PDB Short entry for 2H2F HEADER HYDROLASE 18-MAY-06 2H2F TITLE THE STRUCTURAL BASIS FOR SIRTUIN SUBSTRATE AFFINITY COMPND MOL_ID: 1; COMPND 2 MOLECULE: NAD-DEPENDENT DEACETYLASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: REGULATORY PROTEIN SIR2 HOMOLOG; COMPND 5 EC: 3.5.1.-; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: CELLULAR TUMOR ANTIGEN P53; COMPND 9 CHAIN: B; COMPND 10 SYNONYM: TUMOR SUPPRESSOR P53, PHOSPHOPROTEIN P53, ANTIGEN NY-CO-13; COMPND 11 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMOTOGA MARITIMA; SOURCE 3 ORGANISM_TAXID: 2336; SOURCE 4 GENE: NPDA; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 MOL_ID: 2; SOURCE 8 SYNTHETIC: YES; SOURCE 9 OTHER_DETAILS: THE SEQUENCE OF THE PEPTIDE IS NATURALLY FOUND IN SOURCE 10 HOMO SAPIENS (HUMAN). KEYWDS SIR2TM, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR M.S.COSGROVE,C.WOLBERGER REVDAT 4 30-AUG-23 2H2F 1 REMARK LINK REVDAT 3 27-JUN-12 2H2F 1 AUTHOR VERSN REVDAT 2 24-FEB-09 2H2F 1 VERSN REVDAT 1 05-DEC-06 2H2F 0 JRNL AUTH M.S.COSGROVE,K.BEVER,J.L.AVALOS,S.MUHAMMAD,X.ZHANG, JRNL AUTH 2 C.WOLBERGER JRNL TITL THE STRUCTURAL BASIS OF SIRTUIN SUBSTRATE AFFINITY JRNL REF BIOCHEMISTRY V. 45 7511 2006 JRNL REFN ISSN 0006-2960 JRNL PMID 16768447 JRNL DOI 10.1021/BI0526332 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 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) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 7.96 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 1289818.320 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 14705 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) : 0.206 REMARK 3 FREE R VALUE : 0.246 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 750 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.009 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) : 2.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.33 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.00 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2287 REMARK 3 BIN R VALUE (WORKING SET) : 0.2170 REMARK 3 BIN FREE R VALUE : 0.2450 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.30 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 104 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.024 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1896 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 97 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 23.30 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 38.00 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 3.94000 REMARK 3 B22 (A**2) : 3.19000 REMARK 3 B33 (A**2) : -7.13000 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) : 0.24 REMARK 3 ESD FROM SIGMAA (A) : 0.13 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) : 0.30 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.18 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.100 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 22.90 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.760 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 REMARK 3 KSOL : 0.58 REMARK 3 BSOL : 70469 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 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2H2F COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 24-MAY-06. REMARK 100 THE DEPOSITION ID IS D_1000037844. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-AUG-04 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 9.60 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X25 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.1 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17279 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : 6.200 REMARK 200 R MERGE (I) : 0.09200 REMARK 200 R SYM (I) : 0.06500 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 29.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.18 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.6 REMARK 200 DATA REDUNDANCY IN SHELL : 5.50 REMARK 200 R MERGE FOR SHELL (I) : 0.66000 REMARK 200 R SYM FOR SHELL (I) : 0.55900 REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: PDB ENTRY: 2H2I REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.09 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.42 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG, PH 9.6, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 298K, PH 9.60 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 22.82250 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 52.97650 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 29.65500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 52.97650 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 22.82250 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 29.65500 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 APPLY THE FOLLOWING TO CHAINS: A, B 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 PHE A 33 REMARK 465 ARG A 34 REMARK 465 GLY A 35 REMARK 465 PRO A 36 REMARK 465 ASN A 37 REMARK 465 GLY A 38 REMARK 465 ILE A 39 REMARK 465 TYR A 40 REMARK 465 LYS A 41 REMARK 465 LYS A 42 REMARK 465 TYR A 43 REMARK 465 SER A 44 REMARK 465 LYS B 1 REMARK 465 LYS B 2 REMARK 465 GLY B 3 REMARK 465 GLN B 4 REMARK 465 SER B 5 REMARK 465 THR B 6 REMARK 465 PHE B 14 REMARK 465 LYS B 15 REMARK 465 THR B 16 REMARK 465 GLU B 17 REMARK 465 GLY B 18 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 46 146.65 170.82 REMARK 500 ARG A 102 19.35 57.38 REMARK 500 ARG A 126 -76.81 -82.94 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A1001 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 124 SG REMARK 620 2 CYS A 127 SG 113.8 REMARK 620 3 CYS A 148 SG 109.8 105.8 REMARK 620 4 CYS A 151 SG 91.1 116.1 119.8 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 1001 DBREF 2H2F A 1 246 UNP Q9WYW0 NPD_THEMA 1 246 DBREF 2H2F B 1 18 UNP P04637 P53_HUMAN 372 389 SEQRES 1 A 246 MET LYS MET LYS GLU PHE LEU ASP LEU LEU ASN GLU SER SEQRES 2 A 246 ARG LEU THR VAL THR LEU THR GLY ALA GLY ILE SER THR SEQRES 3 A 246 PRO SER GLY ILE PRO ASP PHE ARG GLY PRO ASN GLY ILE SEQRES 4 A 246 TYR LYS LYS TYR SER GLN ASN VAL PHE ASP ILE ASP PHE SEQRES 5 A 246 PHE TYR SER HIS PRO GLU GLU PHE TYR ARG PHE ALA LYS SEQRES 6 A 246 GLU GLY ILE PHE PRO MET LEU GLN ALA LYS PRO ASN LEU SEQRES 7 A 246 ALA HIS VAL LEU LEU ALA LYS LEU GLU GLU LYS GLY LEU SEQRES 8 A 246 ILE GLU ALA VAL ILE THR GLN ASN ILE ASP ARG LEU HIS SEQRES 9 A 246 GLN ARG ALA GLY SER LYS LYS VAL ILE GLU LEU HIS GLY SEQRES 10 A 246 ASN VAL GLU GLU TYR TYR CYS VAL ARG CYS GLU LYS LYS SEQRES 11 A 246 TYR THR VAL GLU ASP VAL ILE LYS LYS LEU GLU SER SER SEQRES 12 A 246 ASP VAL PRO LEU CYS ASP ASP CYS ASN SER LEU ILE ARG SEQRES 13 A 246 PRO ASN ILE VAL PHE PHE GLY GLU ASN LEU PRO GLN ASP SEQRES 14 A 246 ALA LEU ARG GLU ALA ILE GLY LEU SER SER ARG ALA SER SEQRES 15 A 246 LEU MET ILE VAL LEU GLY SER SER LEU VAL VAL TYR PRO SEQRES 16 A 246 ALA ALA GLU LEU PRO LEU ILE THR VAL ARG SER GLY GLY SEQRES 17 A 246 LYS LEU VAL ILE VAL ASN LEU GLY GLU THR PRO PHE ASP SEQRES 18 A 246 ASP ILE ALA THR LEU LYS TYR ASN MET ASP VAL VAL GLU SEQRES 19 A 246 PHE ALA ARG ARG VAL MET GLU GLU GLY GLY ILE SER SEQRES 1 B 18 LYS LYS GLY GLN SER THR SER ARG HIS LYS LYS LEU MET SEQRES 2 B 18 PHE LYS THR GLU GLY HET ZN A1001 1 HETNAM ZN ZINC ION FORMUL 3 ZN ZN 2+ FORMUL 4 HOH *97(H2 O) HELIX 1 1 MET A 3 SER A 13 1 11 HELIX 2 2 ALA A 22 GLY A 29 5 8 HELIX 3 3 ASP A 49 HIS A 56 1 8 HELIX 4 4 HIS A 56 ILE A 68 1 13 HELIX 5 5 PHE A 69 ALA A 74 5 6 HELIX 6 6 ASN A 77 LYS A 89 1 13 HELIX 7 7 ARG A 102 ALA A 107 1 6 HELIX 8 8 VAL A 133 LEU A 140 1 8 HELIX 9 9 PRO A 167 ALA A 181 1 15 HELIX 10 10 PRO A 195 ALA A 197 5 3 HELIX 11 11 GLU A 198 GLY A 207 1 10 HELIX 12 12 PHE A 220 ALA A 224 5 5 HELIX 13 13 ASP A 231 GLY A 244 1 14 SHEET 1 A 6 VAL A 112 GLU A 114 0 SHEET 2 A 6 ALA A 94 THR A 97 1 N VAL A 95 O ILE A 113 SHEET 3 A 6 THR A 16 THR A 20 1 N THR A 18 O ILE A 96 SHEET 4 A 6 LEU A 183 LEU A 187 1 O LEU A 187 N LEU A 19 SHEET 5 A 6 LYS A 209 VAL A 213 1 O VAL A 211 N MET A 184 SHEET 6 A 6 LEU A 226 TYR A 228 1 O TYR A 228 N ILE A 212 SHEET 1 B 3 LYS A 130 THR A 132 0 SHEET 2 B 3 GLY A 117 CYS A 124 -1 N TYR A 122 O TYR A 131 SHEET 3 B 3 ILE A 155 ILE A 159 -1 O ASN A 158 N GLU A 121 LINK SG CYS A 124 ZN ZN A1001 1555 1555 2.47 LINK SG CYS A 127 ZN ZN A1001 1555 1555 2.33 LINK SG CYS A 148 ZN ZN A1001 1555 1555 2.37 LINK SG CYS A 151 ZN ZN A1001 1555 1555 2.43 CISPEP 1 TYR A 194 PRO A 195 0 -0.64 SITE 1 AC1 4 CYS A 124 CYS A 127 CYS A 148 CYS A 151 CRYST1 45.645 59.310 105.953 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 0.021908 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016861 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009438 0.00000