HEADER CELL CYCLE, REPLICATION 06-JUL-09 3A4C TITLE CRYSTAL STRUCTURE OF CDT1 C TERMINAL DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA REPLICATION FACTOR CDT1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: C TERMINAL DOMAIN, RESIDUES 452-557; COMPND 5 SYNONYM: DOUBLE PARKED HOMOLOG, DUP, RETROVIRAL INSERTION SITE 2 COMPND 6 PROTEIN; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: CDT1, RIS2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET-28A KEYWDS ALPHA-BETA STRUCTURE, CELL CYCLE, DNA REPLICATION, DNA-BINDING, KEYWDS 2 NUCLEUS, PHOSPHOPROTEIN, PROTO-ONCOGENE, UBL CONJUGATION, KEYWDS 3 REPLICATION EXPDTA X-RAY DIFFRACTION AUTHOR Y.CHO,J.H.LEE REVDAT 3 13-MAR-24 3A4C 1 REMARK REVDAT 2 03-NOV-09 3A4C 1 JRNL REVDAT 1 13-OCT-09 3A4C 0 JRNL AUTH B.I.KHAYRUTDINOV,W.J.BAE,Y.M.YUN,J.H.LEE,T.TSUYAMA,J.J.KIM, JRNL AUTH 2 E.HWANG,K.-S.RYU,H.-K.CHEONG,C.CHEONG,J.-S.KO,T.ENOMOTO, JRNL AUTH 3 P.A.KARPLUS,P.GUNTERT,S.TADA,Y.H.JEON,Y.CHO JRNL TITL STRUCTURE OF THE CDT1 C-TERMINAL DOMAIN: CONSERVATION OF THE JRNL TITL 2 WINGED HELIX FOLD IN REPLICATION LICENSING FACTORS JRNL REF PROTEIN SCI. V. 18 2252 2009 JRNL REFN ISSN 0961-8368 JRNL PMID 19722278 JRNL DOI 10.1002/PRO.236 REMARK 2 REMARK 2 RESOLUTION. 1.89 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE) 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.89 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.17 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.290 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.8 REMARK 3 NUMBER OF REFLECTIONS : 11126 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.213 REMARK 3 R VALUE (WORKING SET) : 0.211 REMARK 3 FREE R VALUE : 0.236 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.120 REMARK 3 FREE R VALUE TEST SET COUNT : 570 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 37.1762 - 2.9989 0.99 2831 153 0.2167 0.2540 REMARK 3 2 2.9989 - 2.3804 0.98 2611 163 0.2197 0.2173 REMARK 3 3 2.3804 - 2.0796 0.98 2614 132 0.1920 0.2284 REMARK 3 4 2.0796 - 1.8894 0.95 2500 122 0.1982 0.2276 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 : 0.40 REMARK 3 B_SOL : 58.73 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.260 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.930 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 18.80 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.06 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.25700 REMARK 3 B22 (A**2) : 1.25700 REMARK 3 B33 (A**2) : -2.51400 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 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 : 0.006 859 REMARK 3 ANGLE : 1.028 1163 REMARK 3 CHIRALITY : 0.062 139 REMARK 3 PLANARITY : 0.004 149 REMARK 3 DIHEDRAL : 16.547 332 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL 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 3A4C COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 07-JUL-09. REMARK 100 THE DEPOSITION ID IS D_1000028794. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-AUG-07 REMARK 200 TEMPERATURE (KELVIN) : 113 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PAL/PLS REMARK 200 BEAMLINE : 6C1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : OXFORD ONYX CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11409 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.889 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 15.20 REMARK 200 R MERGE (I) : 0.08100 REMARK 200 R SYM (I) : 0.06400 REMARK 200 FOR THE DATA SET : 67.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.89 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.97 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 15.10 REMARK 200 R MERGE FOR SHELL (I) : 0.37300 REMARK 200 R SYM FOR SHELL (I) : 0.33400 REMARK 200 FOR SHELL : 12.10 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SOLVE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.09 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.74 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 3.8M NACL, 100MM SODIUM CITRATE, 5MM REMARK 280 DTT, PH5.5, 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 48.01750 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 26.28250 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 26.28250 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 24.00875 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 26.28250 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 26.28250 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 72.02625 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 26.28250 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 26.28250 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 24.00875 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 26.28250 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 26.28250 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 72.02625 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 48.01750 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 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 GLN A 499 33.26 -90.17 REMARK 500 ARG A 528 -128.15 50.83 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2KLO RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF THE CDT1 C-TERMINAL DOMAIN DBREF 3A4C A 452 557 UNP Q8R4E9 CDT1_MOUSE 452 557 SEQRES 1 A 106 ARG CYS PRO GLU GLN GLU LEU ARG LEU GLN ARG LEU GLU SEQRES 2 A 106 ARG LEU PRO GLU LEU ALA ARG VAL LEU ARG ASN VAL PHE SEQRES 3 A 106 VAL SER GLU ARG LYS PRO ALA LEU THR MET GLU VAL VAL SEQRES 4 A 106 CYS ALA ARG MET VAL ASP SER CYS GLN THR ALA LEU SER SEQRES 5 A 106 PRO GLY GLU MET GLU LYS HIS LEU VAL LEU LEU ALA GLU SEQRES 6 A 106 LEU LEU PRO ASP TRP LEU SER LEU HIS ARG ILE ARG THR SEQRES 7 A 106 ASP THR TYR VAL LYS LEU ASP LYS ALA VAL ASP LEU ALA SEQRES 8 A 106 GLY LEU THR ALA ARG LEU ALA HIS HIS VAL HIS ALA GLU SEQRES 9 A 106 GLY LEU FORMUL 2 HOH *78(H2 O) HELIX 1 1 CYS A 453 SER A 479 1 27 HELIX 2 2 MET A 487 SER A 497 1 11 HELIX 3 3 SER A 503 LEU A 518 1 16 HELIX 4 4 ASP A 540 GLU A 555 1 16 SHEET 1 A 3 ALA A 484 THR A 486 0 SHEET 2 A 3 ASP A 530 LEU A 535 -1 O VAL A 533 N LEU A 485 SHEET 3 A 3 LEU A 522 ILE A 527 -1 N HIS A 525 O TYR A 532 CRYST1 52.565 52.565 96.035 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 0.019024 0.000000 0.000000 0.00000 SCALE2 0.000000 0.019024 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010413 0.00000