HEADER TRANSFERASE 18-MAY-12 4F99 TITLE HUMAN CDC7 KINASE IN COMPLEX WITH DBF4 AND NUCLEOTIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: CELL DIVISION CYCLE 7-RELATED PROTEIN KINASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: CDC7-RELATED KINASE, HSCDC7, HUCDC7; COMPND 5 EC: 2.7.11.1; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: PROTEIN DBF4 HOMOLOG A; COMPND 9 CHAIN: B; COMPND 10 SYNONYM: ACTIVATOR OF S PHASE KINASE, CHIFFON HOMOLOG A, DBF4-TYPE COMPND 11 ZINC FINGER-CONTAINING PROTEIN 1; COMPND 12 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 EXPRESSION_SYSTEM_STRAIN: ROSETTA-2(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PRSF-DUET; SOURCE 11 MOL_ID: 2; SOURCE 12 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 13 ORGANISM_COMMON: HUMAN; SOURCE 14 ORGANISM_TAXID: 9606; SOURCE 15 GENE: ASK, DBF4, DBF4A, ZDBF1; SOURCE 16 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 17 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 18 EXPRESSION_SYSTEM_STRAIN: ROSETTA-2(DE3); SOURCE 19 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 20 EXPRESSION_SYSTEM_PLASMID: PCDF-DUET KEYWDS SER/THR PROTEIN KINASE, TRANSFERASE, PHOSPHORYLATION, CELL CYCLE, KEYWDS 2 CELL DIVISION, MITOSIS, S PHASE, SERINE/THREONINE-PROTEIN KINASE, KEYWDS 3 DBF4-DEPENDENT KINASE, DDK, ATP-BINDING, NUCLEOTIDE-BINDING, ZINC- KEYWDS 4 BINDING, NUCLEUS EXPDTA X-RAY DIFFRACTION AUTHOR S.HUGHES,P.CHEREPANOV REVDAT 5 13-SEP-23 4F99 1 REMARK SEQADV LINK REVDAT 4 15-NOV-17 4F99 1 REMARK REVDAT 3 16-AUG-17 4F99 1 SOURCE REVDAT 2 12-DEC-12 4F99 1 JRNL REVDAT 1 31-OCT-12 4F99 0 JRNL AUTH S.HUGHES,F.ELUSTONDO,A.DI FONZO,F.G.LEROUX,A.C.WONG, JRNL AUTH 2 A.P.SNIJDERS,S.J.MATTHEWS,P.CHEREPANOV JRNL TITL CRYSTAL STRUCTURE OF HUMAN CDC7 KINASE IN COMPLEX WITH ITS JRNL TITL 2 ACTIVATOR DBF4. JRNL REF NAT.STRUCT.MOL.BIOL. V. 19 1101 2012 JRNL REFN ISSN 1545-9993 JRNL PMID 23064647 JRNL DOI 10.1038/NSMB.2404 REMARK 2 REMARK 2 RESOLUTION. 2.33 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.6.0117 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.33 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 59.52 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 20540 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.194 REMARK 3 R VALUE (WORKING SET) : 0.192 REMARK 3 FREE R VALUE : 0.241 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1051 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.33 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.39 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1218 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.2380 REMARK 3 BIN FREE R VALUE SET COUNT : 55 REMARK 3 BIN FREE R VALUE : 0.2840 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3237 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 29 REMARK 3 SOLVENT ATOMS : 48 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 42.61 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.44000 REMARK 3 B22 (A**2) : 0.44000 REMARK 3 B33 (A**2) : -0.89000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.331 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.236 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.159 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 6.570 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.949 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.919 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3338 ; 0.009 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4510 ; 1.300 ; 1.982 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 397 ; 5.759 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 156 ;34.222 ;24.487 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 596 ;16.343 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 17 ;20.864 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 501 ; 0.084 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2485 ; 0.005 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN USED IF PRESENT IN REMARK 3 THE INPUT REMARK 4 REMARK 4 4F99 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 24-MAY-12. REMARK 100 THE DEPOSITION ID IS D_1000072615. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-SEP-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 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) : 0.9763 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20628 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.330 REMARK 200 RESOLUTION RANGE LOW (A) : 79.140 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 12.10 REMARK 200 R MERGE (I) : 0.10800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.33 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.39 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 10.90 REMARK 200 R MERGE FOR SHELL (I) : 0.68400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: BALBES, MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 3PVG (AUTOMATIC MOLECULAR REPLACEMENT REMARK 200 WITH BALBES). REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 36.89 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.95 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25% PEG-1500, 15% GLYCEROL, PH 7.5, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K 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 118.70500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 30.74000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 30.74000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 59.35250 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 30.74000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 30.74000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 178.05750 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 30.74000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 30.74000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 59.35250 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 30.74000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 30.74000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 178.05750 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 118.70500 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: 6630 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18540 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -63.0 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 ALA A 38 REMARK 465 GLY A 39 REMARK 465 VAL A 40 REMARK 465 GLU A 353 REMARK 465 ARG A 354 REMARK 465 CYS A 355 REMARK 465 SER A 356 REMARK 465 GLN A 357 REMARK 465 ASN A 358 REMARK 465 LYS A 359 REMARK 465 CYS A 360 REMARK 465 SER A 361 REMARK 465 ILE A 362 REMARK 465 CYS A 363 REMARK 465 LEU A 364 REMARK 465 SER A 365 REMARK 465 ARG A 366 REMARK 465 ARG A 367 REMARK 465 GLN A 368 REMARK 465 GLN A 369 REMARK 465 VAL A 370 REMARK 465 ALA A 371 REMARK 465 PRO A 372 REMARK 465 GLY A 513 REMARK 465 MET A 514 REMARK 465 ASP A 515 REMARK 465 SER A 516 REMARK 465 SER A 517 REMARK 465 THR A 518 REMARK 465 PRO A 519 REMARK 465 LYS A 520 REMARK 465 LEU A 521 REMARK 465 THR A 522 REMARK 465 SER A 523 REMARK 465 ASP A 524 REMARK 465 ILE A 525 REMARK 465 GLN A 526 REMARK 465 GLY A 527 REMARK 465 HIS A 528 REMARK 465 ALA A 529 REMARK 465 THR A 530 REMARK 465 ASN A 531 REMARK 465 LEU A 532 REMARK 465 GLU A 533 REMARK 465 GLY A 534 REMARK 465 SER A 573 REMARK 465 LEU A 574 REMARK 465 GLY B 207 REMARK 465 PRO B 208 REMARK 465 GLY B 209 REMARK 465 THR B 210 REMARK 465 ARG B 211 REMARK 465 THR B 212 REMARK 465 GLY B 213 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 293 REMARK 465 LYS B 343 REMARK 465 ASP B 344 REMARK 465 THR B 345 REMARK 465 PRO B 346 REMARK 465 LYS B 347 REMARK 465 LYS B 348 REMARK 465 LYS B 349 REMARK 465 ARG B 350 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 ARG A 373 CG CD NE CZ NH1 NH2 REMARK 470 ARG B 316 CG CD NE CZ NH1 NH2 REMARK 470 GLU B 342 CG CD OE1 OE2 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 557 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 ARG A 557 NE - CZ - NH2 ANGL. DEV. = -3.4 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 -119.40 61.78 REMARK 500 ARG A 176 -3.19 74.42 REMARK 500 ASP A 177 44.30 -142.75 REMARK 500 ASP A 196 86.33 71.88 REMARK 500 GLN B 227 6.10 59.52 REMARK 500 ASN B 322 2.34 -58.03 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 87.4 REMARK 620 3 ADP A 601 O2A 90.6 89.0 REMARK 620 4 ADP A 601 O1B 175.5 89.4 86.2 REMARK 620 5 HOH A 701 O 85.3 170.1 97.7 98.2 REMARK 620 6 HOH A 702 O 98.1 86.0 169.8 84.8 88.4 REMARK 620 N 1 2 3 4 5 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 115.3 REMARK 620 3 HIS B 309 NE2 90.2 126.1 REMARK 620 4 HIS B 315 ND1 113.0 110.0 100.7 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 ZN B 401 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4F99 RELATED DB: PDB REMARK 900 RELATED ID: 4F9A RELATED DB: PDB REMARK 900 RELATED ID: 4F9B RELATED DB: PDB REMARK 900 RELATED ID: 4F9C RELATED DB: PDB REMARK 900 RELATED ID: 3PVG RELATED DB: PDB DBREF 4F99 A 37 359 UNP O00311 CDC7_HUMAN 37 227 DBREF 4F99 A 360 529 UNP O00311 CDC7_HUMAN 360 483 DBREF 4F99 A 530 574 UNP O00311 CDC7_HUMAN 530 574 DBREF 4F99 B 210 350 UNP Q9UBU7 DBF4A_HUMAN 210 350 SEQADV 4F99 MET A 36 UNP O00311 EXPRESSION TAG SEQADV 4F99 GLY B 207 UNP Q9UBU7 EXPRESSION TAG SEQADV 4F99 PRO B 208 UNP Q9UBU7 EXPRESSION TAG SEQADV 4F99 GLY B 209 UNP Q9UBU7 EXPRESSION TAG SEQRES 1 A 361 MET LEU ALA GLY VAL LYS LYS ASP ILE GLU LYS LEU TYR SEQRES 2 A 361 GLU ALA VAL PRO GLN LEU SER ASN VAL PHE LYS ILE GLU SEQRES 3 A 361 ASP LYS ILE GLY GLU GLY THR PHE SER SER VAL TYR LEU SEQRES 4 A 361 ALA THR ALA GLN LEU GLN VAL GLY PRO GLU GLU LYS ILE SEQRES 5 A 361 ALA LEU LYS HIS LEU ILE PRO THR SER HIS PRO ILE ARG SEQRES 6 A 361 ILE ALA ALA GLU LEU GLN CYS LEU THR VAL ALA GLY GLY SEQRES 7 A 361 GLN ASP ASN VAL MET GLY VAL LYS TYR CYS PHE ARG LYS SEQRES 8 A 361 ASN ASP HIS VAL VAL ILE ALA MET PRO TYR LEU GLU HIS SEQRES 9 A 361 GLU SER PHE LEU ASP ILE LEU ASN SER LEU SER PHE GLN SEQRES 10 A 361 GLU VAL ARG GLU TYR MET LEU ASN LEU PHE LYS ALA LEU SEQRES 11 A 361 LYS ARG ILE HIS GLN PHE GLY ILE VAL HIS ARG ASP VAL SEQRES 12 A 361 LYS PRO SER ASN PHE LEU TYR ASN ARG ARG LEU LYS LYS SEQRES 13 A 361 TYR ALA LEU VAL ASP PHE GLY LEU ALA GLN GLY THR HIS SEQRES 14 A 361 ASP THR LYS ILE GLU LEU LEU LYS PHE VAL GLN SER GLU SEQRES 15 A 361 ALA GLN GLN GLU ARG CYS SER GLN ASN LYS CYS SER ILE SEQRES 16 A 361 CYS LEU SER ARG ARG GLN GLN VAL ALA PRO ARG ALA GLY SEQRES 17 A 361 THR PRO GLY PHE ARG ALA PRO GLU VAL LEU THR LYS CYS SEQRES 18 A 361 PRO ASN GLN THR THR ALA ILE ASP MET TRP SER ALA GLY SEQRES 19 A 361 VAL ILE PHE LEU SER LEU LEU SER GLY ARG TYR PRO PHE SEQRES 20 A 361 TYR LYS ALA SER ASP ASP LEU THR ALA LEU ALA GLN ILE SEQRES 21 A 361 MET THR ILE ARG GLY SER ARG GLU THR ILE GLN ALA ALA SEQRES 22 A 361 LYS THR PHE GLY LYS SER ILE LEU CYS SER LYS GLU VAL SEQRES 23 A 361 PRO ALA GLN ASP LEU ARG LYS LEU CYS GLU ARG LEU ARG SEQRES 24 A 361 GLY MET ASP SER SER THR PRO LYS LEU THR SER ASP ILE SEQRES 25 A 361 GLN GLY HIS ALA THR ASN LEU GLU GLY TRP ASN GLU VAL SEQRES 26 A 361 PRO ASP GLU ALA TYR ASP LEU LEU ASP LYS LEU LEU ASP SEQRES 27 A 361 LEU ASN PRO ALA SER ARG ILE THR ALA GLU GLU ALA LEU SEQRES 28 A 361 LEU HIS 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 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 HET ADP A 601 27 HET MG A 602 1 HET ZN B 401 1 HETNAM ADP ADENOSINE-5'-DIPHOSPHATE HETNAM MG MAGNESIUM ION HETNAM ZN ZINC ION FORMUL 3 ADP C10 H15 N5 O10 P2 FORMUL 4 MG MG 2+ FORMUL 5 ZN ZN 2+ FORMUL 6 HOH *48(H2 O) HELIX 1 1 LYS A 41 VAL A 51 1 11 HELIX 2 2 GLN A 53 PHE A 58 1 6 HELIX 3 3 HIS A 97 ALA A 111 1 15 HELIX 4 4 SER A 141 ASN A 147 1 7 HELIX 5 5 SER A 150 PHE A 171 1 22 HELIX 6 6 LYS A 179 SER A 181 5 3 HELIX 7 7 ILE A 208 VAL A 214 5 7 HELIX 8 8 THR A 376 ARG A 380 5 5 HELIX 9 9 ALA A 381 THR A 386 1 6 HELIX 10 10 THR A 393 GLY A 410 1 18 HELIX 11 11 ASP A 419 GLY A 432 1 14 HELIX 12 12 GLY A 432 THR A 442 1 11 HELIX 13 13 ASP A 457 ARG A 466 1 10 HELIX 14 14 PRO A 539 LEU A 550 1 12 HELIX 15 15 THR A 559 LEU A 565 1 7 HELIX 16 16 HIS A 566 LYS A 570 5 5 HELIX 17 17 ASP B 305 LEU B 311 1 7 HELIX 18 18 SER B 312 GLN B 320 1 9 HELIX 19 19 SER B 321 GLN B 323 5 3 HELIX 20 20 TYR B 324 SER B 332 1 9 SHEET 1 A 5 LYS A 59 GLU A 66 0 SHEET 2 A 5 SER A 70 GLN A 78 -1 O THR A 76 N LYS A 59 SHEET 3 A 5 GLU A 84 LEU A 92 -1 O ILE A 87 N ALA A 75 SHEET 4 A 5 HIS A 129 PRO A 135 -1 O ILE A 132 N LYS A 90 SHEET 5 A 5 TYR A 122 LYS A 126 -1 N PHE A 124 O VAL A 131 SHEET 1 B 2 ILE A 173 VAL A 174 0 SHEET 2 B 2 GLN A 201 GLY A 202 -1 O GLN A 201 N VAL A 174 SHEET 1 C 2 PHE A 183 ASN A 186 0 SHEET 2 C 2 LYS A 191 LEU A 194 -1 O ALA A 193 N LEU A 184 SHEET 1 D 3 LYS A 445 CYS A 449 0 SHEET 2 D 3 PHE B 219 ASP B 224 -1 O GLU B 223 N SER A 446 SHEET 3 D 3 PHE B 232 GLN B 235 -1 O PHE B 232 N VAL B 222 SHEET 1 E 2 TYR B 295 CYS B 296 0 SHEET 2 E 2 GLN B 301 LYS B 302 -1 O GLN B 301 N CYS B 296 LINK OD1 ASN A 182 MG MG A 602 1555 1555 2.13 LINK OD2 ASP A 196 MG MG A 602 1555 1555 2.09 LINK O2A ADP A 601 MG MG A 602 1555 1555 1.94 LINK O1B ADP A 601 MG MG A 602 1555 1555 1.97 LINK MG MG A 602 O HOH A 701 1555 1555 2.02 LINK MG MG A 602 O HOH A 702 1555 1555 2.30 LINK SG CYS B 296 ZN ZN B 401 1555 1555 2.32 LINK SG CYS B 299 ZN ZN B 401 1555 1555 2.34 LINK NE2 HIS B 309 ZN ZN B 401 1555 1555 2.15 LINK ND1 HIS B 315 ZN ZN B 401 1555 1555 2.16 CISPEP 1 TYR A 412 PRO A 413 0 -3.79 CISPEP 2 LYS A 570 ASP A 571 0 -19.34 CISPEP 3 LYS B 217 PRO B 218 0 0.40 CISPEP 4 LYS B 248 PRO B 249 0 -3.51 SITE 1 AC1 17 ILE A 64 GLY A 67 SER A 70 VAL A 72 SITE 2 AC1 17 ALA A 88 LYS A 90 MET A 118 PRO A 135 SITE 3 AC1 17 TYR A 136 LEU A 137 HIS A 139 SER A 181 SITE 4 AC1 17 ASN A 182 ASP A 196 MG A 602 HOH A 701 SITE 5 AC1 17 HOH A 702 SITE 1 AC2 5 ASN A 182 ASP A 196 ADP A 601 HOH A 701 SITE 2 AC2 5 HOH A 702 SITE 1 AC3 4 CYS B 296 CYS B 299 HIS B 309 HIS B 315 CRYST1 61.480 61.480 237.410 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 0.016265 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016265 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004212 0.00000