HEADER TRANSFERASE/STRUCTURAL PROTEIN 24-JUL-03 1Q2C TITLE CRYSTAL STRUCTURE OF TETRAHYMENA GCN5 WITH BOUND COENZYME A AND A 19- TITLE 2 RESIDUE HISTONE H4 PEPTIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: HISTONE ACETYLTRANSFERASE GCN5; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 49-209, CATALYTIC DOMAIN; COMPND 5 SYNONYM: HAT A1; COMPND 6 EC: 2.3.1.-; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: HISTONE H4 PEPTIDE; COMPND 10 CHAIN: B; COMPND 11 FRAGMENT: RESIDUES 1-19; COMPND 12 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: TETRAHYMENA THERMOPHILA; SOURCE 3 ORGANISM_TAXID: 5911; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL-21; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PRSETA; SOURCE 9 MOL_ID: 2; SOURCE 10 SYNTHETIC: YES KEYWDS TETRAHYMENA; GCN5; HISTONE H4; X-RAY STRUCTURE, TRANSFERASE- KEYWDS 2 STRUCTURAL PROTEIN COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR A.N.POUX,R.MARMORSTEIN REVDAT 4 14-FEB-24 1Q2C 1 REMARK SEQADV REVDAT 3 18-AUG-10 1Q2C 1 JRNL REVDAT 2 24-FEB-09 1Q2C 1 VERSN REVDAT 1 03-AUG-04 1Q2C 0 JRNL AUTH A.CLEMENTS,A.N.POUX,S.LO,L.PILLUS,S.L.BERGER,R.MARMORSTEIN JRNL TITL STRUCTURAL BASIS FOR HISTONE AND PHOSPHOHISTONE BINDING BY JRNL TITL 2 THE GCN5 HISTONE ACETYLTRANSFERASE JRNL REF MOL.CELL V. 12 461 2003 JRNL REFN ISSN 1097-2765 JRNL PMID 14536085 JRNL DOI 10.1016/S1097-2765(03)00288-0 REMARK 2 REMARK 2 RESOLUTION. 2.25 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.25 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.07 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) (%) : 93.5 REMARK 3 NUMBER OF REFLECTIONS : 10916 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) : 0.252 REMARK 3 FREE R VALUE : 0.279 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1094 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.008 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) : 2.25 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.39 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 95.80 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1634 REMARK 3 BIN R VALUE (WORKING SET) : 0.2570 REMARK 3 BIN FREE R VALUE : 0.2820 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 9.50 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 171 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.022 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1408 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 48 REMARK 3 SOLVENT ATOMS : 47 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 20.20 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.90 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 4.83000 REMARK 3 B22 (A**2) : 4.83000 REMARK 3 B33 (A**2) : -9.66000 REMARK 3 B12 (A**2) : 4.19000 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) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.37 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.27 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.238 REMARK 3 BOND ANGLES (DEGREES) : 5.700 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.30 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.970 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 : 0.43 REMARK 3 BSOL : 45.19 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 : COA_OLD.PAR REMARK 3 PARAMETER FILE 3 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : COA_OLD.TOP REMARK 3 TOPOLOGY FILE 3 : WATER.TOP REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1Q2C COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 30-JUL-03. REMARK 100 THE DEPOSITION ID IS D_1000019827. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-JUN-00 REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : CHESS REMARK 200 BEAMLINE : A1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9213 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA, CCP4 (SCALA) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 23766 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 27.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.5 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.25 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.4 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.85 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.79 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: AMMONIUM SULFATE, TRIS-HCL, MAGNESIUM REMARK 280 CHLORIDE, PH 8.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 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 REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 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 64.37867 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 32.18933 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 0.00000 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 32.18933 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 64.37867 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: 970 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10320 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -7.0 KCAL/MOL 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 SER B 301 REMARK 465 GLY B 302 REMARK 465 ARG B 303 REMARK 465 GLY B 304 REMARK 465 LYS B 305 REMARK 465 GLY B 306 REMARK 465 GLY B 307 REMARK 465 LYS B 316 REMARK 465 ARG B 317 REMARK 465 HIS B 318 REMARK 465 ARG B 319 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 LYS A 103 27.68 45.45 REMARK 500 GLN A 104 -26.93 -153.51 REMARK 500 ASN A 131 7.97 -68.50 REMARK 500 ASN A 163 -123.39 46.61 REMARK 500 LYS B 312 -151.87 43.28 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE COA A 401 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1QSN RELATED DB: PDB REMARK 900 RELATED ID: 1QSR RELATED DB: PDB REMARK 900 RELATED ID: 1QST RELATED DB: PDB REMARK 900 RELATED ID: 1M1D RELATED DB: PDB REMARK 900 RELATED ID: 1PU9 RELATED DB: PDB REMARK 900 RELATED ID: 1PUA RELATED DB: PDB REMARK 900 RELATED ID: 1Q2D RELATED DB: PDB DBREF 1Q2C A 49 210 UNP Q27198 Q27198_TETTH 49 210 DBREF 1Q2C B 301 319 PDB 1Q2C 1Q2C 301 319 SEQADV 1Q2C PHE A 90 UNP Q27198 LEU 90 CLONING ARTIFACT SEQADV 1Q2C ARG A 210 UNP Q27198 ASN 210 CLONING ARTIFACT SEQRES 1 A 162 LEU ASP PHE ASP ILE LEU THR ASN ASP GLY THR HIS ARG SEQRES 2 A 162 ASN MET LYS LEU LEU ILE ASP LEU LYS ASN ILE PHE SER SEQRES 3 A 162 ARG GLN LEU PRO LYS MET PRO LYS GLU TYR ILE VAL LYS SEQRES 4 A 162 LEU VAL PHE ASP ARG HIS HIS GLU SER MET VAL ILE LEU SEQRES 5 A 162 LYS ASN LYS GLN LYS VAL ILE GLY GLY ILE CYS PHE ARG SEQRES 6 A 162 GLN TYR LYS PRO GLN ARG PHE ALA GLU VAL ALA PHE LEU SEQRES 7 A 162 ALA VAL THR ALA ASN GLU GLN VAL ARG GLY TYR GLY THR SEQRES 8 A 162 ARG LEU MET ASN LYS PHE LYS ASP HIS MET GLN LYS GLN SEQRES 9 A 162 ASN ILE GLU TYR LEU LEU THR TYR ALA ASP ASN PHE ALA SEQRES 10 A 162 ILE GLY TYR PHE LYS LYS GLN GLY PHE THR LYS GLU HIS SEQRES 11 A 162 ARG MET PRO GLN GLU LYS TRP LYS GLY TYR ILE LYS ASP SEQRES 12 A 162 TYR ASP GLY GLY THR LEU MET GLU CYS TYR ILE HIS PRO SEQRES 13 A 162 TYR VAL ASP TYR GLY ARG SEQRES 1 B 19 SER GLY ARG GLY LYS GLY GLY LYS GLY LEU GLY LYS GLY SEQRES 2 B 19 GLY ALA LYS ARG HIS ARG HET COA A 401 48 HETNAM COA COENZYME A FORMUL 3 COA C21 H36 N7 O16 P3 S FORMUL 4 HOH *47(H2 O) HELIX 1 1 THR A 59 LEU A 77 1 19 HELIX 2 2 PRO A 81 ASP A 91 1 11 HELIX 3 3 ALA A 130 GLN A 133 5 4 HELIX 4 4 GLY A 136 GLN A 152 1 17 HELIX 5 5 ASN A 163 GLN A 172 1 10 HELIX 6 6 PRO A 181 TRP A 185 5 5 SHEET 1 A 6 ASP A 50 LEU A 54 0 SHEET 2 A 6 HIS A 94 LYS A 101 -1 O SER A 96 N LEU A 54 SHEET 3 A 6 LYS A 105 TYR A 115 -1 O LYS A 105 N LYS A 101 SHEET 4 A 6 PHE A 120 VAL A 128 -1 O PHE A 125 N CYS A 111 SHEET 5 A 6 TYR A 156 ALA A 161 1 O LEU A 158 N ALA A 121 SHEET 6 A 6 THR A 196 TYR A 201 -1 O MET A 198 N THR A 159 SITE 1 AC1 19 GLN A 76 LEU A 77 LEU A 126 ALA A 127 SITE 2 AC1 19 VAL A 128 GLN A 133 VAL A 134 GLY A 138 SITE 3 AC1 19 THR A 139 GLN A 152 PHE A 164 ALA A 165 SITE 4 AC1 19 GLY A 167 TYR A 168 LYS A 171 LYS B 308 SITE 5 AC1 19 LEU B 310 GLY B 314 ALA B 315 CRYST1 65.132 65.132 96.568 90.00 90.00 120.00 P 32 2 1 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 0.015353 0.008864 0.000000 0.00000 SCALE2 0.000000 0.017729 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010355 0.00000