HEADER CELL CYCLE REGULATION 10-SEP-98 1BU2 TITLE X-RAY STRUCTURE OF A VIRAL CYCLIN FROM HERPESVIRUS SAIMIRI COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYCLIN HOMOLOG; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HERPESVIRUS SAIMIRI (STRAIN 11); SOURCE 3 ORGANISM_TAXID: 10383; SOURCE 4 STRAIN: 11; SOURCE 5 GENE: ECLF2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: DH5ALPHADE3 PACYC; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PQE9 KEYWDS CELL CYCLE REGULATION, HERPESVIRUS SAIMIRI, VIRAL CYCLIN EXPDTA X-RAY DIFFRACTION AUTHOR U.SCHULZE-GAHMEN,J.U.JUNG,S.-H.KIM REVDAT 3 07-FEB-24 1BU2 1 REMARK REVDAT 2 24-FEB-09 1BU2 1 VERSN REVDAT 1 15-JUN-99 1BU2 0 JRNL AUTH U.SCHULZE-GAHMEN,J.U.JUNG,S.H.KIM JRNL TITL CRYSTAL STRUCTURE OF A VIRAL CYCLIN, A POSITIVE REGULATOR OF JRNL TITL 2 CYCLIN-DEPENDENT KINASE 6. JRNL REF STRUCTURE FOLD.DES. V. 7 245 1999 JRNL REFN ISSN 0969-2126 JRNL PMID 10368294 JRNL DOI 10.1016/S0969-2126(99)80035-5 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH J.U.JUNG,M.STAEGER,R.C.DESROSIER REMARK 1 TITL VIRUS-ENCODED CYCLIN REMARK 1 REF MOL.CELL.BIOL. V. 14 7235 1994 REMARK 1 REFN ISSN 0270-7306 REMARK 2 REMARK 2 RESOLUTION. 3.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 0.3 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 93.7 REMARK 3 NUMBER OF REFLECTIONS : 6121 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 SET) : 0.242 REMARK 3 FREE R VALUE : 0.325 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 11.100 REMARK 3 FREE R VALUE TEST SET COUNT : 678 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.012 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 3.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.19 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 90.80 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 856 REMARK 3 BIN R VALUE (WORKING SET) : 0.3350 REMARK 3 BIN FREE R VALUE : 0.4360 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 10.50 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 100 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.044 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1671 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 69.20 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 64.70 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 4.86000 REMARK 3 B22 (A**2) : -19.64000 REMARK 3 B33 (A**2) : 14.78000 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 COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.39 REMARK 3 ESD FROM SIGMAA (A) : 0.48 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.53 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.60 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.009 REMARK 3 BOND ANGLES (DEGREES) : 1.500 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 19.70 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.800 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : GROUP REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : NULL REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: BULK SOLVENT MODEL USED REMARK 4 REMARK 4 1BU2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000172089. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NOV-95 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X12B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9471 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 6501 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.000 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 200 DATA REDUNDANCY : 4.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.95000 REMARK 200 FOR THE DATA SET : 11.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL 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: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CNS 0.3 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 58.18 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.94 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 7.0 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z 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 18.96000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 65.28500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 30.72000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 65.28500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 18.96000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 30.72000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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 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 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 22 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 28 CG CD CE NZ REMARK 470 LEU A 33 CG CD1 CD2 REMARK 470 LYS A 36 CG CD CE NZ REMARK 470 THR A 38 OG1 CG2 REMARK 470 SER A 39 OG REMARK 470 GLU A 42 CG CD OE1 OE2 REMARK 470 GLN A 44 CG CD OE1 NE2 REMARK 470 SER A 65 OG REMARK 470 LYS A 91 CG CD CE NZ REMARK 470 LYS A 92 CG CD CE NZ REMARK 470 THR A 115 OG1 CG2 REMARK 470 LEU A 122 CG CD1 CD2 REMARK 470 ASP A 125 CG OD1 OD2 REMARK 470 ILE A 157 CG1 CG2 CD1 REMARK 470 ILE A 165 CG1 CG2 CD1 REMARK 470 LEU A 169 CG CD1 CD2 REMARK 470 GLN A 172 CG CD OE1 NE2 REMARK 470 LYS A 183 CG CD CE NZ REMARK 470 ILE A 207 CG1 CG2 CD1 REMARK 470 ASP A 210 CG OD1 OD2 REMARK 470 THR A 212 OG1 CG2 REMARK 470 CYS A 214 SG REMARK 470 THR A 218 OG1 CG2 REMARK 470 CYS A 219 SG REMARK 470 GLU A 222 CG CD OE1 OE2 REMARK 470 SER A 225 OG REMARK 470 ILE A 227 CG1 CG2 CD1 REMARK 470 ASN A 229 CG OD1 ND2 REMARK 470 PHE A 230 CG CD1 CD2 CE1 CE2 CZ REMARK 470 SER A 231 OG REMARK 470 THR A 232 OG1 CG2 REMARK 470 ASN A 233 CG OD1 ND2 REMARK 470 THR A 234 OG1 CG2 REMARK 470 ARG A 236 CG CD NE CZ NH1 NH2 REMARK 470 THR A 237 OG1 CG2 REMARK 470 LYS A 239 CG CD CE NZ REMARK 470 ASP A 240 CG OD1 OD2 REMARK 470 GLN A 241 CG CD OE1 NE2 REMARK 470 VAL A 242 CG1 CG2 REMARK 470 PHE A 246 CG CD1 CD2 CE1 CE2 CZ REMARK 470 LEU A 248 CG CD1 CD2 REMARK 470 TYR A 249 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 ASP A 250 CG OD1 OD2 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 ARG A 30 7.11 -69.61 REMARK 500 THR A 38 -14.38 72.16 REMARK 500 LEU A 40 95.98 -43.48 REMARK 500 THR A 45 -78.54 -82.84 REMARK 500 GLU A 46 -81.57 -56.26 REMARK 500 LYS A 86 -49.62 -143.20 REMARK 500 ARG A 109 -61.18 -93.40 REMARK 500 LYS A 112 74.60 -114.28 REMARK 500 PRO A 113 101.51 -56.99 REMARK 500 MET A 114 136.97 -35.93 REMARK 500 CYS A 124 91.06 36.83 REMARK 500 ASP A 125 47.73 13.43 REMARK 500 TRP A 145 22.66 49.00 REMARK 500 GLU A 167 29.08 -65.86 REMARK 500 PRO A 188 2.13 -64.33 REMARK 500 ALA A 191 27.17 -69.76 REMARK 500 LEU A 192 25.40 -148.86 REMARK 500 CYS A 214 -164.23 -72.04 REMARK 500 ARG A 215 41.96 -106.85 REMARK 500 GLU A 222 -13.00 -47.11 REMARK 500 SER A 226 101.53 45.73 REMARK 500 ILE A 227 159.16 158.43 REMARK 500 LEU A 228 -47.53 -134.76 REMARK 500 REMARK 500 REMARK: NULL DBREF 1BU2 A 22 250 UNP Q01043 CGH2_SHV21 22 250 SEQRES 1 A 229 ARG VAL LEU ASN ASN LEU LYS LEU ARG GLU LEU LEU LEU SEQRES 2 A 229 PRO LYS PHE THR SER LEU TRP GLU ILE GLN THR GLU VAL SEQRES 3 A 229 THR VAL ASP ASN ARG THR ILE LEU LEU THR TRP MET HIS SEQRES 4 A 229 LEU LEU CYS GLU SER PHE GLU LEU ASP LYS SER VAL PHE SEQRES 5 A 229 PRO LEU SER VAL SER ILE LEU ASP ARG TYR LEU CYS LYS SEQRES 6 A 229 LYS GLN GLY THR LYS LYS THR LEU GLN LYS ILE GLY ALA SEQRES 7 A 229 ALA CYS VAL LEU ILE GLY SER LYS ILE ARG THR VAL LYS SEQRES 8 A 229 PRO MET THR VAL SER LYS LEU THR TYR LEU SER CYS ASP SEQRES 9 A 229 CYS PHE THR ASN LEU GLU LEU ILE ASN GLN GLU LYS ASP SEQRES 10 A 229 ILE LEU GLU ALA LEU LYS TRP ASP THR GLU ALA VAL LEU SEQRES 11 A 229 ALA THR ASP PHE LEU ILE PRO LEU CYS ASN ALA LEU LYS SEQRES 12 A 229 ILE PRO GLU ASP LEU TRP PRO GLN LEU TYR GLU ALA ALA SEQRES 13 A 229 SER THR THR ILE CYS LYS ALA LEU ILE GLN PRO ASN ILE SEQRES 14 A 229 ALA LEU LEU SER PRO GLY LEU ILE CYS ALA GLY GLY LEU SEQRES 15 A 229 LEU THR THR ILE GLU THR ASP ASN THR ASN CYS ARG PRO SEQRES 16 A 229 TRP THR CYS TYR LEU GLU ASP LEU SER SER ILE LEU ASN SEQRES 17 A 229 PHE SER THR ASN THR VAL ARG THR VAL LYS ASP GLN VAL SEQRES 18 A 229 SER GLU ALA PHE SER LEU TYR ASP HELIX 1 1 LEU A 24 LEU A 29 1 6 HELIX 2 2 VAL A 49 SER A 65 1 17 HELIX 3 3 LYS A 70 CYS A 85 1 16 HELIX 4 4 LEU A 94 ILE A 108 1 15 HELIX 5 5 VAL A 116 TYR A 121 1 6 HELIX 6 6 ASN A 129 ALA A 142 1 14 HELIX 7 7 ALA A 152 ALA A 162 5 11 HELIX 8 8 TRP A 170 ILE A 186 1 17 HELIX 9 9 ILE A 190 LEU A 192 5 3 HELIX 10 10 PRO A 195 THR A 209 1 15 HELIX 11 11 PRO A 216 ASP A 223 5 8 HELIX 12 12 PHE A 230 GLU A 244 1 15 CRYST1 37.920 61.440 130.570 90.00 90.00 90.00 P 21 21 21 4 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 0.026371 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016276 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007659 0.00000