HEADER NUCLEAR PROTEIN 20-MAY-19 6RRV TITLE CRYSTAL STRUCTURE OF THE SIR4 H-BRCT DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: REGULATORY PROTEIN SIR4; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: SILENT INFORMATION REGULATOR 4; COMPND 5 ENGINEERED: YES; COMPND 6 OTHER_DETAILS: FRAGMENT (RESIDUES 961-1085) SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 3 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 4 ORGANISM_TAXID: 4932; SOURCE 5 GENE: SIR4, ASD1, STE9, UTH2, YDR227W, YD9934.12; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_VARIANT: STAR KEYWDS HETEROCHROMATIN, NUCLEAR PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR I.DESHPANDE,J.J.KEUSCH,K.CHALLA,V.IESMANTAVICIUS,S.M.GASSER,H.GUT REVDAT 4 15-MAY-24 6RRV 1 REMARK REVDAT 3 23-OCT-19 6RRV 1 JRNL REVDAT 2 25-SEP-19 6RRV 1 JRNL REVDAT 1 18-SEP-19 6RRV 0 JRNL AUTH I.DESHPANDE,J.J.KEUSCH,K.CHALLA,V.IESMANTAVICIUS,S.M.GASSER, JRNL AUTH 2 H.GUT JRNL TITL THE SIR4 H-BRCT DOMAIN INTERACTS WITH PHOSPHO-PROTEINS TO JRNL TITL 2 SEQUESTER AND REPRESS YEAST HETEROCHROMATIN. JRNL REF EMBO J. V. 38 01744 2019 JRNL REFN ESSN 1460-2075 JRNL PMID 31515872 JRNL DOI 10.15252/EMBJ.2019101744 REMARK 2 REMARK 2 RESOLUTION. 1.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.14_3260: ???) 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.89 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 2.010 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.4 REMARK 3 NUMBER OF REFLECTIONS : 43698 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.118 REMARK 3 R VALUE (WORKING SET) : 0.117 REMARK 3 FREE R VALUE : 0.142 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.050 REMARK 3 FREE R VALUE TEST SET COUNT : 2206 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 42.9244 - 2.7715 0.99 2808 135 0.1483 0.1715 REMARK 3 2 2.7715 - 2.1998 0.99 2682 160 0.1275 0.1353 REMARK 3 3 2.1998 - 1.9218 0.99 2716 137 0.1110 0.1399 REMARK 3 4 1.9218 - 1.7460 0.99 2695 154 0.1086 0.1289 REMARK 3 5 1.7460 - 1.6209 0.99 2703 144 0.0959 0.1265 REMARK 3 6 1.6209 - 1.5253 0.99 2659 144 0.0929 0.1198 REMARK 3 7 1.5253 - 1.4489 0.99 2708 144 0.0909 0.1207 REMARK 3 8 1.4489 - 1.3859 0.98 2656 143 0.0938 0.1291 REMARK 3 9 1.3859 - 1.3325 0.97 2641 146 0.0982 0.1392 REMARK 3 10 1.3325 - 1.2865 0.96 2558 152 0.1006 0.1508 REMARK 3 11 1.2865 - 1.2463 0.96 2584 151 0.0992 0.1334 REMARK 3 12 1.2463 - 1.2107 0.94 2565 121 0.1030 0.1376 REMARK 3 13 1.2107 - 1.1788 0.93 2536 126 0.1028 0.1434 REMARK 3 14 1.1788 - 1.1500 0.93 2518 134 0.0965 0.1326 REMARK 3 15 1.1500 - 1.1239 0.89 2420 115 0.1029 0.1312 REMARK 3 16 1.1239 - 1.1000 0.76 2043 100 0.1123 0.1563 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 0.90 REMARK 3 SHRINKAGE RADIUS : 0.50 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.070 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 12.320 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) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL 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 : 0.010 1209 REMARK 3 ANGLE : 1.249 1646 REMARK 3 CHIRALITY : 0.084 171 REMARK 3 PLANARITY : 0.006 222 REMARK 3 DIHEDRAL : 16.227 486 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 6RRV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 21-MAY-19. REMARK 100 THE DEPOSITION ID IS D_1292102493. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-MAY-12 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) : 0.999 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 S 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 43703 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.100 REMARK 200 RESOLUTION RANGE LOW (A) : 42.900 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.2 REMARK 200 DATA REDUNDANCY : 3.400 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.03400 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 20.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.13 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) : 0.12800 REMARK 200 <I/SIGMA(I)> FOR SHELL : 7.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SHELXCD REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 35.78 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.92 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 35% PEG 2000 MME 150 MM POTASSIUM REMARK 280 BROMIDE, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 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 34.83000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 19.06500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 34.83000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 19.06500 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 170 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8380 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -5.0 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 NH2 ARG A1075 LIES ON A SPECIAL POSITION. REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG A1029 NE - CZ - NH2 ANGL. DEV. = -3.4 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A1409 DISTANCE = 6.15 ANGSTROMS REMARK 525 HOH A1410 DISTANCE = 6.41 ANGSTROMS REMARK 525 HOH A1411 DISTANCE = 6.46 ANGSTROMS REMARK 525 HOH A1412 DISTANCE = 6.59 ANGSTROMS REMARK 525 HOH A1413 DISTANCE = 6.72 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 1101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue BR A 1102 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6QSZ RELATED DB: PDB REMARK 900 6QSZ CONTAINS THE SAME PROTEIN DOMAIN IN COMPLEX WITH ESC1 PS1450 REMARK 900 PEPTIDE REMARK 900 RELATED ID: 6QTM RELATED DB: PDB REMARK 900 6QTM CONTAINS THE SAME PROTEIN DOMAIN IN COMPLEX WITH TY5 PS1095 REMARK 900 PEPTIDE REMARK 900 RELATED ID: 6RR0 RELATED DB: PDB REMARK 900 6RR0 CONTAINS THE SAME PROTEIN DOMAIN IN COMPLEX WITH UBP10 PT123 REMARK 900 PEPTIDE DBREF 6RRV A 961 1085 UNP P11978 SIR4_YEAST 961 1085 SEQADV 6RRV GLY A 959 UNP P11978 EXPRESSION TAG SEQADV 6RRV PRO A 960 UNP P11978 EXPRESSION TAG SEQRES 1 A 127 GLY PRO LYS PRO LYS ASN THR LYS GLU ASN LEU SER LYS SEQRES 2 A 127 SER SER TRP ARG GLN GLU TRP LEU ALA ASN LEU LYS LEU SEQRES 3 A 127 ILE SER VAL SER LEU VAL ASP GLU PHE PRO SER GLU LEU SEQRES 4 A 127 SER ASP SER ASP ARG GLN ILE ILE ASN GLU LYS MET GLN SEQRES 5 A 127 LEU LEU LYS ASP ILE PHE ALA ASN ASN LEU LYS SER ALA SEQRES 6 A 127 ILE SER ASN ASN PHE ARG GLU SER ASP ILE ILE ILE LEU SEQRES 7 A 127 LYS GLY GLU ILE GLU ASP TYR PRO MET SER SER GLU ILE SEQRES 8 A 127 LYS ILE TYR TYR ASN GLU LEU GLN ASN LYS PRO ASP ALA SEQRES 9 A 127 LYS LYS ALA ARG PHE TRP SER PHE MET LYS THR GLN ARG SEQRES 10 A 127 PHE VAL SER ASN MET GLY PHE ASP ILE GLN HET CL A1101 1 HET BR A1102 1 HETNAM CL CHLORIDE ION HETNAM BR BROMIDE ION FORMUL 2 CL CL 1- FORMUL 3 BR BR 1- FORMUL 4 HOH *213(H2 O) HELIX 1 AA1 ASN A 968 LYS A 983 1 16 HELIX 2 AA2 SER A 998 ASN A 1019 1 22 HELIX 3 AA3 ASN A 1027 SER A 1031 5 5 HELIX 4 AA4 GLU A 1039 TYR A 1043 5 5 HELIX 5 AA5 SER A 1047 ASN A 1058 1 12 HELIX 6 AA6 PHE A 1070 MET A 1080 1 11 SHEET 1 AA1 4 ALA A1023 SER A1025 0 SHEET 2 AA1 4 SER A 986 LEU A 989 1 N VAL A 987 O ALA A1023 SHEET 3 AA1 4 ILE A1033 LEU A1036 1 O ILE A1035 N SER A 988 SHEET 4 AA1 4 ARG A1066 SER A1069 1 O ARG A1066 N ILE A1034 SITE 1 AC1 1 ARG A1075 SITE 1 AC2 2 SER A 970 MET A1045 CRYST1 69.660 38.130 48.620 90.00 118.09 90.00 C 1 2 1 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 0.014355 0.000000 0.007663 0.00000 SCALE2 0.000000 0.026226 0.000000 0.00000 SCALE3 0.000000 0.000000 0.023314 0.00000