HEADER CELL CYCLE 11-MAR-20 6YA8 TITLE CDC7-DBF4 BOUND TO ADP-BEF3 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, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR S.D.DICK,P.CHEREPANOV REVDAT 4 24-JAN-24 6YA8 1 REMARK REVDAT 3 19-AUG-20 6YA8 1 JRNL LINK REVDAT 2 01-JUL-20 6YA8 1 JRNL REVDAT 1 27-MAY-20 6YA8 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. 1.79 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.18RC4_3812 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.79 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 58.86 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 3 NUMBER OF REFLECTIONS : 42930 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.167 REMARK 3 R VALUE (WORKING SET) : 0.166 REMARK 3 FREE R VALUE : 0.197 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.140 REMARK 3 FREE R VALUE TEST SET COUNT : 2208 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 58.8600 - 4.5100 1.00 2853 145 0.1681 0.1894 REMARK 3 2 4.5100 - 3.5800 1.00 2664 126 0.1376 0.1632 REMARK 3 3 3.5800 - 3.1300 1.00 2632 144 0.1624 0.1924 REMARK 3 4 3.1300 - 2.8400 1.00 2572 159 0.1719 0.1989 REMARK 3 5 2.8400 - 2.6400 1.00 2551 157 0.1714 0.2101 REMARK 3 6 2.6400 - 2.4800 1.00 2573 122 0.1727 0.2209 REMARK 3 7 2.4800 - 2.3600 1.00 2549 133 0.1676 0.2150 REMARK 3 8 2.3600 - 2.2600 1.00 2580 121 0.1610 0.1693 REMARK 3 9 2.2600 - 2.1700 1.00 2539 128 0.1619 0.1901 REMARK 3 10 2.1700 - 2.0900 1.00 2544 145 0.1631 0.1985 REMARK 3 11 2.0900 - 2.0300 1.00 2501 158 0.1648 0.2124 REMARK 3 12 2.0300 - 1.9700 1.00 2474 149 0.1636 0.1763 REMARK 3 13 1.9700 - 1.9200 1.00 2524 146 0.1813 0.2215 REMARK 3 14 1.9200 - 1.8700 0.99 2506 145 0.1924 0.2451 REMARK 3 15 1.8700 - 1.8300 0.95 2429 114 0.2198 0.2542 REMARK 3 16 1.8300 - 1.7900 0.89 2231 116 0.2350 0.2888 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL 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) : 0.186 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 17.600 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 21.66 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.29 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 3693 REMARK 3 ANGLE : 0.934 5004 REMARK 3 CHIRALITY : 0.054 556 REMARK 3 PLANARITY : 0.005 638 REMARK 3 DIHEDRAL : 18.634 1408 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 38:348) REMARK 3 ORIGIN FOR THE GROUP (A): -16.6245 18.0084 0.5750 REMARK 3 T TENSOR REMARK 3 T11: 0.1351 T22: 0.1081 REMARK 3 T33: 0.1235 T12: 0.0083 REMARK 3 T13: -0.0047 T23: 0.0000 REMARK 3 L TENSOR REMARK 3 L11: 0.4690 L22: 0.4639 REMARK 3 L33: 1.1450 L12: 0.0668 REMARK 3 L13: 0.0630 L23: 0.2711 REMARK 3 S TENSOR REMARK 3 S11: -0.0029 S12: -0.0180 S13: 0.0352 REMARK 3 S21: 0.1195 S22: -0.0195 S23: -0.0325 REMARK 3 S31: -0.0152 S32: -0.0573 S33: -0.0062 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN A AND RESID 349:465) REMARK 3 ORIGIN FOR THE GROUP (A): -21.9134 3.1910 -22.9022 REMARK 3 T TENSOR REMARK 3 T11: 0.1344 T22: 0.1272 REMARK 3 T33: 0.1054 T12: 0.0099 REMARK 3 T13: 0.0041 T23: 0.0210 REMARK 3 L TENSOR REMARK 3 L11: 0.3000 L22: 0.5945 REMARK 3 L33: -0.0045 L12: 0.1581 REMARK 3 L13: 0.0085 L23: -0.0670 REMARK 3 S TENSOR REMARK 3 S11: -0.0196 S12: -0.0218 S13: -0.0177 REMARK 3 S21: -0.0325 S22: 0.0088 S23: -0.0545 REMARK 3 S31: 0.0183 S32: 0.0137 S33: 0.0003 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: (CHAIN A AND RESID 466:572) REMARK 3 ORIGIN FOR THE GROUP (A): -16.1717 22.5127 -26.1054 REMARK 3 T TENSOR REMARK 3 T11: 0.1621 T22: 0.1564 REMARK 3 T33: 0.1600 T12: 0.0066 REMARK 3 T13: 0.0117 T23: 0.0356 REMARK 3 L TENSOR REMARK 3 L11: 0.4029 L22: 0.3597 REMARK 3 L33: 0.2693 L12: 0.1578 REMARK 3 L13: 0.0287 L23: 0.1422 REMARK 3 S TENSOR REMARK 3 S11: 0.0167 S12: 0.2736 S13: 0.0898 REMARK 3 S21: -0.2432 S22: 0.0140 S23: -0.0993 REMARK 3 S31: -0.1484 S32: 0.0252 S33: 0.0597 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: (CHAIN B AND RESID 207:238) REMARK 3 ORIGIN FOR THE GROUP (A): -25.5755 -11.5714 -23.4996 REMARK 3 T TENSOR REMARK 3 T11: 0.1671 T22: 0.1461 REMARK 3 T33: 0.2257 T12: 0.0088 REMARK 3 T13: -0.0130 T23: 0.0478 REMARK 3 L TENSOR REMARK 3 L11: 0.3094 L22: 0.4406 REMARK 3 L33: 0.6619 L12: 0.1353 REMARK 3 L13: -0.1369 L23: 0.2401 REMARK 3 S TENSOR REMARK 3 S11: -0.2120 S12: 0.0670 S13: 0.0905 REMARK 3 S21: -0.0638 S22: 0.0123 S23: 0.0363 REMARK 3 S31: 0.1211 S32: 0.0799 S33: -0.2111 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: (CHAIN B AND RESID 239:301) REMARK 3 ORIGIN FOR THE GROUP (A): -30.2464 6.3977 -12.2724 REMARK 3 T TENSOR REMARK 3 T11: 0.1852 T22: 0.1588 REMARK 3 T33: 0.2328 T12: -0.0003 REMARK 3 T13: -0.0094 T23: 0.0224 REMARK 3 L TENSOR REMARK 3 L11: 0.0291 L22: 0.1792 REMARK 3 L33: 0.1325 L12: -0.0778 REMARK 3 L13: 0.0235 L23: 0.0713 REMARK 3 S TENSOR REMARK 3 S11: 0.0716 S12: -0.0037 S13: -0.1964 REMARK 3 S21: -0.0061 S22: 0.0457 S23: 0.1450 REMARK 3 S31: 0.1386 S32: -0.0903 S33: 0.0031 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: (CHAIN B AND RESID 302:346) REMARK 3 ORIGIN FOR THE GROUP (A): -14.6183 7.8681 16.1413 REMARK 3 T TENSOR REMARK 3 T11: 0.2514 T22: 0.1661 REMARK 3 T33: 0.2467 T12: 0.0131 REMARK 3 T13: -0.0031 T23: 0.0365 REMARK 3 L TENSOR REMARK 3 L11: 0.2461 L22: 0.1964 REMARK 3 L33: 0.1408 L12: -0.1637 REMARK 3 L13: -0.2138 L23: 0.0581 REMARK 3 S TENSOR REMARK 3 S11: 0.0258 S12: -0.1574 S13: -0.1037 REMARK 3 S21: 0.2285 S22: -0.0790 S23: 0.0646 REMARK 3 S31: 0.0965 S32: 0.0465 S33: -0.0115 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 6YA8 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_1292105685. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-DEC-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.57 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I04 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97957 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 42930 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.790 REMARK 200 RESOLUTION RANGE LOW (A) : 58.860 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : 11.50 REMARK 200 R MERGE (I) : 0.06980 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 23.6600 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.79 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.85 REMARK 200 COMPLETENESS FOR SHELL (%) : 91.2 REMARK 200 DATA REDUNDANCY IN SHELL : 11.50 REMARK 200 R MERGE FOR SHELL (I) : NULL 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: 4F99 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.20 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.17 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M MMT PH 6.57, 21% PEG 1500, 15% REMARK 280 V/V ACETONITRILE, 20MM MGCL2, VAPOR DIFFUSION, HANGING DROP, REMARK 280 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 117.72000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 30.57500 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 30.57500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 58.86000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 30.57500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 30.57500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 176.58000 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 30.57500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 30.57500 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 58.86000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 30.57500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 30.57500 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 176.58000 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 117.72000 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: 8290 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 21460 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -69.0 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 GLN A 333 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 ALA A 532 REMARK 465 GLY A 533 REMARK 465 SER A 573 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 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 F2 BEF A 603 O HOH A 901 1.87 REMARK 500 F2 BEF A 603 O HOH A 883 1.99 REMARK 500 O HOH A 860 O HOH A 901 2.12 REMARK 500 O HOH A 821 O HOH A 892 2.16 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 -120.60 54.86 REMARK 500 ARG A 176 -4.40 72.35 REMARK 500 ASP A 177 41.79 -141.30 REMARK 500 ASP A 196 83.66 76.34 REMARK 500 ASP A 205 40.11 -103.80 REMARK 500 TRP A 535 6.80 81.95 REMARK 500 LEU A 550 31.01 -93.56 REMARK 500 ASP A 571 -6.49 86.32 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 A 602 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN A 182 OD1 REMARK 620 2 ASP A 196 OD2 92.5 REMARK 620 3 ADP A 601 O1B 179.3 86.8 REMARK 620 4 ADP A 601 O1A 89.5 93.6 90.3 REMARK 620 5 HOH A 827 O 88.3 176.8 92.4 89.6 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 604 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 196 OD1 REMARK 620 2 ASP A 196 OD2 63.4 REMARK 620 3 ADP A 601 O3B 89.7 84.6 REMARK 620 4 HOH A 808 O 89.0 89.6 174.0 REMARK 620 5 HOH A 870 O 95.1 158.0 91.0 95.0 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 605 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 351 SG REMARK 620 2 CYS A 353 SG 110.1 REMARK 620 3 CYS A 360 SG 112.7 107.3 REMARK 620 4 CYS A 363 SG 104.9 109.2 112.7 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 BEF A 603 BE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ADP A 601 O1B REMARK 620 2 BEF A 603 F1 125.3 REMARK 620 3 BEF A 603 F2 90.1 96.7 REMARK 620 4 BEF A 603 F3 107.1 125.8 96.1 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 120.3 REMARK 620 3 HIS B 309 NE2 102.2 108.7 REMARK 620 4 HIS B 315 ND1 106.5 115.3 101.4 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 ADP A 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 602 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue BEF A 603 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 604 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 605 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN B 401 DBREF 6YA8 A 37 345 UNP O00311 CDC7_HUMAN 37 227 DBREF 6YA8 A 346 467 UNP O00311 CDC7_HUMAN 346 467 DBREF 6YA8 A 534 574 UNP O00311 CDC7_HUMAN 534 574 DBREF 6YA8 B 210 350 UNP Q9UBU7 DBF4A_HUMAN 210 350 SEQADV 6YA8 MET A 36 UNP O00311 INITIATING METHIONINE SEQADV 6YA8 ALA A 468 UNP O00311 LINKER SEQADV 6YA8 GLY A 469 UNP O00311 LINKER SEQADV 6YA8 ALA A 532 UNP O00311 LINKER SEQADV 6YA8 GLY A 533 UNP O00311 LINKER SEQADV 6YA8 GLY B 207 UNP Q9UBU7 EXPRESSION TAG SEQADV 6YA8 PRO B 208 UNP Q9UBU7 EXPRESSION TAG SEQADV 6YA8 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 6YA8 SEP B 226 SER MODIFIED RESIDUE HET SEP B 226 10 HET ADP A 601 27 HET MG A 602 1 HET BEF A 603 4 HET MG A 604 1 HET ZN A 605 1 HET ZN B 401 1 HETNAM SEP PHOSPHOSERINE HETNAM ADP ADENOSINE-5'-DIPHOSPHATE HETNAM MG MAGNESIUM ION HETNAM BEF BERYLLIUM TRIFLUORIDE ION HETNAM ZN ZINC ION HETSYN SEP PHOSPHONOSERINE FORMUL 2 SEP C3 H8 N O6 P FORMUL 3 ADP C10 H15 N5 O10 P2 FORMUL 4 MG 2(MG 2+) FORMUL 5 BEF BE F3 1- FORMUL 7 ZN 2(ZN 2+) FORMUL 9 HOH *302(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 149 1 9 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 THR A 376 ARG A 380 5 5 HELIX 10 AB1 ALA A 381 THR A 386 1 6 HELIX 11 AB2 THR A 393 GLY A 410 1 18 HELIX 12 AB3 ASP A 419 GLY A 432 1 14 HELIX 13 AB4 GLY A 432 PHE A 443 1 12 HELIX 14 AB5 ASP A 457 GLY A 467 1 11 HELIX 15 AB6 PRO A 539 LEU A 550 1 12 HELIX 16 AB7 THR A 559 LEU A 565 1 7 HELIX 17 AB8 HIS A 566 LYS A 570 5 5 HELIX 18 AB9 ASP B 305 LEU B 311 1 7 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 HIS A 91 N SER A 71 SHEET 4 AA1 5 HIS A 129 PRO A 135 -1 O ILE A 132 N LYS A 90 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 GLN B 301 N CYS B 296 LINK C MET B 225 N SEP B 226 1555 1555 1.33 LINK C SEP B 226 N GLN B 227 1555 1555 1.33 LINK OD1 ASN A 182 MG MG A 602 1555 1555 2.11 LINK OD2 ASP A 196 MG MG A 602 1555 1555 2.10 LINK OD1 ASP A 196 MG MG A 604 1555 1555 2.09 LINK OD2 ASP A 196 MG MG A 604 1555 1555 2.12 LINK SG CYS A 351 ZN ZN A 605 1555 1555 2.29 LINK SG CYS A 353 ZN ZN A 605 1555 1555 2.35 LINK SG CYS A 360 ZN ZN A 605 1555 1555 2.32 LINK SG CYS A 363 ZN ZN A 605 1555 1555 2.41 LINK O1B ADP A 601 MG MG A 602 1555 1555 2.06 LINK O1A ADP A 601 MG MG A 602 1555 1555 1.98 LINK O1B ADP A 601 BE BEF A 603 1555 1555 1.76 LINK O3B ADP A 601 MG MG A 604 1555 1555 2.12 LINK MG MG A 602 O HOH A 827 1555 1555 2.09 LINK MG MG A 604 O HOH A 808 1555 1555 2.06 LINK MG MG A 604 O HOH A 870 1555 1555 2.13 LINK SG CYS B 296 ZN ZN B 401 1555 1555 2.24 LINK SG CYS B 299 ZN ZN B 401 1555 1555 2.38 LINK NE2 HIS B 309 ZN ZN B 401 1555 1555 2.01 LINK ND1 HIS B 315 ZN ZN B 401 1555 1555 2.05 CISPEP 1 TYR A 412 PRO A 413 0 -5.35 CISPEP 2 LYS B 217 PRO B 218 0 1.90 CISPEP 3 LYS B 248 PRO B 249 0 6.98 SITE 1 AC1 23 SER A 70 VAL A 72 ALA A 88 LYS A 90 SITE 2 AC1 23 MET A 118 MET A 134 PRO A 135 TYR A 136 SITE 3 AC1 23 LEU A 137 HIS A 139 SER A 181 ASN A 182 SITE 4 AC1 23 LEU A 184 ASP A 196 MG A 602 BEF A 603 SITE 5 AC1 23 MG A 604 HOH A 794 HOH A 796 HOH A 799 SITE 6 AC1 23 HOH A 807 HOH A 827 HOH A 870 SITE 1 AC2 5 ASN A 182 ASP A 196 ADP A 601 BEF A 603 SITE 2 AC2 5 HOH A 827 SITE 1 AC3 13 ASP A 177 LYS A 179 ASN A 182 ASP A 196 SITE 2 AC3 13 ADP A 601 MG A 602 MG A 604 HOH A 749 SITE 3 AC3 13 HOH A 808 HOH A 827 HOH A 883 HOH A 901 SITE 4 AC3 13 HOH A 930 SITE 1 AC4 5 ASP A 196 ADP A 601 BEF A 603 HOH A 808 SITE 2 AC4 5 HOH A 870 SITE 1 AC5 4 CYS A 351 CYS A 353 CYS A 360 CYS A 363 SITE 1 AC6 4 CYS B 296 CYS B 299 HIS B 309 HIS B 315 CRYST1 61.150 61.150 235.440 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 0.016353 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016353 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004247 0.00000