HEADER CELL CYCLE 19-AUG-10 3OIP TITLE CRYSTAL STRUCTURE OF YEAST TELOMERE PROTEIN CDC13 OB1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: CELL DIVISION CONTROL PROTEIN 13; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 3 ORGANISM_COMMON: BREWER'S YEAST,LAGER BEER YEAST,YEAST; SOURCE 4 ORGANISM_TAXID: 4932; SOURCE 5 GENE: CDC13, YDL220C; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS OB FOLD, DIMER, CELL CYCLE EXPDTA X-RAY DIFFRACTION AUTHOR J.SUN,Y.YANG,K.WAN,N.MAO,T.Y.YU,Y.C.LIN,D.C.DEZWAAN,B.C.FREEMAN, AUTHOR 2 J.J.LIN,N.F.LUE,M.LEI REVDAT 4 22-MAY-24 3OIP 1 REMARK REVDAT 3 26-JUL-23 3OIP 1 JRNL SEQADV REVDAT 2 08-NOV-17 3OIP 1 REMARK REVDAT 1 03-NOV-10 3OIP 0 JRNL AUTH J.SUN,Y.YANG,K.WAN,N.MAO,T.Y.YU,Y.C.LIN,D.C.DEZWAAN, JRNL AUTH 2 B.C.FREEMAN,J.J.LIN,N.F.LUE,M.LEI JRNL TITL STRUCTURAL BASES OF DIMERIZATION OF YEAST TELOMERE PROTEIN JRNL TITL 2 CDC13 AND ITS INTERACTION WITH THE CATALYTIC SUBUNIT OF DNA JRNL TITL 3 POLYMERASE ALPHA. JRNL REF CELL RES. V. 21 258 2011 JRNL REFN ISSN 1001-0602 JRNL PMID 20877309 JRNL DOI 10.1038/CR.2010.138 REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.5_2) 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) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.78 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.150 REMARK 3 COMPLETENESS FOR RANGE (%) : 90.9 REMARK 3 NUMBER OF REFLECTIONS : 7492 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.209 REMARK 3 R VALUE (WORKING SET) : 0.203 REMARK 3 FREE R VALUE : 0.257 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.580 REMARK 3 FREE R VALUE TEST SET COUNT : 793 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 34.7848 - 4.5477 0.99 1291 158 0.2081 0.2456 REMARK 3 2 4.5477 - 3.6108 0.99 1222 159 0.1637 0.2389 REMARK 3 3 3.6108 - 3.1548 0.98 1200 135 0.1989 0.2343 REMARK 3 4 3.1548 - 2.8665 0.96 1153 130 0.2140 0.3319 REMARK 3 5 2.8665 - 2.6611 0.87 1043 128 0.2458 0.3163 REMARK 3 6 2.6611 - 2.5040 0.65 790 83 0.2770 0.3354 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 : 0.37 REMARK 3 B_SOL : 62.30 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.300 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -17.70810 REMARK 3 B22 (A**2) : 10.51510 REMARK 3 B33 (A**2) : 7.19310 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 : 0.008 1632 REMARK 3 ANGLE : 1.198 2193 REMARK 3 CHIRALITY : 0.089 257 REMARK 3 PLANARITY : 0.004 274 REMARK 3 DIHEDRAL : 20.256 611 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 3OIP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-AUG-10. REMARK 100 THE DEPOSITION ID IS D_1000061165. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-DEC-08 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 : APS REMARK 200 BEAMLINE : 21-ID-D REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97856 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MAR SCANNER 300 MM PLATE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7955 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 100.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.4 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL 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 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SHARP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.23 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.13 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 21% PEG 3350, 0.2M NACL, 0.1M HEPES, REMARK 280 10MM DTT, PH 7.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X+1/2,Y+1/2,-Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 31.25750 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 34.32050 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 31.25750 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 34.32050 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2810 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 20350 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -11.0 KCAL/MOL 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 125.03000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 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 ARG A 61 REMARK 465 GLY A 62 REMARK 465 ASP A 63 REMARK 465 GLN A 64 REMARK 465 ASP A 106 REMARK 465 SER A 107 REMARK 465 GLY A 108 REMARK 465 ALA A 109 REMARK 465 SER A 110 REMARK 465 PRO A 111 REMARK 465 SER A 162 REMARK 465 THR A 163 REMARK 465 ASN A 164 REMARK 465 SER A 165 REMARK 465 SER A 166 REMARK 465 LYS A 167 REMARK 465 HIS A 168 REMARK 465 SER A 169 REMARK 465 GLN A 226 REMARK 465 LYS A 227 REMARK 465 SER A 228 REMARK 465 LYS A 229 REMARK 465 ALA A 230 REMARK 465 ALA A 231 REMARK 465 ALA A 232 REMARK 465 ILE A 233 REMARK 465 ASN A 234 REMARK 465 PRO A 235 REMARK 465 PHE A 236 REMARK 465 PHE A 237 REMARK 465 VAL A 238 REMARK 465 PRO A 239 REMARK 465 ASN A 240 REMARK 465 ARG A 241 REMARK 465 LEU A 242 REMARK 465 GLY A 243 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 ARG A 122 NE2 HIS A 208 2.15 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 HIS A 12 -157.09 -140.88 REMARK 500 SER A 20 142.44 -171.93 REMARK 500 THR A 47 -141.22 -111.17 REMARK 500 LEU A 123 88.38 77.92 REMARK 500 THR A 157 -36.27 -36.65 REMARK 500 THR A 160 -97.51 -84.41 REMARK 500 TYR A 209 90.58 -49.37 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3OIQ RELATED DB: PDB DBREF 3OIP A 12 243 UNP P32797 CDC13_YEAST 12 243 SEQADV 3OIP SER A 11 UNP P32797 EXPRESSION TAG SEQRES 1 A 233 SER HIS LYS ASN ARG ILE PHE VAL SER SER SER LYS ASP SEQRES 2 A 233 PHE GLU GLY TYR PRO SER LYS ALA ILE VAL PRO VAL GLN SEQRES 3 A 233 PHE VAL ALA LEU LEU THR SER ILE HIS LEU THR GLU THR SEQRES 4 A 233 LYS CYS LEU LEU GLY PHE SER ASN PHE GLU ARG ARG GLY SEQRES 5 A 233 ASP GLN SER GLN GLU ASP GLN TYR LEU ILE LYS LEU LYS SEQRES 6 A 233 PHE LYS ASP ARG GLY SER GLU ARG LEU ALA ARG ILE THR SEQRES 7 A 233 ILE SER LEU LEU CYS GLN TYR PHE ASP ILE GLU LEU PRO SEQRES 8 A 233 ASP LEU ASP SER ASP SER GLY ALA SER PRO THR VAL ILE SEQRES 9 A 233 LEU ARG ASP ILE HIS LEU GLU ARG LEU CYS PHE SER SER SEQRES 10 A 233 CYS LYS ALA LEU TYR VAL SER LYS HIS GLY ASN TYR THR SEQRES 11 A 233 LEU PHE LEU GLU ASP ILE LYS PRO LEU ASP LEU VAL SER SEQRES 12 A 233 VAL ILE SER THR ILE SER THR LYS SER THR ASN SER SER SEQRES 13 A 233 LYS HIS SER SER SER GLU LEU ILE SER GLU CYS ASP LEU SEQRES 14 A 233 ASN ASN SER LEU VAL ASP ILE PHE ASN ASN LEU ILE GLU SEQRES 15 A 233 MET ASN ARG ASP GLU LYS ASN ARG PHE LYS PHE VAL LYS SEQRES 16 A 233 LEU ILE HIS TYR ASP ILE GLU LEU LYS LYS PHE VAL GLN SEQRES 17 A 233 ASP GLN GLN LYS VAL LEU SER GLN LYS SER LYS ALA ALA SEQRES 18 A 233 ALA ILE ASN PRO PHE PHE VAL PRO ASN ARG LEU GLY FORMUL 2 HOH *25(H2 O) HELIX 1 1 SER A 20 TYR A 27 5 8 HELIX 2 2 ASP A 78 PHE A 96 1 19 HELIX 3 3 ASP A 117 ARG A 122 1 6 HELIX 4 4 ASP A 150 THR A 160 1 11 HELIX 5 5 CYS A 177 ASP A 196 1 20 HELIX 6 6 LYS A 202 LEU A 206 5 5 HELIX 7 7 ASP A 210 GLN A 221 1 12 SHEET 1 A 8 ILE A 16 PHE A 17 0 SHEET 2 A 8 VAL A 113 LEU A 115 0 SHEET 3 A 8 CYS A 51 SER A 56 0 SHEET 4 A 8 TYR A 70 LYS A 73 -1 O TYR A 70 N PHE A 55 SHEET 5 A 8 ASN A 138 PRO A 148 1 O LEU A 141 N LYS A 73 SHEET 6 A 8 PHE A 125 LYS A 135 -1 N SER A 127 O LYS A 147 SHEET 7 A 8 ALA A 31 LEU A 46 -1 N VAL A 35 O ALA A 130 SHEET 8 A 8 VAL A 113 LEU A 115 -1 O LEU A 115 N ILE A 44 CRYST1 62.515 68.641 52.815 90.00 90.00 90.00 P 21 21 2 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 0.015996 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014569 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018934 0.00000