REMARK 465 ASP A 473 REMARK 465 LYS A 474 REMARK 465 SER A 475 REMARK 465 GLU A 476 REMARK 465 SER A 477 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 O3' C5P A 504 O3P C5P A 505 1.27 REMARK 500 O HOH A 703 O HOH A 1011 1.85 REMARK 500 O HOH A 627 O HOH A 987 1.87 REMARK 500 O HOH A 682 O HOH A 1004 1.95 REMARK 500 O HOH A 875 O HOH A 1021 2.02 REMARK 500 O HOH A 924 O HOH A 990 2.04 REMARK 500 O HOH A 884 O HOH A 1022 2.07 REMARK 500 O HOH A 648 O HOH A 773 2.08 REMARK 500 ND1 HIS A 174 O HOH A 601 2.09 REMARK 500 O1P C5P A 506 O HOH A 602 2.10 REMARK 500 O HOH A 747 O HOH A 953 2.11 REMARK 500 O HOH A 601 O HOH A 941 2.13 REMARK 500 O HOH A 939 O HOH A 1002 2.15 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 O HOH A 771 O HOH A 898 2959 1.94 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 ARG A 132 -40.45 -134.69 REMARK 500 LEU A 134 139.58 -179.75 REMARK 500 ARG A 197 45.01 -85.50 REMARK 500 ASN A 215 71.91 -158.38 REMARK 500 GLU A 220 -17.73 72.97 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 A1054 DISTANCE = 6.01 ANGSTROMS REMARK 525 HOH A1055 DISTANCE = 6.12 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 ZN A 503 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 0 NE2 REMARK 620 2 GLU A 230 OE1 43.8 REMARK 620 3 GLU A 230 OE2 42.3 2.0 REMARK 620 4 HOH A 608 O 78.4 57.8 57.1 REMARK 620 5 HOH A 654 O 82.4 112.9 110.9 78.6 REMARK 620 6 HOH A 750 O 91.6 116.9 117.3 169.3 96.5 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 502 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 32 ND1 REMARK 620 2 ASP A 34 OD2 105.9 REMARK 620 3 C5P A 505 O1P 107.4 92.0 REMARK 620 4 HOH A 686 O 113.1 128.5 106.3 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 501 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 36 OD2 REMARK 620 2 HIS A 106 NE2 91.0 REMARK 620 3 ASP A 165 OD2 84.9 93.7 REMARK 620 4 C5P A 505 O2P 175.1 89.9 90.3 REMARK 620 5 HOH A 686 O 76.9 113.8 146.8 107.1 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 ZN A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue C5P A 504 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue C5P A 505 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue C5P A 506 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5X4H RELATED DB: PDB REMARK 900 RELATED ID: 5X4I RELATED DB: PDB REMARK 900 RELATED ID: 5X4J RELATED DB: PDB DBREF 5X4K A 1 477 UNP Q8TZE0 Q8TZE0_PYRFU 1 477 SEQADV 5X4K MSE A -22 UNP Q8TZE0 EXPRESSION TAG SEQADV 5X4K SER A -21 UNP Q8TZE0 EXPRESSION TAG SEQADV 5X4K TYR A -20 UNP Q8TZE0 EXPRESSION TAG SEQADV 5X4K TYR A -19 UNP Q8TZE0 EXPRESSION TAG SEQADV 5X4K HIS A -18 UNP Q8TZE0 EXPRESSION TAG SEQADV 5X4K HIS A -17 UNP Q8TZE0 EXPRESSION TAG SEQADV 5X4K HIS A -16 UNP Q8TZE0 EXPRESSION TAG SEQADV 5X4K HIS A -15 UNP Q8TZE0 EXPRESSION TAG SEQADV 5X4K HIS A -14 UNP Q8TZE0 EXPRESSION TAG SEQADV 5X4K HIS A -13 UNP Q8TZE0 EXPRESSION TAG SEQADV 5X4K LEU A -12 UNP Q8TZE0 EXPRESSION TAG SEQADV 5X4K GLU A -11 UNP Q8TZE0 EXPRESSION TAG SEQADV 5X4K SER A -10 UNP Q8TZE0 EXPRESSION TAG SEQADV 5X4K THR A -9 UNP Q8TZE0 EXPRESSION TAG SEQADV 5X4K SER A -8 UNP Q8TZE0 EXPRESSION TAG SEQADV 5X4K LEU A -7 UNP Q8TZE0 EXPRESSION TAG SEQADV 5X4K TYR A -6 UNP Q8TZE0 EXPRESSION TAG SEQADV 5X4K LYS A -5 UNP Q8TZE0 EXPRESSION TAG SEQADV 5X4K LYS A -4 UNP Q8TZE0 EXPRESSION TAG SEQADV 5X4K ALA A -3 UNP Q8TZE0 EXPRESSION TAG SEQADV 5X4K GLY A -2 UNP Q8TZE0 EXPRESSION TAG SEQADV 5X4K SER A -1 UNP Q8TZE0 EXPRESSION TAG SEQADV 5X4K HIS A 0 UNP Q8TZE0 EXPRESSION TAG SEQADV 5X4K ALA A 83 UNP Q8TZE0 ASP 83 ENGINEERED MUTATION SEQRES 1 A 500 MSE SER TYR TYR HIS HIS HIS HIS HIS HIS LEU GLU SER SEQRES 2 A 500 THR SER LEU TYR LYS LYS ALA GLY SER HIS MSE ASP LYS SEQRES 3 A 500 GLU GLY PHE LEU ASN LYS VAL ARG GLU ALA VAL ASP VAL SEQRES 4 A 500 VAL LYS LEU HIS ILE GLU LEU GLY HIS THR ILE ARG ILE SEQRES 5 A 500 ILE SER HIS ARG ASP ALA ASP GLY ILE THR SER ALA ALA SEQRES 6 A 500 ILE LEU ALA LYS ALA LEU GLY ARG GLU GLY ALA SER PHE SEQRES 7 A 500 HIS ILE SER ILE VAL LYS GLN VAL SER GLU ASP LEU LEU SEQRES 8 A 500 ARG GLU LEU LYS ASP GLU ASP TYR LYS ILE PHE ILE PHE SEQRES 9 A 500 SER ALA LEU GLY SER GLY SER LEU SER LEU ILE LYS GLU SEQRES 10 A 500 TYR LEU LYS GLU LYS THR VAL ILE ILE LEU ASP HIS HIS SEQRES 11 A 500 PRO PRO GLU ASN VAL LYS LEU GLU GLU LYS HIS ILE LEU SEQRES 12 A 500 VAL ASN PRO VAL GLN PHE GLY ALA ASN SER VAL ARG ASP SEQRES 13 A 500 LEU SER GLY SER GLY VAL THR TYR PHE PHE ALA ARG GLU SEQRES 14 A 500 LEU ASN GLU LYS ASN ARG ASP LEU ALA TYR ILE ALA ILE SEQRES 15 A 500 VAL GLY ALA VAL GLY ASP MSE GLN GLU ASN ASP GLY VAL SEQRES 16 A 500 PHE HIS GLY MSE ASN LEU ASP ILE ILE GLU ASP GLY LYS SEQRES 17 A 500 SER LEU GLY ILE LEU GLU VAL LYS LYS GLU LEU ARG LEU SEQRES 18 A 500 PHE GLY ARG GLU THR ARG PRO LEU TYR GLN MSE LEU ALA SEQRES 19 A 500 TYR ALA THR ASN PRO GLU ILE PRO GLU VAL THR GLY ASP SEQRES 20 A 500 GLU ARG LYS ALA ILE GLU TRP LEU LYS ASN LYS GLY PHE SEQRES 21 A 500 ASN PRO GLU LYS LYS TYR TRP GLU LEU SER GLU GLU GLU SEQRES 22 A 500 LYS LYS LYS LEU HIS ASP PHE LEU ILE ILE HIS MSE ILE SEQRES 23 A 500 LYS HIS GLY ALA GLY LYS GLU ASP ILE ASP ARG LEU ILE SEQRES 24 A 500 GLY ASP VAL VAL ILE SER PRO LEU TYR PRO GLU GLY ASP SEQRES 25 A 500 PRO ARG HIS GLU ALA ARG GLU PHE ALA THR LEU LEU ASN SEQRES 26 A 500 ALA THR GLY ARG LEU ASN LEU GLY ASN LEU GLY VAL ALA SEQRES 27 A 500 VAL CYS LEU GLY ASP GLU GLU ALA PHE ARG LYS ALA LEU SEQRES 28 A 500 LYS MSE VAL GLU ASP TYR LYS ARG GLU GLN ILE GLU ALA SEQRES 29 A 500 ARG LYS TRP LEU LEU GLN ASN TRP ASN SER GLU VAL TRP SEQRES 30 A 500 GLU GLY ASP HIS VAL TYR VAL LEU TYR VAL GLY LYS SER SEQRES 31 A 500 ILE ARG ASP THR LEU VAL GLY ILE ALA ALA SER MSE ALA SEQRES 32 A 500 ILE ASN ALA GLY LEU ALA ASP PRO GLU LYS PRO VAL ILE SEQRES 33 A 500 VAL PHE ALA ASP THR ASP GLU ASP PRO ASN LEU LEU LYS SEQRES 34 A 500 GLY SER ALA ARG THR THR GLU ARG ALA LEU ALA LYS GLY SEQRES 35 A 500 TYR ASN LEU GLY GLU ALA LEU ARG LYS ALA ALA GLU LEU SEQRES 36 A 500 VAL ASN GLY GLU GLY GLY GLY HIS ALA ILE ALA ALA GLY SEQRES 37 A 500 ILE ARG ILE PRO ARG ALA ARG LEU ALA GLU PHE ARG LYS SEQRES 38 A 500 LEU ILE ASP LYS ILE LEU GLY GLU GLN VAL SER LYS GLY SEQRES 39 A 500 GLY ASP LYS SER GLU SER MODRES 5X4K MSE A 1 MET MODIFIED RESIDUE MODRES 5X4K MSE A 166 MET MODIFIED RESIDUE MODRES 5X4K MSE A 176 MET MODIFIED RESIDUE MODRES 5X4K MSE A 209 MET MODIFIED RESIDUE MODRES 5X4K MSE A 262 MET MODIFIED RESIDUE MODRES 5X4K MSE A 330 MET MODIFIED RESIDUE MODRES 5X4K MSE A 379 MET MODIFIED RESIDUE HET MSE A 1 8 HET MSE A 166 8 HET MSE A 176 8 HET MSE A 209 8 HET MSE A 262 16 HET MSE A 330 8 HET MSE A 379 8 HET ZN A 501 1 HET ZN A 502 1 HET ZN A 503 1 HET C5P A 504 21 HET C5P A 505 21 HET C5P A 506 21 HETNAM MSE SELENOMETHIONINE HETNAM ZN ZINC ION HETNAM C5P CYTIDINE-5'-MONOPHOSPHATE FORMUL 1 MSE 7(C5 H11 N O2 SE) FORMUL 2 ZN 3(ZN 2+) FORMUL 5 C5P 3(C9 H14 N3 O8 P) FORMUL 8 HOH *455(H2 O) HELIX 1 AA1 ASP A 2 LEU A 23 1 22 HELIX 2 AA2 ASP A 34 GLU A 51 1 18 HELIX 3 AA3 SER A 64 GLU A 74 1 11 HELIX 4 AA4 GLY A 85 GLY A 87 5 3 HELIX 5 AA5 SER A 88 LEU A 96 1 9 HELIX 6 AA6 ASN A 122 GLY A 127 5 6 HELIX 7 AA7 SER A 135 ASN A 148 1 14 HELIX 8 AA8 GLU A 149 ASP A 153 5 5 HELIX 9 AA9 LEU A 154 ASP A 165 1 12 HELIX 10 AB1 MSE A 176 LEU A 187 1 12 HELIX 11 AB2 PRO A 205 TYR A 212 1 8 HELIX 12 AB3 ASP A 224 LYS A 235 1 12 HELIX 13 AB4 LYS A 242 LEU A 246 5 5 HELIX 14 AB5 SER A 247 HIS A 265 1 19 HELIX 15 AB6 GLY A 268 ARG A 274 1 7 HELIX 16 AB7 ASP A 289 HIS A 292 5 4 HELIX 17 AB8 GLU A 293 LEU A 307 1 15 HELIX 18 AB9 LEU A 309 LEU A 318 1 10 HELIX 19 AC1 ASP A 320 LYS A 329 1 10 HELIX 20 AC2 MSE A 330 VAL A 353 1 24 HELIX 21 AC3 ARG A 369 THR A 371 5 3 HELIX 22 AC4 LEU A 372 ALA A 383 1 12 HELIX 23 AC5 THR A 412 LYS A 418 1 7 HELIX 24 AC6 ASN A 421 GLU A 431 1 11 HELIX 25 AC7 ARG A 452 VAL A 468 1 17 SHEET 1 AA1 5 PHE A 55 VAL A 60 0 SHEET 2 AA1 5 ILE A 27 HIS A 32 1 N ILE A 29 O HIS A 56 SHEET 3 AA1 5 ILE A 78 SER A 82 1 O ILE A 80 N ARG A 28 SHEET 4 AA1 5 THR A 100 LEU A 104 1 O LEU A 104 N PHE A 81 SHEET 5 AA1 5 HIS A 118 VAL A 121 1 O VAL A 121 N ILE A 103 SHEET 1 AA2 2 GLU A 191 LEU A 196 0 SHEET 2 AA2 2 ILE A 276 ILE A 281 -1 O VAL A 279 N LYS A 193 SHEET 1 AA3 6 TRP A 354 GLU A 355 0 SHEET 2 AA3 6 TYR A 360 TYR A 363 -1 O VAL A 361 N TRP A 354 SHEET 3 AA3 6 VAL A 392 THR A 398 1 O PHE A 395 N LEU A 362 SHEET 4 AA3 6 ASP A 401 ARG A 410 -1 O ARG A 410 N VAL A 392 SHEET 5 AA3 6 ALA A 443 PRO A 449 -1 O ALA A 444 N ALA A 409 SHEET 6 AA3 6 GLU A 436 GLY A 439 -1 N GLU A 436 O ARG A 447 LINK C HIS A 0 N MSE A 1 1555 1555 1.33 LINK C MSE A 1 N ASP A 2 1555 1555 1.33 LINK C ASP A 165 N MSE A 166 1555 1555 1.33 LINK C MSE A 166 N GLN A 167 1555 1555 1.33 LINK C GLY A 175 N MSE A 176 1555 1555 1.33 LINK C MSE A 176 N ASN A 177 1555 1555 1.34 LINK C GLN A 208 N MSE A 209 1555 1555 1.33 LINK C MSE A 209 N LEU A 210 1555 1555 1.34 LINK C HIS A 261 N AMSE A 262 1555 1555 1.33 LINK C HIS A 261 N BMSE A 262 1555 1555 1.33 LINK C AMSE A 262 N ILE A 263 1555 1555 1.33 LINK C BMSE A 262 N ILE A 263 1555 1555 1.33 LINK C LYS A 329 N MSE A 330 1555 1555 1.33 LINK C MSE A 330 N VAL A 331 1555 1555 1.33 LINK C ASER A 378 N MSE A 379 1555 1555 1.33 LINK C BSER A 378 N MSE A 379 1555 1555 1.33 LINK C MSE A 379 N ALA A 380 1555 1555 1.34 LINK NE2 HIS A 0 ZN ZN A 503 1555 1555 2.03 LINK ND1 HIS A 32 ZN ZN A 502 1555 1555 2.02 LINK OD2 ASP A 34 ZN ZN A 502 1555 1555 2.04 LINK OD2 ASP A 36 ZN ZN A 501 1555 1555 2.41 LINK NE2 HIS A 106 ZN ZN A 501 1555 1555 2.19 LINK OD2 ASP A 165 ZN ZN A 501 1555 1555 1.95 LINK OE1 GLU A 230 ZN ZN A 503 1555 2949 2.63 LINK OE2 GLU A 230 ZN ZN A 503 1555 2949 2.50 LINK ZN ZN A 501 O2P C5P A 505 1555 1555 2.13 LINK ZN ZN A 501 O HOH A 686 1555 1555 1.91 LINK ZN ZN A 502 O1P C5P A 505 1555 1555 1.91 LINK ZN ZN A 502 O HOH A 686 1555 1555 2.35 LINK ZN ZN A 503 O HOH A 608 1555 2959 2.41 LINK ZN ZN A 503 O HOH A 654 1555 1555 1.92 LINK ZN ZN A 503 O HOH A 750 1555 2959 2.15 CISPEP 1 ASN A 215 PRO A 216 0 4.04 SITE 1 AC1 6 ASP A 36 HIS A 106 ASP A 165 ZN A 502 SITE 2 AC1 6 C5P A 505 HOH A 686 SITE 1 AC2 5 HIS A 32 ASP A 34 ZN A 501 C5P A 505 SITE 2 AC2 5 HOH A 686 SITE 1 AC3 2 HIS A 0 HOH A 654 SITE 1 AC4 16 HIS A 32 HIS A 107 LYS A 406 SER A 408 SITE 2 AC4 16 ARG A 410 GLY A 437 GLY A 438 GLY A 439 SITE 3 AC4 16 ALA A 444 GLY A 445 C5P A 505 HOH A 628 SITE 4 AC4 16 HOH A 633 HOH A 706 HOH A 714 HOH A 903 SITE 1 AC5 20 HIS A 32 ASP A 34 HIS A 106 HIS A 107 SITE 2 AC5 20 ASP A 165 MSE A 166 ASN A 169 ARG A 410 SITE 3 AC5 20 HIS A 440 ILE A 442 ALA A 443 ZN A 501 SITE 4 AC5 20 ZN A 502 C5P A 504 C5P A 506 HOH A 609 SITE 5 AC5 20 HOH A 747 HOH A 787 HOH A 801 HOH A 904 SITE 1 AC6 15 THR A 214 TYR A 334 LYS A 335 GLN A 338 SITE 2 AC6 15 ILE A 375 SER A 378 ASN A 382 ARG A 410 SITE 3 AC6 15 C5P A 505 HOH A 602 HOH A 605 HOH A 624 SITE 4 AC6 15 HOH A 629 HOH A 648 HOH A 777 CRYST1 58.426 66.172 59.929 90.00 112.22 90.00 P 1 21 1 2 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 0.017116 0.000000 0.006991 0.00000 SCALE2 0.000000 0.015112 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018025 0.00000