HEADER PROTEIN BINDING 09-JUL-02 1IXV TITLE CRYSTAL STRUCTURE ANALYSIS OF HOMOLOG OF ONCOPROTEIN GANKYRIN, AN TITLE 2 INTERACTOR OF RB AND CDK4/6 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROBABLE 26S PROTEASOME REGULATORY SUBUNIT P28; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 3 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 4 ORGANISM_TAXID: 4932; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET28B-NAS6P KEYWDS ANKYRIN REPEATS, PROTEIN BINDING EXPDTA X-RAY DIFFRACTION AUTHOR B.PADMANABHAN,N.ADACHI,K.KATAOKA,M.HORIKOSHI REVDAT 4 27-DEC-23 1IXV 1 SEQADV REVDAT 3 24-FEB-09 1IXV 1 VERSN REVDAT 2 17-FEB-04 1IXV 1 JRNL REVDAT 1 16-DEC-03 1IXV 0 JRNL AUTH B.PADMANABHAN,N.ADACHI,K.KATAOKA,M.HORIKOSHI JRNL TITL CRYSTAL STRUCTURE OF THE HOMOLOG OF THE ONCOPROTEIN JRNL TITL 2 GANKYRIN, AN INTERACTOR OF RB AND CDK4/6 JRNL REF J.BIOL.CHEM. V. 279 1546 2004 JRNL REFN ISSN 0021-9258 JRNL PMID 14583612 JRNL DOI 10.1074/JBC.M310266200 REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.0 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 : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.45 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.0 REMARK 3 NUMBER OF REFLECTIONS : 11582 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) : 0.194 REMARK 3 FREE R VALUE : 0.234 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 588 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.010 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) : 2.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.44 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.80 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1779 REMARK 3 BIN R VALUE (WORKING SET) : 0.2220 REMARK 3 BIN FREE R VALUE : 0.3110 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.70 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 87 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.033 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1814 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 102 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 13.20 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 17.90 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.78000 REMARK 3 B22 (A**2) : 2.16000 REMARK 3 B33 (A**2) : -0.38000 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) : 0.25 REMARK 3 ESD FROM SIGMAA (A) : 0.20 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) : 0.31 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.30 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.300 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 21.30 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.840 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.200 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.860 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.250 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.380 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.34 REMARK 3 BSOL : 23.20 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 : WATER_REP.PARAM 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: NULL REMARK 4 REMARK 4 1IXV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 11-JUL-02. REMARK 100 THE DEPOSITION ID IS D_1000005386. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-JAN-02 REMARK 200 TEMPERATURE (KELVIN) : 278.0 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : BL-18B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : SCALA, CCP4 (SCALA) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11582 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.08500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.46 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.9 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.21600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MIR REMARK 200 SOFTWARE USED: SOLVE, CCP4 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.13 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.42 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG8000, TRIS-HCL, PH 6.5, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 298K 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 20.71650 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 49.04750 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 30.86800 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 49.04750 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 20.71650 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 30.86800 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 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 1 REMARK 465 SER A 2 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 TYR A 67 68.40 -119.89 REMARK 500 ASP A 69 -174.93 -68.76 REMARK 500 REMARK 500 REMARK: NULL DBREF 1IXV A 1 228 UNP P50086 PSDA_YEAST 1 228 SEQADV 1IXV VAL A 229 UNP P50086 CLONING ARTIFACT SEQADV 1IXV ASP A 230 UNP P50086 CLONING ARTIFACT SEQADV 1IXV ALA A 231 UNP P50086 CLONING ARTIFACT SEQRES 1 A 231 MET SER ASN TYR PRO LEU HIS GLN ALA CYS MET GLU ASN SEQRES 2 A 231 GLU PHE PHE LYS VAL GLN GLU LEU LEU HIS SER LYS PRO SEQRES 3 A 231 SER LEU LEU LEU GLN LYS ASP GLN ASP GLY ARG ILE PRO SEQRES 4 A 231 LEU HIS TRP SER VAL SER PHE GLN ALA HIS GLU ILE THR SEQRES 5 A 231 SER PHE LEU LEU SER LYS MET GLU ASN VAL ASN LEU ASP SEQRES 6 A 231 ASP TYR PRO ASP ASP SER GLY TRP THR PRO PHE HIS ILE SEQRES 7 A 231 ALA CYS SER VAL GLY ASN LEU GLU VAL VAL LYS SER LEU SEQRES 8 A 231 TYR ASP ARG PRO LEU LYS PRO ASP LEU ASN LYS ILE THR SEQRES 9 A 231 ASN GLN GLY VAL THR CYS LEU HIS LEU ALA VAL GLY LYS SEQRES 10 A 231 LYS TRP PHE GLU VAL SER GLN PHE LEU ILE GLU ASN GLY SEQRES 11 A 231 ALA SER VAL ARG ILE LYS ASP LYS PHE ASN GLN ILE PRO SEQRES 12 A 231 LEU HIS ARG ALA ALA SER VAL GLY SER LEU LYS LEU ILE SEQRES 13 A 231 GLU LEU LEU CYS GLY LEU GLY LYS SER ALA VAL ASN TRP SEQRES 14 A 231 GLN ASP LYS GLN GLY TRP THR PRO LEU PHE HIS ALA LEU SEQRES 15 A 231 ALA GLU GLY HIS GLY ASP ALA ALA VAL LEU LEU VAL GLU SEQRES 16 A 231 LYS TYR GLY ALA GLU TYR ASP LEU VAL ASP ASN LYS GLY SEQRES 17 A 231 ALA LYS ALA GLU ASP VAL ALA LEU ASN GLU GLN VAL LYS SEQRES 18 A 231 LYS PHE PHE LEU ASN ASN VAL VAL ASP ALA FORMUL 2 HOH *102(H2 O) HELIX 1 1 TYR A 4 ASN A 13 1 10 HELIX 2 2 GLU A 14 LYS A 25 1 12 HELIX 3 3 PRO A 26 LEU A 29 5 4 HELIX 4 4 ILE A 38 PHE A 46 1 9 HELIX 5 5 ALA A 48 SER A 57 1 10 HELIX 6 6 ASN A 63 TYR A 67 5 5 HELIX 7 7 THR A 74 GLY A 83 1 10 HELIX 8 8 ASN A 84 ASP A 93 1 10 HELIX 9 9 THR A 109 LYS A 117 1 9 HELIX 10 10 TRP A 119 ASN A 129 1 11 HELIX 11 11 ILE A 142 GLY A 151 1 10 HELIX 12 12 SER A 152 GLY A 161 1 10 HELIX 13 13 THR A 176 GLU A 184 1 9 HELIX 14 14 HIS A 186 GLY A 198 1 13 HELIX 15 15 ALA A 211 ALA A 215 5 5 HELIX 16 16 ASN A 217 VAL A 228 1 12 CRYST1 41.433 61.736 98.095 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 0.024135 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016198 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010194 0.00000