HEADER CELL CYCLE 11-MAR-20 6YA7 TITLE CDC7-DBF4 BOUND TO AN MCM2-S40 DERIVED BIVALENT SUBSTRATE 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; COMPND 15 MOL_ID: 3; COMPND 16 MOLECULE: DNA REPLICATION LICENSING FACTOR MCM2; COMPND 17 CHAIN: C; COMPND 18 SYNONYM: MINICHROMOSOME MAINTENANCE PROTEIN 2 HOMOLOG,NUCLEAR PROTEIN COMPND 19 BM28; COMPND 20 EC: 3.6.4.12; COMPND 21 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: HOMO SAPIENS; SOURCE 7 EXPRESSION_SYSTEM_COMMON: HUMAN; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 9 MOL_ID: 2; SOURCE 10 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 11 ORGANISM_COMMON: HUMAN; SOURCE 12 ORGANISM_TAXID: 9606; SOURCE 13 GENE: DBF4, ASK, DBF4A, ZDBF1; SOURCE 14 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 15 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 16 MOL_ID: 3; SOURCE 17 SYNTHETIC: YES; SOURCE 18 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 19 ORGANISM_COMMON: HUMAN; SOURCE 20 ORGANISM_TAXID: 9606 KEYWDS KINASE, CDC7, DBF4, CELL CYCLE, BIVALENT SUBSTRATE, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR S.D.DICK,P.CHEREPANOV REVDAT 4 24-JAN-24 6YA7 1 LINK REVDAT 3 19-AUG-20 6YA7 1 JRNL LINK REVDAT 2 01-JUL-20 6YA7 1 JRNL REVDAT 1 27-MAY-20 6YA7 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. 1.67 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.67 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 60.20 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 54918 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.158 REMARK 3 R VALUE (WORKING SET) : 0.156 REMARK 3 FREE R VALUE : 0.185 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.990 REMARK 3 FREE R VALUE TEST SET COUNT : 2739 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 60.2000 - 4.5300 1.00 2909 144 0.1671 0.2134 REMARK 3 2 4.5300 - 3.6000 1.00 2731 135 0.1334 0.1612 REMARK 3 3 3.6000 - 3.1400 1.00 2650 144 0.1473 0.1582 REMARK 3 4 3.1400 - 2.8600 1.00 2621 161 0.1585 0.1957 REMARK 3 5 2.8600 - 2.6500 1.00 2621 156 0.1616 0.1875 REMARK 3 6 2.6500 - 2.4900 1.00 2604 126 0.1595 0.1582 REMARK 3 7 2.4900 - 2.3700 1.00 2623 141 0.1566 0.1771 REMARK 3 8 2.3700 - 2.2700 1.00 2607 123 0.1514 0.1745 REMARK 3 9 2.2700 - 2.1800 1.00 2601 132 0.1514 0.1878 REMARK 3 10 2.1800 - 2.1000 1.00 2563 152 0.1456 0.1685 REMARK 3 11 2.1000 - 2.0400 1.00 2573 143 0.1511 0.1820 REMARK 3 12 2.0400 - 1.9800 1.00 2554 155 0.1515 0.1766 REMARK 3 13 1.9800 - 1.9300 1.00 2535 159 0.1560 0.2007 REMARK 3 14 1.9300 - 1.8800 1.00 2549 139 0.1569 0.1963 REMARK 3 15 1.8800 - 1.8400 1.00 2574 123 0.1642 0.2026 REMARK 3 16 1.8400 - 1.8000 1.00 2591 129 0.1651 0.2184 REMARK 3 17 1.8000 - 1.7600 1.00 2544 126 0.1708 0.1866 REMARK 3 18 1.7600 - 1.7300 1.00 2559 120 0.1869 0.2431 REMARK 3 19 1.7300 - 1.7000 1.00 2585 112 0.1960 0.2652 REMARK 3 20 1.7000 - 1.6700 1.00 2585 119 0.2212 0.2300 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) : 0.144 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 17.167 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 17.27 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.91 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 : 0.010 3838 REMARK 3 ANGLE : 1.151 5191 REMARK 3 CHIRALITY : 0.067 576 REMARK 3 PLANARITY : 0.007 664 REMARK 3 DIHEDRAL : 20.184 1461 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 39:349) REMARK 3 ORIGIN FOR THE GROUP (A): -16.7662 11.2239 -0.2344 REMARK 3 T TENSOR REMARK 3 T11: 0.1062 T22: 0.0564 REMARK 3 T33: 0.0861 T12: -0.0036 REMARK 3 T13: 0.0096 T23: -0.0041 REMARK 3 L TENSOR REMARK 3 L11: 0.4677 L22: 0.1538 REMARK 3 L33: 0.9617 L12: -0.0063 REMARK 3 L13: 0.0685 L23: -0.0948 REMARK 3 S TENSOR REMARK 3 S11: -0.0016 S12: -0.0041 S13: 0.0570 REMARK 3 S21: 0.0408 S22: -0.0454 S23: -0.0034 REMARK 3 S31: 0.0004 S32: -0.0203 S33: -0.0740 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN A AND RESID 350:467) REMARK 3 ORIGIN FOR THE GROUP (A): -12.7613 26.4894 -22.4443 REMARK 3 T TENSOR REMARK 3 T11: 0.1053 T22: 0.0777 REMARK 3 T33: 0.0980 T12: 0.0004 REMARK 3 T13: 0.0004 T23: -0.0065 REMARK 3 L TENSOR REMARK 3 L11: 0.0985 L22: 0.6164 REMARK 3 L33: 0.0598 L12: 0.1099 REMARK 3 L13: 0.0284 L23: -0.0680 REMARK 3 S TENSOR REMARK 3 S11: -0.0315 S12: -0.0229 S13: 0.0441 REMARK 3 S21: -0.0120 S22: 0.0301 S23: 0.0163 REMARK 3 S31: -0.0212 S32: 0.0025 S33: 0.0001 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: (CHAIN A AND RESID 468:573) REMARK 3 ORIGIN FOR THE GROUP (A): -19.6454 7.5195 -26.1358 REMARK 3 T TENSOR REMARK 3 T11: 0.1343 T22: 0.0910 REMARK 3 T33: 0.1090 T12: -0.0048 REMARK 3 T13: -0.0026 T23: -0.0102 REMARK 3 L TENSOR REMARK 3 L11: 0.1869 L22: 0.2569 REMARK 3 L33: 0.2628 L12: -0.0426 REMARK 3 L13: 0.1862 L23: -0.2140 REMARK 3 S TENSOR REMARK 3 S11: 0.0235 S12: 0.0917 S13: -0.0699 REMARK 3 S21: -0.2177 S22: -0.0377 S23: 0.0663 REMARK 3 S31: 0.1188 S32: 0.0013 S33: -0.0128 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: (CHAIN B AND RESID 207:238) REMARK 3 ORIGIN FOR THE GROUP (A): -9.0119 42.0290 -22.2939 REMARK 3 T TENSOR REMARK 3 T11: 0.1469 T22: 0.1246 REMARK 3 T33: 0.1778 T12: 0.0128 REMARK 3 T13: 0.0100 T23: -0.0265 REMARK 3 L TENSOR REMARK 3 L11: 0.0785 L22: 0.1721 REMARK 3 L33: 0.0778 L12: 0.0849 REMARK 3 L13: -0.0298 L23: -0.0057 REMARK 3 S TENSOR REMARK 3 S11: -0.1339 S12: -0.0194 S13: -0.0728 REMARK 3 S21: -0.1473 S22: 0.0616 S23: 0.0151 REMARK 3 S31: -0.0767 S32: 0.0565 S33: -0.0048 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: (CHAIN B AND RESID 239:256) REMARK 3 ORIGIN FOR THE GROUP (A): 2.2929 17.5743 -24.1033 REMARK 3 T TENSOR REMARK 3 T11: 0.1305 T22: 0.1390 REMARK 3 T33: 0.1737 T12: 0.0081 REMARK 3 T13: 0.0288 T23: -0.0126 REMARK 3 L TENSOR REMARK 3 L11: 0.1036 L22: 0.0212 REMARK 3 L33: 0.0323 L12: -0.0091 REMARK 3 L13: -0.0279 L23: -0.0268 REMARK 3 S TENSOR REMARK 3 S11: 0.0153 S12: -0.1174 S13: 0.1287 REMARK 3 S21: 0.0570 S22: -0.0375 S23: -0.1194 REMARK 3 S31: -0.0397 S32: 0.1898 S33: -0.0079 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: (CHAIN B AND RESID 291:348) REMARK 3 ORIGIN FOR THE GROUP (A): -15.2237 19.8699 15.7434 REMARK 3 T TENSOR REMARK 3 T11: 0.1997 T22: 0.1582 REMARK 3 T33: 0.1614 T12: -0.0096 REMARK 3 T13: -0.0108 T23: -0.0241 REMARK 3 L TENSOR REMARK 3 L11: 0.2559 L22: 0.3654 REMARK 3 L33: 0.1903 L12: -0.3688 REMARK 3 L13: 0.1242 L23: -0.1468 REMARK 3 S TENSOR REMARK 3 S11: 0.0095 S12: -0.0336 S13: 0.0338 REMARK 3 S21: 0.3994 S22: -0.0139 S23: -0.1068 REMARK 3 S31: -0.1262 S32: 0.0278 S33: -0.0002 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 6YA7 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_1292105860. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-APR-14 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 : DIAMOND REMARK 200 BEAMLINE : I03 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97625 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 : 54941 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.670 REMARK 200 RESOLUTION RANGE LOW (A) : 60.200 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 12.50 REMARK 200 R MERGE (I) : 0.09800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 19.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.67 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.71 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.72400 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 (%): 41.91 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.12 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 117.39500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 31.14000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 31.14000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 58.69750 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 31.14000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 31.14000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 176.09250 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 31.14000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 31.14000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 58.69750 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 31.14000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 31.14000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 176.09250 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 117.39500 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 9740 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 22170 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -142.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 LEU A 37 REMARK 465 ALA A 38 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 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 349 REMARK 465 ARG B 350 REMARK 465 ARG C 33 REMARK 465 ARG C 34 REMARK 465 THR C 35 REMARK 465 ASP C 36 REMARK 465 ALA C 37 REMARK 465 PRO C 47 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 O ASP B 254 O HOH B 501 2.02 REMARK 500 O1B ADP A 604 O HOH A 701 2.11 REMARK 500 O HOH A 820 O HOH A 879 2.18 REMARK 500 O HOH A 881 O HOH B 544 2.18 REMARK 500 O3B ADP A 604 O HOH A 702 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 CYS A 388 CB CYS A 388 SG -0.120 REMARK 500 REMARK 500 REMARK: NULL 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 ARG A 155 NE - CZ - NH1 ANGL. DEV. = -3.3 DEGREES REMARK 500 ARG A 155 NE - CZ - NH2 ANGL. DEV. = 3.3 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 ASN A 127 -121.77 56.44 REMARK 500 ARG A 176 -14.54 77.40 REMARK 500 ASP A 196 84.03 75.11 REMARK 500 ARG A 373 13.75 -150.03 REMARK 500 LEU A 550 31.05 -93.41 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 ASN A 182 OD1 REMARK 620 2 ASP A 196 OD2 114.0 REMARK 620 3 ADP A 604 O1A 95.4 108.5 REMARK 620 4 HOH A 722 O 81.5 164.1 72.1 REMARK 620 5 7O5 C 40 S1G 112.3 95.7 131.7 73.8 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 601 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 351 SG REMARK 620 2 CYS A 353 SG 110.2 REMARK 620 3 CYS A 360 SG 110.6 108.6 REMARK 620 4 CYS A 363 SG 105.3 108.7 113.3 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 117.6 REMARK 620 3 HIS B 309 NE2 103.2 108.0 REMARK 620 4 HIS B 315 ND1 110.0 112.7 104.1 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 ZN 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 ZN A 603 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ADP 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 Ligand 7O5 C 40 bound to THR C REMARK 800 39 DBREF 6YA7 A 37 345 UNP O00311 CDC7_HUMAN 37 227 DBREF 6YA7 A 346 466 UNP O00311 CDC7_HUMAN 346 466 DBREF 6YA7 A 534 574 UNP O00311 CDC7_HUMAN 534 574 DBREF 6YA7 B 210 350 UNP Q9UBU7 DBF4A_HUMAN 210 350 DBREF 6YA7 C 33 47 UNP P49736 MCM2_HUMAN 33 47 SEQADV 6YA7 GLY A 467 UNP O00311 LINKER SEQADV 6YA7 ALA A 468 UNP O00311 LINKER SEQADV 6YA7 GLY A 469 UNP O00311 LINKER SEQADV 6YA7 ALA A 470 UNP O00311 LINKER SEQADV 6YA7 GLY A 471 UNP O00311 LINKER SEQADV 6YA7 GLY B 207 UNP Q9UBU7 EXPRESSION TAG SEQADV 6YA7 PRO B 208 UNP Q9UBU7 EXPRESSION TAG SEQADV 6YA7 GLY B 209 UNP Q9UBU7 EXPRESSION TAG SEQADV 6YA7 7O5 C 40 UNP P49736 SER 40 CONFLICT SEQRES 1 A 358 LEU ALA GLY VAL LYS LYS ASP ILE GLU LYS LEU TYR GLU SEQRES 2 A 358 ALA VAL PRO GLN LEU SER ASN VAL PHE LYS ILE GLU ASP SEQRES 3 A 358 LYS ILE GLY GLU GLY THR PHE SER SER VAL TYR LEU ALA SEQRES 4 A 358 THR ALA GLN LEU GLN VAL GLY PRO GLU GLU LYS ILE ALA SEQRES 5 A 358 LEU LYS HIS LEU ILE PRO THR SER HIS PRO ILE ARG ILE SEQRES 6 A 358 ALA ALA GLU LEU GLN CYS LEU THR VAL ALA GLY GLY GLN SEQRES 7 A 358 ASP ASN VAL MET GLY VAL LYS TYR CYS PHE ARG LYS ASN SEQRES 8 A 358 ASP HIS VAL VAL ILE ALA MET PRO TYR LEU GLU HIS GLU SEQRES 9 A 358 SER PHE LEU ASP ILE LEU ASN SER LEU SER PHE GLN GLU SEQRES 10 A 358 VAL ARG GLU TYR MET LEU ASN LEU PHE LYS ALA LEU LYS SEQRES 11 A 358 ARG ILE HIS GLN PHE GLY ILE VAL HIS ARG ASP VAL LYS SEQRES 12 A 358 PRO SER ASN PHE LEU TYR ASN ARG ARG LEU LYS LYS TYR SEQRES 13 A 358 ALA LEU VAL ASP PHE GLY LEU ALA GLN GLY THR HIS ASP SEQRES 14 A 358 THR LYS ILE GLU LEU LEU LYS PHE VAL GLN SER GLU ALA SEQRES 15 A 358 GLN GLN GLU ARG CYS SER GLN ASN LYS PRO ALA SER LEU SEQRES 16 A 358 THR CYS ASP CYS TYR ALA THR ASP LYS VAL CYS SER ILE SEQRES 17 A 358 CYS LEU SER ARG ARG GLN GLN VAL ALA PRO ARG ALA GLY SEQRES 18 A 358 THR PRO GLY PHE ARG ALA PRO GLU VAL LEU THR LYS CYS SEQRES 19 A 358 PRO ASN GLN THR THR ALA ILE ASP MET TRP SER ALA GLY SEQRES 20 A 358 VAL ILE PHE LEU SER LEU LEU SER GLY ARG TYR PRO PHE SEQRES 21 A 358 TYR LYS ALA SER ASP ASP LEU THR ALA LEU ALA GLN ILE SEQRES 22 A 358 MET THR ILE ARG GLY SER ARG GLU THR ILE GLN ALA ALA SEQRES 23 A 358 LYS THR PHE GLY LYS SER ILE LEU CYS SER LYS GLU VAL SEQRES 24 A 358 PRO ALA GLN ASP LEU ARG LYS LEU CYS GLU ARG LEU ARG SEQRES 25 A 358 GLY ALA GLY ALA GLY GLY TRP ASN GLU VAL PRO ASP GLU SEQRES 26 A 358 ALA TYR ASP LEU LEU ASP LYS LEU LEU ASP LEU ASN PRO SEQRES 27 A 358 ALA SER ARG ILE THR ALA GLU GLU ALA LEU LEU HIS PRO SEQRES 28 A 358 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 SER 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 SEQRES 1 C 15 ARG ARG THR ASP ALA LEU THR 7O5 SEP PRO GLY ARG ASP SEQRES 2 C 15 LEU PRO MODRES 6YA7 SEP C 41 SER MODIFIED RESIDUE HET 7O5 C 40 10 HET SEP C 41 10 HET ZN A 601 1 HET ZN A 602 1 HET ZN A 603 1 HET ADP A 604 27 HET ZN B 401 1 HETNAM 7O5 (2~{S})-2-AZANYL-3-(2-SULFANYLETHANOYLAMINO)PROPANOIC HETNAM 2 7O5 ACID HETNAM SEP PHOSPHOSERINE HETNAM ZN ZINC ION HETNAM ADP ADENOSINE-5'-DIPHOSPHATE HETSYN SEP PHOSPHONOSERINE FORMUL 3 7O5 C5 H10 N2 O3 S FORMUL 3 SEP C3 H8 N O6 P FORMUL 4 ZN 4(ZN 2+) FORMUL 7 ADP C10 H15 N5 O10 P2 FORMUL 9 HOH *366(H2 O) HELIX 1 AA1 GLY A 39 VAL A 51 1 13 HELIX 2 AA2 PRO A 52 ASN A 56 5 5 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 ALA A 470 VAL A 538 5 7 HELIX 15 AB6 PRO A 539 LEU A 550 1 12 HELIX 16 AB7 THR A 559 LEU A 564 1 6 HELIX 17 AB8 LEU A 565 LYS A 570 5 6 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 SER B 321 GLN B 323 5 3 HELIX 21 AC3 TYR B 324 SER B 332 1 9 SHEET 1 AA1 5 PHE A 58 GLU A 66 0 SHEET 2 AA1 5 SER A 70 ALA A 77 -1 O LEU A 74 N ASP A 62 SHEET 3 AA1 5 GLU A 85 LEU A 92 -1 O ILE A 87 N ALA A 75 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 THR C 39 N 7O5 C 40 1555 1555 1.33 LINK C 7O5 C 40 N SEP C 41 1555 1555 1.33 LINK C SEP C 41 N PRO C 42 1555 1555 1.35 LINK OD1 ASN A 182 ZN ZN A 602 1555 1555 2.05 LINK OD2 ASP A 196 ZN ZN A 602 1555 1555 1.97 LINK SG CYS A 351 ZN ZN A 601 1555 1555 2.36 LINK SG CYS A 353 ZN ZN A 601 1555 1555 2.29 LINK SG CYS A 360 ZN ZN A 601 1555 1555 2.33 LINK SG CYS A 363 ZN ZN A 601 1555 1555 2.40 LINK SG CYS A 449 ZN ZN A 603 1555 1555 2.24 LINK ZN ZN A 602 O1A ADP A 604 1555 1555 1.76 LINK ZN ZN A 602 O HOH A 722 1555 1555 2.46 LINK ZN ZN A 602 S1G 7O5 C 40 1555 1555 2.33 LINK SG CYS B 296 ZN ZN B 401 1555 1555 2.29 LINK SG CYS B 299 ZN ZN B 401 1555 1555 2.30 LINK NE2 HIS B 309 ZN ZN B 401 1555 1555 2.06 LINK ND1 HIS B 315 ZN ZN B 401 1555 1555 2.10 CISPEP 1 TYR A 412 PRO A 413 0 -3.45 CISPEP 2 LYS B 217 PRO B 218 0 3.78 CISPEP 3 LYS B 248 PRO B 249 0 11.63 SITE 1 AC1 4 CYS A 351 CYS A 353 CYS A 360 CYS A 363 SITE 1 AC2 5 ASN A 182 ASP A 196 ADP A 604 HOH A 722 SITE 2 AC2 5 7O5 C 40 SITE 1 AC3 3 CYS A 449 LYS A 451 MET B 239 SITE 1 AC4 23 GLY A 67 SER A 70 VAL A 72 ALA A 88 SITE 2 AC4 23 LYS A 90 MET A 118 PRO A 135 TYR A 136 SITE 3 AC4 23 LEU A 137 HIS A 139 SER A 181 ASN A 182 SITE 4 AC4 23 LEU A 184 ASP A 196 ZN A 602 HOH A 701 SITE 5 AC4 23 HOH A 702 HOH A 717 HOH A 722 HOH A 730 SITE 6 AC4 23 HOH A 757 HOH A 813 7O5 C 40 SITE 1 AC5 4 CYS B 296 CYS B 299 HIS B 309 HIS B 315 SITE 1 AC6 17 THR A 68 PHE A 69 ASP A 177 LYS A 179 SITE 2 AC6 17 ASN A 182 ASP A 196 LEU A 199 GLY A 375 SITE 3 AC6 17 THR A 376 ZN A 602 ADP A 604 HOH A 702 SITE 4 AC6 17 HOH A 722 THR C 39 SEP C 41 HOH C 108 SITE 5 AC6 17 HOH C 109 CRYST1 62.280 62.280 234.790 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 0.016057 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016057 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004259 0.00000