HEADER TRANSFERASE 16-MAR-05 1Z4R TITLE HUMAN GCN5 ACETYLTRANSFERASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: GENERAL CONTROL OF AMINO ACID SYNTHESIS PROTEIN 5-LIKE 2; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 497-662; COMPND 5 SYNONYM: HISTONE ACETYLTRANSFERASE GCN5, HSGCN5, STAF97; COMPND 6 EC: 2.3.1.48; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: GCN5; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS GCN5, ACETYLTRANSFERASE, SGC, STRUCTURAL GENOMICS, STRUCTURAL KEYWDS 2 GENOMICS CONSORTIUM, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR A.DONG,G.BERNSTEIN,A.SCHUETZ,T.ANTOSHENKO,H.WU,P.LOPPNAU,M.SUNDSTROM, AUTHOR 2 C.ARROWSMITH,A.EDWARDS,A.BOCHKAREV,A.PLOTNIKOV,STRUCTURAL GENOMICS AUTHOR 3 CONSORTIUM (SGC) REVDAT 4 23-AUG-23 1Z4R 1 REMARK SEQADV REVDAT 3 20-MAY-08 1Z4R 1 JRNL VERSN REVDAT 2 05-APR-05 1Z4R 1 AUTHOR REVDAT 1 29-MAR-05 1Z4R 0 JRNL AUTH A.SCHUETZ,G.BERNSTEIN,A.DONG,T.ANTOSHENKO,H.WU,P.LOPPNAU, JRNL AUTH 2 A.BOCHKAREV,A.N.PLOTNIKOV JRNL TITL CRYSTAL STRUCTURE OF A BINARY COMPLEX BETWEEN HUMAN GCN5 JRNL TITL 2 HISTONE ACETYLTRANSFERASE DOMAIN AND ACETYL COENZYME A JRNL REF PROTEINS V. 68 403 2007 JRNL REFN ISSN 0887-3585 JRNL PMID 17410582 JRNL DOI 10.1002/PROT.21407 REMARK 2 REMARK 2 RESOLUTION. 1.74 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) : 1.74 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.98 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 762661.160 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 94.3 REMARK 3 NUMBER OF REFLECTIONS : 14729 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) : 0.197 REMARK 3 FREE R VALUE : 0.240 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.000 REMARK 3 FREE R VALUE TEST SET COUNT : 592 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.010 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) : 1.74 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.85 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 71.60 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1750 REMARK 3 BIN R VALUE (WORKING SET) : 0.2750 REMARK 3 BIN FREE R VALUE : 0.2970 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.70 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 86 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.032 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1330 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 51 REMARK 3 SOLVENT ATOMS : 131 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 20.90 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.90 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 3.09000 REMARK 3 B22 (A**2) : 3.09000 REMARK 3 B33 (A**2) : -6.19000 REMARK 3 B12 (A**2) : 2.58000 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) : 0.20 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) : 0.26 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.17 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : 1.200 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 22.90 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.870 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) : 1.250 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.920 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.160 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.040 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.37 REMARK 3 BSOL : 47.65 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 : COA_XPLOR_PAR.TXT REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER_REP.TOP REMARK 3 TOPOLOGY FILE 3 : COA_XPLOR_TOP.TXT REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1Z4R COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 17-MAR-05. REMARK 100 THE DEPOSITION ID IS D_1000032296. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-MAR-05 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU FR-E REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : VERIMAX REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : CRYSTALCLEAR (MSC/RIGAKU) REMARK 200 DATA SCALING SOFTWARE : D*TREK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15315 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.680 REMARK 200 RESOLUTION RANGE LOW (A) : 32.980 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 87.2 REMARK 200 DATA REDUNDANCY : 6.710 REMARK 200 R MERGE (I) : 0.05600 REMARK 200 R SYM (I) : 0.05600 REMARK 200 FOR THE DATA SET : 19.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.68 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.74 REMARK 200 COMPLETENESS FOR SHELL (%) : 87.2 REMARK 200 DATA REDUNDANCY IN SHELL : 1.73 REMARK 200 R MERGE FOR SHELL (I) : 0.16900 REMARK 200 R SYM FOR SHELL (I) : 0.16900 REMARK 200 FOR SHELL : 3.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 1YGH REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.50 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 15% (V/V) ETHANOL, 100 MM TRIS, PH REMARK 280 7.0, VAPOR DIFFUSION, TEMPERATURE 300K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+5/6 REMARK 290 6555 X-Y,X,Z+1/6 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 62.11333 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 124.22667 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 93.17000 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 155.28333 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 31.05667 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 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 GLY A 495 REMARK 465 ILE A 659 REMARK 465 PRO A 660 REMARK 465 TYR A 661 REMARK 465 THR A 662 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 LEU A 508 -58.31 -157.64 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 ACO A 401 DBREF 1Z4R A 497 662 UNP Q92830 GCNL2_HUMAN 497 662 SEQADV 1Z4R GLY A 495 UNP Q92830 CLONING ARTIFACT SEQADV 1Z4R SER A 496 UNP Q92830 CLONING ARTIFACT SEQRES 1 A 168 GLY SER GLY ILE ILE GLU PHE HIS VAL ILE GLY ASN SER SEQRES 2 A 168 LEU THR PRO LYS ALA ASN ARG ARG VAL LEU LEU TRP LEU SEQRES 3 A 168 VAL GLY LEU GLN ASN VAL PHE SER HIS GLN LEU PRO ARG SEQRES 4 A 168 MET PRO LYS GLU TYR ILE ALA ARG LEU VAL PHE ASP PRO SEQRES 5 A 168 LYS HIS LYS THR LEU ALA LEU ILE LYS ASP GLY ARG VAL SEQRES 6 A 168 ILE GLY GLY ILE CYS PHE ARG MET PHE PRO THR GLN GLY SEQRES 7 A 168 PHE THR GLU ILE VAL PHE CYS ALA VAL THR SER ASN GLU SEQRES 8 A 168 GLN VAL LYS GLY TYR GLY THR HIS LEU MET ASN HIS LEU SEQRES 9 A 168 LYS GLU TYR HIS ILE LYS HIS ASN ILE LEU TYR PHE LEU SEQRES 10 A 168 THR TYR ALA ASP GLU TYR ALA ILE GLY TYR PHE LYS LYS SEQRES 11 A 168 GLN GLY PHE SER LYS ASP ILE LYS VAL PRO LYS SER ARG SEQRES 12 A 168 TYR LEU GLY TYR ILE LYS ASP TYR GLU GLY ALA THR LEU SEQRES 13 A 168 MET GLU CYS GLU LEU ASN PRO ARG ILE PRO TYR THR HET ACO A 401 51 HETNAM ACO ACETYL COENZYME *A FORMUL 2 ACO C23 H38 N7 O17 P3 S FORMUL 3 HOH *131(H2 O) HELIX 1 1 ASN A 513 LEU A 531 1 19 HELIX 2 2 PRO A 535 PHE A 544 1 10 HELIX 3 3 SER A 583 GLN A 586 5 4 HELIX 4 4 GLY A 589 HIS A 605 1 17 HELIX 5 5 ASP A 615 TYR A 617 5 3 HELIX 6 6 ALA A 618 GLN A 625 1 8 HELIX 7 7 PRO A 634 LEU A 639 1 6 SHEET 1 A 7 ILE A 499 ILE A 504 0 SHEET 2 A 7 LYS A 549 LYS A 555 -1 O ALA A 552 N HIS A 502 SHEET 3 A 7 ARG A 558 PHE A 568 -1 O PHE A 565 N LYS A 549 SHEET 4 A 7 PHE A 573 VAL A 581 -1 O GLU A 575 N ARG A 566 SHEET 5 A 7 TYR A 609 ALA A 614 1 O LEU A 611 N ILE A 576 SHEET 6 A 7 THR A 649 GLU A 654 -1 O MET A 651 N THR A 612 SHEET 7 A 7 PHE A 627 SER A 628 -1 N SER A 628 O GLU A 652 SITE 1 AC1 34 HIS A 502 ALA A 512 ASN A 513 ARG A 515 SITE 2 AC1 34 TRP A 519 GLN A 530 LEU A 531 ILE A 576 SITE 3 AC1 34 VAL A 577 PHE A 578 CYS A 579 ALA A 580 SITE 4 AC1 34 VAL A 581 GLN A 586 VAL A 587 LYS A 588 SITE 5 AC1 34 GLY A 589 TYR A 590 GLY A 591 THR A 592 SITE 6 AC1 34 THR A 612 TYR A 613 ASP A 615 TYR A 617 SITE 7 AC1 34 GLY A 620 TYR A 621 LYS A 624 HOH A1002 SITE 8 AC1 34 HOH A1008 HOH A1013 HOH A1024 HOH A1033 SITE 9 AC1 34 HOH A1036 HOH A1044 CRYST1 38.090 38.090 186.340 90.00 90.00 120.00 P 61 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 0.026254 0.015158 0.000000 0.00000 SCALE2 0.000000 0.030315 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005367 0.00000