HEADER REPLICATION 27-MAY-04 1WG3 TITLE STRUCTURAL ANALYSIS OF YEAST NUCLEOSOME-ASSEMBLY FACTOR CIA1P COMPND MOL_ID: 1; COMPND 2 MOLECULE: ANTI-SILENCING PROTEIN 1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: ANTI-SILENCING FUNCTION 1; COMPND 5 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: PGEX5X-2-CIA1-DELTAC2 KEYWDS BETA-SANDWICH, RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE, RSGI, KEYWDS 2 STRUCTURAL GENOMICS, REPLICATION EXPDTA X-RAY DIFFRACTION AUTHOR B.PADMANABHAN,K.KATAOKA,T.UMEHARA,N.ADACHI,S.YOKOYAMA,M.HORIKOSHI, AUTHOR 2 RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE (RSGI) REVDAT 4 25-OCT-23 1WG3 1 SEQADV REVDAT 3 24-FEB-09 1WG3 1 VERSN REVDAT 2 17-OCT-06 1WG3 1 JRNL REVDAT 1 14-JUN-05 1WG3 0 JRNL AUTH B.PADMANABHAN,K.KATAOKA,T.UMEHARA,N.ADACHI,S.YOKOYAMA, JRNL AUTH 2 M.HORIKOSHI JRNL TITL STRUCTURAL SIMILARITY BETWEEN HISTONE CHAPERONE CIA1P/ASF1P JRNL TITL 2 AND DNA-BINDING PROTEIN NF-{KAPPA}B JRNL REF J.BIOCHEM.(TOKYO) V. 138 821 2005 JRNL REFN ISSN 0021-924X JRNL PMID 16428312 JRNL DOI 10.1093/JB/MVI182 REMARK 2 REMARK 2 RESOLUTION. 3.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 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) : 3.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.42 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 7860443.030 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 91.1 REMARK 3 NUMBER OF REFLECTIONS : 4033 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) : 0.198 REMARK 3 FREE R VALUE : 0.274 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.300 REMARK 3 FREE R VALUE TEST SET COUNT : 212 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.019 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) (%) : 93.00 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 633 REMARK 3 BIN R VALUE (WORKING SET) : 0.2550 REMARK 3 BIN FREE R VALUE : 0.3530 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.80 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 32 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.062 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1307 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 119 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 36.80 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -2.25000 REMARK 3 B22 (A**2) : -2.91000 REMARK 3 B33 (A**2) : 5.16000 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) : 0.30 REMARK 3 ESD FROM SIGMAA (A) : 0.27 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) : 0.43 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.44 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : 1.400 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 26.40 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.090 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) : 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 : FLAT MODEL REMARK 3 KSOL : 0.31 REMARK 3 BSOL : 70.95 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 1WG3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 01-JUN-04. REMARK 100 THE DEPOSITION ID IS D_1000023542. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-OCT-01 REMARK 200 TEMPERATURE (KELVIN) : 298 REMARK 200 PH : 7.5 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 : DPS REMARK 200 DATA SCALING SOFTWARE : CCP4 (SCALA) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 4606 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.950 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL 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 : 5.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.95 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.13 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.28700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: 1ROC REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.54 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG8K, AS, TRIS-HCL, PH 7.5, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 293K 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 53.31450 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 23.52400 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 53.31450 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 23.52400 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 LEU A 168 REMARK 465 TYR A 169 REMARK 465 PRO A 170 REMARK 465 PRO A 171 REMARK 465 GLU A 172 REMARK 465 GLN A 173 REMARK 465 PRO A 174 REMARK 465 GLY A 175 REMARK 465 VAL A 176 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 LYS A 136 CG CD CE NZ 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 SER A 3 11.88 -69.05 REMARK 500 SER A 6 35.74 -72.77 REMARK 500 MET A 8 102.83 -19.93 REMARK 500 ASN A 20 -22.20 81.98 REMARK 500 ALA A 23 -171.19 -57.60 REMARK 500 SER A 54 150.50 -44.96 REMARK 500 SER A 57 -67.70 -179.45 REMARK 500 ASP A 59 -27.66 -168.70 REMARK 500 ASP A 61 21.86 39.64 REMARK 500 PRO A 92 133.61 -30.95 REMARK 500 LEU A 96 25.71 -171.84 REMARK 500 ASP A 109 27.30 47.37 REMARK 500 ASN A 132 63.57 -152.25 REMARK 500 PRO A 133 170.86 -44.60 REMARK 500 VAL A 137 108.89 -56.80 REMARK 500 ASP A 140 43.21 -76.70 REMARK 500 HIS A 141 9.09 -150.65 REMARK 500 ALA A 148 -5.47 -49.61 REMARK 500 LYS A 150 68.86 -112.38 REMARK 500 ASN A 157 74.26 -119.76 REMARK 500 TRP A 160 -121.61 -91.82 REMARK 500 ASP A 161 -107.68 -76.92 REMARK 500 GLU A 163 -12.32 -162.58 REMARK 500 ASN A 164 58.91 73.49 REMARK 500 GLU A 165 -53.13 -11.51 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: AR_001000281.1 RELATED DB: TARGETDB DBREF 1WG3 A 8 176 UNP P32447 ASF1_YEAST 1 169 SEQADV 1WG3 ALA A 2 UNP P32447 CLONING ARTIFACT SEQADV 1WG3 SER A 3 UNP P32447 CLONING ARTIFACT SEQADV 1WG3 GLY A 4 UNP P32447 CLONING ARTIFACT SEQADV 1WG3 SER A 5 UNP P32447 CLONING ARTIFACT SEQADV 1WG3 SER A 6 UNP P32447 CLONING ARTIFACT SEQADV 1WG3 GLY A 7 UNP P32447 CLONING ARTIFACT SEQRES 1 A 175 ALA SER GLY SER SER GLY MET SER ILE VAL SER LEU LEU SEQRES 2 A 175 GLY ILE LYS VAL LEU ASN ASN PRO ALA LYS PHE THR ASP SEQRES 3 A 175 PRO TYR GLU PHE GLU ILE THR PHE GLU CYS LEU GLU SER SEQRES 4 A 175 LEU LYS HIS ASP LEU GLU TRP LYS LEU THR TYR VAL GLY SEQRES 5 A 175 SER SER ARG SER LEU ASP HIS ASP GLN GLU LEU ASP SER SEQRES 6 A 175 ILE LEU VAL GLY PRO VAL PRO VAL GLY VAL ASN LYS PHE SEQRES 7 A 175 VAL PHE SER ALA ASP PRO PRO SER ALA GLU LEU ILE PRO SEQRES 8 A 175 ALA SER GLU LEU VAL SER VAL THR VAL ILE LEU LEU SER SEQRES 9 A 175 CYS SER TYR ASP GLY ARG GLU PHE VAL ARG VAL GLY TYR SEQRES 10 A 175 TYR VAL ASN ASN GLU TYR ASP GLU GLU GLU LEU ARG GLU SEQRES 11 A 175 ASN PRO PRO ALA LYS VAL GLN VAL ASP HIS ILE VAL ARG SEQRES 12 A 175 ASN ILE LEU ALA GLU LYS PRO ARG VAL THR ARG PHE ASN SEQRES 13 A 175 ILE VAL TRP ASP ASN GLU ASN GLU GLY ASP LEU TYR PRO SEQRES 14 A 175 PRO GLU GLN PRO GLY VAL FORMUL 2 HOH *119(H2 O) HELIX 1 1 SER A 87 ILE A 91 5 5 HELIX 2 2 GLU A 127 GLU A 131 5 5 HELIX 3 3 GLN A 138 ASP A 140 5 3 SHEET 1 A 3 VAL A 11 LYS A 17 0 SHEET 2 A 3 TYR A 29 CYS A 37 -1 O THR A 34 N GLY A 15 SHEET 3 A 3 GLY A 75 ALA A 83 -1 O GLY A 75 N CYS A 37 SHEET 1 B 5 GLN A 62 VAL A 69 0 SHEET 2 B 5 LEU A 45 VAL A 52 -1 N TYR A 51 O GLN A 62 SHEET 3 B 5 VAL A 99 TYR A 108 -1 O VAL A 101 N VAL A 52 SHEET 4 B 5 ARG A 111 TYR A 124 -1 O ARG A 111 N TYR A 108 SHEET 5 B 5 ILE A 142 ILE A 146 -1 O VAL A 143 N GLU A 123 SHEET 1 C 5 GLN A 62 VAL A 69 0 SHEET 2 C 5 LEU A 45 VAL A 52 -1 N TYR A 51 O GLN A 62 SHEET 3 C 5 VAL A 99 TYR A 108 -1 O VAL A 101 N VAL A 52 SHEET 4 C 5 ARG A 111 TYR A 124 -1 O ARG A 111 N TYR A 108 SHEET 5 C 5 ARG A 152 ARG A 155 -1 O ARG A 152 N GLY A 117 CISPEP 1 ASN A 21 PRO A 22 0 0.28 CRYST1 106.629 47.048 40.686 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 0.009378 0.000000 0.000000 0.00000 SCALE2 0.000000 0.021255 0.000000 0.00000 SCALE3 0.000000 0.000000 0.024579 0.00000