HEADER CELL CYCLE 11-MAR-20 6YA6 TITLE MINIMAL CONSTRUCT OF CDC7-DBF4 BOUND TO XL413 COMPND MOL_ID: 1; COMPND 2 MOLECULE: CELL DIVISION CYCLE 7-RELATED PROTEIN KINASE,CELL DIVISION COMPND 3 CYCLE 7-RELATED PROTEIN KINASE,CELL DIVISION CYCLE 7-RELATED PROTEIN COMPND 4 KINASE; COMPND 5 CHAIN: A; COMPND 6 SYNONYM: HUCDC7,HUCDC7,HUCDC7; COMPND 7 EC: 2.7.11.1,2.7.11.1,2.7.11.1; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: PROTEIN DBF4 HOMOLOG A; COMPND 11 CHAIN: B; COMPND 12 SYNONYM: ACTIVATOR OF S PHASE KINASE,CHIFFON HOMOLOG A,DBF4-TYPE ZINC COMPND 13 FINGER-CONTAINING PROTEIN 1; COMPND 14 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: CDC7, CDC7L1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 10 ORGANISM_COMMON: HUMAN; SOURCE 11 ORGANISM_TAXID: 9606; SOURCE 12 GENE: DBF4, ASK, DBF4A, ZDBF1; SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS KINASE, CDC7, DBF4, CELL CYCLE, BIVALENT SUBSTRATE, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR S.D.DICK,P.CHEREPANOV REVDAT 4 24-JAN-24 6YA6 1 REMARK REVDAT 3 19-AUG-20 6YA6 1 JRNL REVDAT 2 01-JUL-20 6YA6 1 JRNL REVDAT 1 27-MAY-20 6YA6 0 JRNL AUTH S.D.DICK,S.FEDERICO,S.M.HUGHES,V.E.PYE,N.O'REILLY, JRNL AUTH 2 P.CHEREPANOV JRNL TITL STRUCTURAL BASIS FOR THE ACTIVATION AND TARGET SITE JRNL TITL 2 SPECIFICITY OF CDC7 KINASE. JRNL REF STRUCTURE V. 28 954 2020 JRNL REFN ISSN 0969-2126 JRNL PMID 32521228 JRNL DOI 10.1016/J.STR.2020.05.010 REMARK 2 REMARK 2 RESOLUTION. 1.44 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX DEV_3707 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) : 1.44 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.85 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 82484 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.168 REMARK 3 R VALUE (WORKING SET) : 0.167 REMARK 3 FREE R VALUE : 0.193 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.020 REMARK 3 FREE R VALUE TEST SET COUNT : 4139 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 42.8500 - 4.4700 1.00 2935 146 0.1640 0.1882 REMARK 3 2 4.4700 - 3.5500 1.00 2766 133 0.1433 0.1775 REMARK 3 3 3.5500 - 3.1000 1.00 2683 154 0.1577 0.1792 REMARK 3 4 3.1000 - 2.8200 1.00 2657 158 0.1683 0.1949 REMARK 3 5 2.8200 - 2.6200 1.00 2658 164 0.1692 0.1874 REMARK 3 6 2.6200 - 2.4600 1.00 2654 122 0.1642 0.1887 REMARK 3 7 2.4600 - 2.3400 1.00 2655 142 0.1627 0.2030 REMARK 3 8 2.3400 - 2.2400 1.00 2651 129 0.1639 0.1831 REMARK 3 9 2.2400 - 2.1500 1.00 2630 139 0.1599 0.1958 REMARK 3 10 2.1500 - 2.0800 1.00 2605 146 0.1654 0.1699 REMARK 3 11 2.0800 - 2.0100 1.00 2618 149 0.1634 0.2142 REMARK 3 12 2.0100 - 1.9500 1.00 2570 163 0.1621 0.1880 REMARK 3 13 1.9500 - 1.9000 1.00 2589 156 0.1665 0.2136 REMARK 3 14 1.9000 - 1.8600 1.00 2584 131 0.1746 0.2057 REMARK 3 15 1.8600 - 1.8100 1.00 2618 119 0.1732 0.1874 REMARK 3 16 1.8100 - 1.7800 1.00 2613 152 0.1695 0.1746 REMARK 3 17 1.7800 - 1.7400 1.00 2588 132 0.1709 0.1810 REMARK 3 18 1.7400 - 1.7100 1.00 2572 147 0.1633 0.2114 REMARK 3 19 1.7100 - 1.6800 1.00 2592 134 0.1663 0.2132 REMARK 3 20 1.6800 - 1.6500 1.00 2601 144 0.1696 0.1836 REMARK 3 21 1.6500 - 1.6200 1.00 2554 123 0.1767 0.1746 REMARK 3 22 1.6200 - 1.6000 1.00 2646 129 0.1737 0.2257 REMARK 3 23 1.6000 - 1.5700 1.00 2572 133 0.1876 0.1954 REMARK 3 24 1.5700 - 1.5500 1.00 2590 112 0.1828 0.2127 REMARK 3 25 1.5500 - 1.5300 1.00 2594 127 0.1933 0.1961 REMARK 3 26 1.5300 - 1.5100 1.00 2592 130 0.1988 0.2464 REMARK 3 27 1.5100 - 1.4900 0.99 2590 130 0.2081 0.2298 REMARK 3 28 1.4900 - 1.4700 0.97 2474 125 0.2119 0.2246 REMARK 3 29 1.4700 - 1.4600 0.96 2478 125 0.2261 0.2709 REMARK 3 30 1.4600 - 1.4400 0.94 2416 145 0.2394 0.2493 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) : 0.129 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 17.007 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 13.58 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.95 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 : 0.006 3684 REMARK 3 ANGLE : 0.888 4980 REMARK 3 CHIRALITY : 0.080 550 REMARK 3 PLANARITY : 0.005 636 REMARK 3 DIHEDRAL : 18.203 1388 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 6 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: (CHAIN A AND RESID 38:214) REMARK 3 ORIGIN FOR THE GROUP (A): 20.9311 14.9032 58.7437 REMARK 3 T TENSOR REMARK 3 T11: 0.0771 T22: 0.1066 REMARK 3 T33: 0.0952 T12: -0.0003 REMARK 3 T13: 0.0048 T23: 0.0123 REMARK 3 L TENSOR REMARK 3 L11: 0.0970 L22: 0.1435 REMARK 3 L33: 1.0011 L12: -0.0560 REMARK 3 L13: 0.0551 L23: 0.0573 REMARK 3 S TENSOR REMARK 3 S11: -0.0106 S12: -0.0218 S13: -0.0281 REMARK 3 S21: 0.0205 S22: -0.0078 S23: -0.0219 REMARK 3 S31: -0.0029 S32: 0.0657 S33: -0.0069 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN A AND RESID 215:450 OR CHAIN D AND RESID 1:1) REMARK 3 ORIGIN FOR THE GROUP (A): 1.4402 17.7602 38.0657 REMARK 3 T TENSOR REMARK 3 T11: 0.0761 T22: 0.1204 REMARK 3 T33: 0.1036 T12: 0.0044 REMARK 3 T13: 0.0106 T23: -0.0024 REMARK 3 L TENSOR REMARK 3 L11: 0.4273 L22: 0.0965 REMARK 3 L33: 0.0524 L12: -0.2981 REMARK 3 L13: 0.0218 L23: -0.0938 REMARK 3 S TENSOR REMARK 3 S11: 0.0350 S12: 0.0212 S13: -0.0897 REMARK 3 S21: 0.0146 S22: -0.0265 S23: 0.0544 REMARK 3 S31: 0.0171 S32: -0.0144 S33: -0.0066 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: (CHAIN A AND RESID 451:573) REMARK 3 ORIGIN FOR THE GROUP (A): 21.3067 16.5916 30.6833 REMARK 3 T TENSOR REMARK 3 T11: 0.0640 T22: 0.1514 REMARK 3 T33: 0.0963 T12: 0.0074 REMARK 3 T13: 0.0199 T23: 0.0035 REMARK 3 L TENSOR REMARK 3 L11: 0.2462 L22: 0.2911 REMARK 3 L33: 0.3156 L12: 0.0125 REMARK 3 L13: 0.0881 L23: -0.0262 REMARK 3 S TENSOR REMARK 3 S11: 0.0038 S12: 0.1943 S13: -0.0310 REMARK 3 S21: -0.0596 S22: 0.0298 S23: -0.0699 REMARK 3 S31: 0.0157 S32: 0.0642 S33: 0.0175 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: (CHAIN B AND RESID 207:254) REMARK 3 ORIGIN FOR THE GROUP (A): -2.8525 26.4124 35.4799 REMARK 3 T TENSOR REMARK 3 T11: 0.0959 T22: 0.1181 REMARK 3 T33: 0.1626 T12: -0.0123 REMARK 3 T13: 0.0127 T23: 0.0320 REMARK 3 L TENSOR REMARK 3 L11: 0.3436 L22: -0.1890 REMARK 3 L33: 0.0951 L12: -0.0830 REMARK 3 L13: -0.0865 L23: 0.1410 REMARK 3 S TENSOR REMARK 3 S11: 0.0184 S12: 0.0937 S13: -0.0628 REMARK 3 S21: 0.0717 S22: -0.0338 S23: -0.0038 REMARK 3 S31: -0.0027 S32: -0.0330 S33: -0.0158 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: (CHAIN B AND RESID 293:314 OR CHAIN D AND RESID 2:2) REMARK 3 ORIGIN FOR THE GROUP (A): -1.6126 20.5604 68.4010 REMARK 3 T TENSOR REMARK 3 T11: 0.2228 T22: 0.4297 REMARK 3 T33: 0.2772 T12: 0.1014 REMARK 3 T13: 0.0404 T23: 0.1355 REMARK 3 L TENSOR REMARK 3 L11: 0.0402 L22: 0.0692 REMARK 3 L33: 0.3142 L12: 0.0396 REMARK 3 L13: 0.0387 L23: 0.0706 REMARK 3 S TENSOR REMARK 3 S11: -0.1639 S12: 0.1093 S13: 0.0639 REMARK 3 S21: 0.0552 S22: 0.1209 S23: 0.3232 REMARK 3 S31: -0.4791 S32: -0.3628 S33: -0.0085 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: (CHAIN B AND RESID 315:346) REMARK 3 ORIGIN FOR THE GROUP (A): 16.2952 10.1513 76.2319 REMARK 3 T TENSOR REMARK 3 T11: 0.1427 T22: 0.1553 REMARK 3 T33: 0.1517 T12: 0.0106 REMARK 3 T13: 0.0450 T23: 0.0367 REMARK 3 L TENSOR REMARK 3 L11: 0.1297 L22: -0.0113 REMARK 3 L33: 0.1766 L12: 0.0303 REMARK 3 L13: -0.0378 L23: -0.0269 REMARK 3 S TENSOR REMARK 3 S11: -0.0139 S12: -0.1931 S13: -0.1278 REMARK 3 S21: 0.1270 S22: 0.0572 S23: 0.0162 REMARK 3 S31: -0.0011 S32: -0.0603 S33: 0.0055 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 6YA6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 11-MAR-20. REMARK 100 THE DEPOSITION ID IS D_1292105862. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-NOV-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : BM14 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0332 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 82613 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.440 REMARK 200 RESOLUTION RANGE LOW (A) : 59.610 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 9.100 REMARK 200 R MERGE (I) : 0.04900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 26.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.44 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.49 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.58400 REMARK 200 R SYM FOR SHELL (I) : NULL 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: 5MH9 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.72 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.15 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M PCTP PH7, 18% PEG 1500, 8% MPD, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 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+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 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 116.95500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 30.82000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 30.82000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 58.47750 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 30.82000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 30.82000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 175.43250 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 30.82000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 30.82000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 58.47750 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 30.82000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 30.82000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 175.43250 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 116.95500 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: 7530 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 21730 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -47.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 MET A 36 REMARK 465 LEU A 37 REMARK 465 SER A 334 REMARK 465 GLU A 335 REMARK 465 ALA A 336 REMARK 465 GLN A 337 REMARK 465 GLN A 338 REMARK 465 GLU A 339 REMARK 465 ARG A 340 REMARK 465 CYS A 341 REMARK 465 SER A 342 REMARK 465 GLN A 343 REMARK 465 ASN A 344 REMARK 465 LYS A 345 REMARK 465 LEU A 574 REMARK 465 VAL B 255 REMARK 465 ASP B 256 REMARK 465 LYS B 257 REMARK 465 PRO B 258 REMARK 465 SER B 259 REMARK 465 SER B 260 REMARK 465 MET B 261 REMARK 465 GLN B 262 REMARK 465 LYS B 263 REMARK 465 GLN B 264 REMARK 465 THR B 265 REMARK 465 GLN B 266 REMARK 465 VAL B 267 REMARK 465 LYS B 268 REMARK 465 LEU B 269 REMARK 465 ARG B 270 REMARK 465 ILE B 271 REMARK 465 GLN B 272 REMARK 465 THR B 273 REMARK 465 ASP B 274 REMARK 465 GLY B 275 REMARK 465 ASP B 276 REMARK 465 LYS B 277 REMARK 465 TYR B 278 REMARK 465 GLY B 279 REMARK 465 GLY B 280 REMARK 465 THR B 281 REMARK 465 SER B 282 REMARK 465 ILE B 283 REMARK 465 GLN B 284 REMARK 465 LEU B 285 REMARK 465 GLN B 286 REMARK 465 LEU B 287 REMARK 465 LYS B 288 REMARK 465 GLU B 289 REMARK 465 LYS B 290 REMARK 465 LYS B 291 REMARK 465 LYS B 292 REMARK 465 LYS B 347 REMARK 465 LYS B 348 REMARK 465 LYS B 349 REMARK 465 ARG B 350 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 OD1 ASN B 322 O HOH B 501 2.14 REMARK 500 O HOH A 918 O HOH A 1001 2.17 REMARK 500 OD2 ASP B 344 O HOH B 502 2.19 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 127 -121.58 55.91 REMARK 500 ARG A 176 -17.89 79.98 REMARK 500 ASP A 196 86.75 81.15 REMARK 500 ARG A 373 8.98 -152.82 REMARK 500 LEU A 550 32.41 -91.58 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 ZN A 602 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 351 SG REMARK 620 2 CYS A 353 SG 110.5 REMARK 620 3 CYS A 360 SG 112.7 107.0 REMARK 620 4 CYS A 363 SG 104.8 108.2 113.7 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 401 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 296 SG REMARK 620 2 CYS B 299 SG 115.7 REMARK 620 3 HIS B 309 NE2 98.8 112.9 REMARK 620 4 HIS B 315 ND1 108.1 111.2 109.4 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 0SX A 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 602 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PEG A 603 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue BO3 A 604 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN B 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL B 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IMD B 403 DBREF 6YA6 A 37 345 UNP O00311 CDC7_HUMAN 37 227 DBREF 6YA6 A 346 467 UNP O00311 CDC7_HUMAN 346 467 DBREF 6YA6 A 534 574 UNP O00311 CDC7_HUMAN 534 574 DBREF 6YA6 B 210 350 UNP Q9UBU7 DBF4A_HUMAN 210 350 SEQADV 6YA6 MET A 36 UNP O00311 INITIATING METHIONINE SEQADV 6YA6 ALA A 468 UNP O00311 LINKER SEQADV 6YA6 GLY A 469 UNP O00311 LINKER SEQADV 6YA6 ALA A 470 UNP O00311 LINKER SEQADV 6YA6 GLY A 471 UNP O00311 LINKER SEQADV 6YA6 GLY B 207 UNP Q9UBU7 EXPRESSION TAG SEQADV 6YA6 PRO B 208 UNP Q9UBU7 EXPRESSION TAG SEQADV 6YA6 GLY B 209 UNP Q9UBU7 EXPRESSION TAG SEQRES 1 A 359 MET LEU ALA GLY VAL LYS LYS ASP ILE GLU LYS LEU TYR SEQRES 2 A 359 GLU ALA VAL PRO GLN LEU SER ASN VAL PHE LYS ILE GLU SEQRES 3 A 359 ASP LYS ILE GLY GLU GLY THR PHE SER SER VAL TYR LEU SEQRES 4 A 359 ALA THR ALA GLN LEU GLN VAL GLY PRO GLU GLU LYS ILE SEQRES 5 A 359 ALA LEU LYS HIS LEU ILE PRO THR SER HIS PRO ILE ARG SEQRES 6 A 359 ILE ALA ALA GLU LEU GLN CYS LEU THR VAL ALA GLY GLY SEQRES 7 A 359 GLN ASP ASN VAL MET GLY VAL LYS TYR CYS PHE ARG LYS SEQRES 8 A 359 ASN ASP HIS VAL VAL ILE ALA MET PRO TYR LEU GLU HIS SEQRES 9 A 359 GLU SER PHE LEU ASP ILE LEU ASN SER LEU SER PHE GLN SEQRES 10 A 359 GLU VAL ARG GLU TYR MET LEU ASN LEU PHE LYS ALA LEU SEQRES 11 A 359 LYS ARG ILE HIS GLN PHE GLY ILE VAL HIS ARG ASP VAL SEQRES 12 A 359 LYS PRO SER ASN PHE LEU TYR ASN ARG ARG LEU LYS LYS SEQRES 13 A 359 TYR ALA LEU VAL ASP PHE GLY LEU ALA GLN GLY THR HIS SEQRES 14 A 359 ASP THR LYS ILE GLU LEU LEU LYS PHE VAL GLN SER GLU SEQRES 15 A 359 ALA GLN GLN GLU ARG CYS SER GLN ASN LYS PRO ALA SER SEQRES 16 A 359 LEU THR CYS ASP CYS TYR ALA THR ASP LYS VAL CYS SER SEQRES 17 A 359 ILE CYS LEU SER ARG ARG GLN GLN VAL ALA PRO ARG ALA SEQRES 18 A 359 GLY THR PRO GLY PHE ARG ALA PRO GLU VAL LEU THR LYS SEQRES 19 A 359 CYS PRO ASN GLN THR THR ALA ILE ASP MET TRP SER ALA SEQRES 20 A 359 GLY VAL ILE PHE LEU SER LEU LEU SER GLY ARG TYR PRO SEQRES 21 A 359 PHE TYR LYS ALA SER ASP ASP LEU THR ALA LEU ALA GLN SEQRES 22 A 359 ILE MET THR ILE ARG GLY SER ARG GLU THR ILE GLN ALA SEQRES 23 A 359 ALA LYS THR PHE GLY LYS SER ILE LEU CYS SER LYS GLU SEQRES 24 A 359 VAL PRO ALA GLN ASP LEU ARG LYS LEU CYS GLU ARG LEU SEQRES 25 A 359 ARG GLY ALA GLY ALA GLY GLY TRP ASN GLU VAL PRO ASP SEQRES 26 A 359 GLU ALA TYR ASP LEU LEU ASP LYS LEU LEU ASP LEU ASN SEQRES 27 A 359 PRO ALA SER ARG ILE THR ALA GLU GLU ALA LEU LEU HIS SEQRES 28 A 359 PRO PHE PHE LYS ASP MET SER LEU SEQRES 1 B 144 GLY PRO GLY THR ARG THR GLY ARG LEU LYS LYS PRO PHE SEQRES 2 B 144 VAL LYS VAL GLU ASP MET SEP GLN LEU TYR ARG PRO PHE SEQRES 3 B 144 TYR LEU GLN LEU THR ASN MET PRO PHE ILE ASN TYR SER SEQRES 4 B 144 ILE GLN LYS PRO CYS SER PRO PHE ASP VAL ASP LYS PRO SEQRES 5 B 144 SER SER MET GLN LYS GLN THR GLN VAL LYS LEU ARG ILE SEQRES 6 B 144 GLN THR ASP GLY ASP LYS TYR GLY GLY THR SER ILE GLN SEQRES 7 B 144 LEU GLN LEU LYS GLU LYS LYS LYS LYS GLY TYR CYS GLU SEQRES 8 B 144 CYS CYS LEU GLN LYS TYR GLU ASP LEU GLU THR HIS LEU SEQRES 9 B 144 LEU SER GLU GLN HIS ARG ASN PHE ALA GLN SER ASN GLN SEQRES 10 B 144 TYR GLN VAL VAL ASP ASP ILE VAL SER LYS LEU VAL PHE SEQRES 11 B 144 ASP PHE VAL GLU TYR GLU LYS ASP THR PRO LYS LYS LYS SEQRES 12 B 144 ARG MODRES 6YA6 SEP B 226 SER MODIFIED RESIDUE HET SEP B 226 10 HET 0SX A 601 20 HET ZN A 602 1 HET PEG A 603 7 HET BO3 A 604 4 HET ZN B 401 1 HET CL B 402 1 HET IMD B 403 5 HETNAM SEP PHOSPHOSERINE HETNAM 0SX 8-CHLORO-2-[(2S)-PYRROLIDIN-2-YL][1]BENZOFURO[3,2- HETNAM 2 0SX D]PYRIMIDIN-4(3H)-ONE HETNAM ZN ZINC ION HETNAM PEG DI(HYDROXYETHYL)ETHER HETNAM BO3 BORIC ACID HETNAM CL CHLORIDE ION HETNAM IMD IMIDAZOLE HETSYN SEP PHOSPHONOSERINE FORMUL 2 SEP C3 H8 N O6 P FORMUL 3 0SX C14 H12 CL N3 O2 FORMUL 4 ZN 2(ZN 2+) FORMUL 5 PEG C4 H10 O3 FORMUL 6 BO3 B H3 O3 FORMUL 8 CL CL 1- FORMUL 9 IMD C3 H5 N2 1+ FORMUL 10 HOH *464(H2 O) HELIX 1 AA1 ALA A 38 VAL A 51 1 14 HELIX 2 AA2 PRO A 52 VAL A 57 5 6 HELIX 3 AA3 HIS A 97 ALA A 111 1 15 HELIX 4 AA4 SER A 141 LEU A 146 1 6 HELIX 5 AA5 SER A 150 PHE A 171 1 22 HELIX 6 AA6 LYS A 179 SER A 181 5 3 HELIX 7 AA7 ILE A 208 VAL A 214 5 7 HELIX 8 AA8 CYS A 360 SER A 365 1 6 HELIX 9 AA9 ALA A 381 THR A 386 1 6 HELIX 10 AB1 THR A 393 GLY A 410 1 18 HELIX 11 AB2 ASP A 419 GLY A 432 1 14 HELIX 12 AB3 GLY A 432 PHE A 443 1 12 HELIX 13 AB4 ASP A 457 GLY A 467 1 11 HELIX 14 AB5 PRO A 539 LEU A 550 1 12 HELIX 15 AB6 THR A 559 LEU A 564 1 6 HELIX 16 AB7 LEU A 565 LYS A 570 5 6 HELIX 17 AB8 GLY B 207 ARG B 211 5 5 HELIX 18 AB9 ASP B 305 LEU B 310 1 6 HELIX 19 AC1 SER B 312 GLN B 320 1 9 HELIX 20 AC2 TYR B 324 SER B 332 1 9 SHEET 1 AA1 5 LYS A 59 GLU A 66 0 SHEET 2 AA1 5 SER A 70 GLN A 78 -1 O LEU A 74 N GLU A 61 SHEET 3 AA1 5 GLU A 84 LEU A 92 -1 O ILE A 87 N ALA A 75 SHEET 4 AA1 5 HIS A 129 PRO A 135 -1 O MET A 134 N ALA A 88 SHEET 5 AA1 5 TYR A 122 LYS A 126 -1 N TYR A 122 O ALA A 133 SHEET 1 AA2 2 ILE A 173 VAL A 174 0 SHEET 2 AA2 2 GLN A 201 GLY A 202 -1 O GLN A 201 N VAL A 174 SHEET 1 AA3 2 PHE A 183 ASN A 186 0 SHEET 2 AA3 2 LYS A 191 LEU A 194 -1 O LYS A 191 N ASN A 186 SHEET 1 AA4 2 LYS A 358 VAL A 359 0 SHEET 2 AA4 2 GLY B 213 ARG B 214 -1 O GLY B 213 N VAL A 359 SHEET 1 AA5 3 LYS A 445 CYS A 449 0 SHEET 2 AA5 3 PHE B 219 ASP B 224 -1 O GLU B 223 N SER A 446 SHEET 3 AA5 3 PHE B 232 GLN B 235 -1 O PHE B 232 N VAL B 222 SHEET 1 AA6 2 GLY B 294 CYS B 296 0 SHEET 2 AA6 2 GLN B 301 TYR B 303 -1 O TYR B 303 N GLY B 294 LINK C MET B 225 N SEP B 226 1555 1555 1.32 LINK C SEP B 226 N GLN B 227 1555 1555 1.33 LINK SG CYS A 351 ZN ZN A 602 1555 1555 2.29 LINK SG CYS A 353 ZN ZN A 602 1555 1555 2.28 LINK SG CYS A 360 ZN ZN A 602 1555 1555 2.33 LINK SG CYS A 363 ZN ZN A 602 1555 1555 2.37 LINK SG CYS B 296 ZN ZN B 401 1555 1555 2.28 LINK SG CYS B 299 ZN ZN B 401 1555 1555 2.32 LINK NE2 HIS B 309 ZN ZN B 401 1555 1555 2.03 LINK ND1 HIS B 315 ZN ZN B 401 1555 1555 2.05 CISPEP 1 TYR A 412 PRO A 413 0 -4.51 CISPEP 2 LYS B 217 PRO B 218 0 0.90 CISPEP 3 LYS B 248 PRO B 249 0 3.82 SITE 1 AC1 13 SER A 70 VAL A 72 ALA A 88 LYS A 90 SITE 2 AC1 13 MET A 134 PRO A 135 TYR A 136 LEU A 137 SITE 3 AC1 13 ASN A 182 LEU A 184 VAL A 195 ASP A 196 SITE 4 AC1 13 HOH A 742 SITE 1 AC2 4 CYS A 351 CYS A 353 CYS A 360 CYS A 363 SITE 1 AC3 8 GLU A 66 GLY A 67 SER A 70 SER A 71 SITE 2 AC3 8 HIS A 91 LEU A 92 ILE A 93 HOH A 964 SITE 1 AC4 2 GLU A 85 HOH A 803 SITE 1 AC5 4 CYS B 296 CYS B 299 HIS B 309 HIS B 315 SITE 1 AC6 2 ASN A 127 ARG B 214 SITE 1 AC7 5 GLN A 53 TYR A 122 THR B 237 PHE B 336 SITE 2 AC7 5 GLU B 340 CRYST1 61.640 61.640 233.910 90.00 90.00 90.00 P 41 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 0.016223 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016223 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004275 0.00000