HEADER TRANSCRIPTION 21-NOV-12 3ZCO TITLE CRYSTAL STRUCTURE OF S. CEREVISIAE SIR3 C-TERMINAL DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: REGULATORY PROTEIN SIR3; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: C-TERMINAL DOMAIN, RESIDUES 840-978; COMPND 5 SYNONYM: SILENT INFORMATION REGULATOR 3; COMPND 6 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: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) KEYWDS TRANSCRIPTION, WINGED-HELIX LIKE DOMAIN, DIMERIZATION EXPDTA X-RAY DIFFRACTION AUTHOR M.OPPIKOFER,S.KUENG,J.J.KEUSCH,M.HASSLER,A.G.LADURNER,H.GUT, AUTHOR 2 S.M.GASSER REVDAT 2 08-MAY-24 3ZCO 1 REMARK REVDAT 1 03-APR-13 3ZCO 0 JRNL AUTH M.OPPIKOFER,S.KUENG,J.J.KEUSCH,M.HASSLER,A.G.LADURNER,H.GUT, JRNL AUTH 2 S.M.GASSER JRNL TITL DIMERIZATION OF SIR3 VIA ITS C-TERMINAL WINGED HELIX DOMAIN JRNL TITL 2 IS ESSENTIAL FOR YEAST HETEROCHROMATIN FORMATION. JRNL REF EMBO J. V. 32 437 2013 JRNL REFN ISSN 0261-4189 JRNL PMID 23299941 JRNL DOI 10.1038/EMBOJ.2012.343 REMARK 2 REMARK 2 RESOLUTION. 2.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : BUSTER 2.11.2 REMARK 3 AUTHORS : BRICOGNE,BLANC,BRANDL,FLENSBURG,KELLER, REMARK 3 : PACIOREK,ROVERSI,SHARFF,SMART,VONRHEIN, REMARK 3 : WOMACK,MATTHEWS,TEN EYCK,TRONRUD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.13 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 5076 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 + TEST SET) : 0.218 REMARK 3 R VALUE (WORKING SET) : 0.211 REMARK 3 FREE R VALUE : 0.263 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 14.340 REMARK 3 FREE R VALUE TEST SET COUNT : 728 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 5 REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 2.70 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 3.02 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.98 REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 1437 REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.2622 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1238 REMARK 3 BIN R VALUE (WORKING SET) : 0.2529 REMARK 3 BIN FREE R VALUE : 0.3225 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 13.85 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 199 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1010 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) : 88.88 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 101.7 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.00600 REMARK 3 B22 (A**2) : -1.00600 REMARK 3 B33 (A**2) : 2.01190 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) : 0.707 REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : 0.525 REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 0.307 REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : 0.560 REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : 0.315 REMARK 3 REMARK 3 REFERENCES: BLOW, D. (2002) ACTA CRYST D58, 792-797 REMARK 3 CRUICKSHANK, D.W.J. (1999) ACTA CRYST D55, 583-601 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.955 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.917 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 1025 ; 2.000 ; HARMONIC REMARK 3 BOND ANGLES : 1381 ; 2.000 ; HARMONIC REMARK 3 TORSION ANGLES : 378 ; 2.000 ; SINUSOIDAL REMARK 3 TRIGONAL CARBON PLANES : 24 ; 2.000 ; HARMONIC REMARK 3 GENERAL PLANES : 139 ; 5.000 ; HARMONIC REMARK 3 ISOTROPIC THERMAL FACTORS : 1025 ; 20.000 ; HARMONIC REMARK 3 BAD NON-BONDED CONTACTS : NULL ; NULL ; NULL REMARK 3 IMPROPER TORSIONS : NULL ; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES : NULL ; NULL ; NULL REMARK 3 CHIRAL IMPROPER TORSION : 141 ; 5.000 ; SEMIHARMONIC REMARK 3 SUM OF OCCUPANCIES : NULL ; NULL ; NULL REMARK 3 UTILITY DISTANCES : NULL ; NULL ; NULL REMARK 3 UTILITY ANGLES : NULL ; NULL ; NULL REMARK 3 UTILITY TORSION : NULL ; NULL ; NULL REMARK 3 IDEAL-DIST CONTACT TERM : 1213 ; 4.000 ; SEMIHARMONIC REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 1.34 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 2.42 REMARK 3 OTHER TORSION ANGLES (DEGREES) : 22.60 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN A REMARK 3 ORIGIN FOR THE GROUP (A): -13.8891 16.2468 -1.8620 REMARK 3 T TENSOR REMARK 3 T11: 0.1730 T22: -0.0948 REMARK 3 T33: -0.1940 T12: 0.3173 REMARK 3 T13: 0.2816 T23: 0.1202 REMARK 3 L TENSOR REMARK 3 L11: 8.2091 L22: 7.0048 REMARK 3 L33: 3.6815 L12: -1.4090 REMARK 3 L13: 0.2747 L23: 0.8820 REMARK 3 S TENSOR REMARK 3 S11: -0.4793 S12: -0.1451 S13: -0.4713 REMARK 3 S21: -0.6907 S22: 0.2499 S23: -0.4801 REMARK 3 S31: -0.2575 S32: 0.1704 S33: 0.2294 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3ZCO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 21-NOV-12. REMARK 100 THE DEPOSITION ID IS D_1290054858. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X10SA 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 : SI(111) REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 5076 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.700 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 8.200 REMARK 200 R MERGE (I) : 0.05000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 25.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.77 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 8.40 REMARK 200 R MERGE FOR SHELL (I) : 0.54000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: AUTOSHARP REMARK 200 STARTING MODEL: NONE REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.50 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30% PEG 4000, 0.2 M AMMONIUM ACETATE, REMARK 280 0.1 M SODIUM CITRATE PH 5.6 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 1 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 -Y,-X,-Z+1/3 REMARK 290 5555 -X+Y,Y,-Z+2/3 REMARK 290 6555 X,X-Y,-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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 37.04667 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 18.52333 REMARK 290 SMTRY1 4 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 18.52333 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 37.04667 REMARK 290 SMTRY1 6 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 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: 1710 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13280 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -8.3 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 0.500000 -0.866025 0.000000 0.00000 REMARK 350 BIOMT2 2 -0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 18.52333 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 GLY A 838 REMARK 465 PRO A 839 REMARK 465 SER A 840 REMARK 465 GLU A 841 REMARK 465 ALA A 842 REMARK 465 ILE A 843 REMARK 465 ASN A 844 REMARK 465 GLY A 845 REMARK 465 PHE A 846 REMARK 465 LYS A 847 REMARK 465 ASP A 848 REMARK 465 ASP A 976 REMARK 465 CYS A 977 REMARK 465 ILE A 978 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 ASN A 877 -121.79 34.84 REMARK 500 ARG A 878 -49.89 61.34 REMARK 500 ALA A 950 53.40 -60.30 REMARK 500 REMARK 500 REMARK: NULL DBREF 3ZCO A 840 978 UNP P06701 SIR3_YEAST 840 978 SEQADV 3ZCO GLY A 838 UNP P06701 EXPRESSION TAG SEQADV 3ZCO PRO A 839 UNP P06701 EXPRESSION TAG SEQRES 1 A 141 GLY PRO SER GLU ALA ILE ASN GLY PHE LYS ASP GLU THR SEQRES 2 A 141 ILE SER LYS LYS ILE ILE GLY MET SER LEU LEU MET ARG SEQRES 3 A 141 THR PHE LEU TYR THR LEU ALA GLN GLU THR GLU GLY THR SEQRES 4 A 141 ASN ARG HIS THR LEU ALA LEU GLU THR VAL LEU ILE LYS SEQRES 5 A 141 MET VAL LYS MET LEU ARG ASP ASN PRO GLY TYR LYS ALA SEQRES 6 A 141 SER LYS GLU ILE LYS LYS VAL ILE CYS GLY ALA TRP GLU SEQRES 7 A 141 PRO ALA ILE THR ILE GLU LYS LEU LYS GLN PHE SER TRP SEQRES 8 A 141 ILE SER VAL VAL ASN ASP LEU VAL GLY GLU LYS LEU VAL SEQRES 9 A 141 VAL VAL VAL LEU GLU GLU PRO SER ALA SER ILE MET VAL SEQRES 10 A 141 GLU LEU LYS LEU PRO LEU GLU ILE ASN TYR ALA PHE SER SEQRES 11 A 141 MET ASP GLU GLU PHE LYS ASN MET ASP CYS ILE HELIX 1 1 THR A 850 GLY A 857 1 8 HELIX 2 2 SER A 859 GLU A 874 1 16 HELIX 3 3 LEU A 883 ASN A 897 1 15 HELIX 4 4 TYR A 900 CYS A 911 1 12 HELIX 5 5 THR A 919 LYS A 924 1 6 HELIX 6 6 SER A 927 GLU A 938 1 12 HELIX 7 7 LEU A 958 ASP A 969 1 12 HELIX 8 8 GLU A 970 LYS A 973 5 4 SHEET 1 AA 3 THR A 880 ALA A 882 0 SHEET 2 AA 3 ILE A 952 LEU A 956 -1 O VAL A 954 N LEU A 881 SHEET 3 AA 3 VAL A 941 LEU A 945 -1 O VAL A 942 N GLU A 955 CRYST1 75.320 75.320 55.570 90.00 90.00 120.00 P 32 1 2 6 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 0.013277 0.007665 0.000000 0.00000 SCALE2 0.000000 0.015331 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017995 0.00000