HEADER TRANSFERASE 16-DEC-04 1Y9W TITLE STRUCTURAL GENOMICS, 1.9A CRYSTAL STRUCTURE OF AN ACETYLTRANSFERASE TITLE 2 FROM BACILLUS CEREUS ATCC 14579 COMPND MOL_ID: 1; COMPND 2 MOLECULE: ACETYLTRANSFERASE; COMPND 3 CHAIN: A, B; COMPND 4 EC: 2.3.1.-; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS CEREUS; SOURCE 3 ORGANISM_TAXID: 226900; SOURCE 4 STRAIN: ATCC 14579; SOURCE 5 GENE: GI:29896479; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET15B KEYWDS BACILLUS CEREUS, ACETYLTRANSFERASE, STRUCTURAL GENOMICS, PROTEIN KEYWDS 2 STRUCTURE INITIATIVE, PSI, MIDWEST CENTER FOR STRUCTURAL GENOMICS, KEYWDS 3 MCSG, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR R.ZHANG,H.LI,F.COLLART,A.JOACHIMIAK,MIDWEST CENTER FOR STRUCTURAL AUTHOR 2 GENOMICS (MCSG) REVDAT 4 14-FEB-24 1Y9W 1 REMARK REVDAT 3 13-JUL-11 1Y9W 1 VERSN REVDAT 2 24-FEB-09 1Y9W 1 VERSN REVDAT 1 01-FEB-05 1Y9W 0 JRNL AUTH R.ZHANG,H.LI,F.COLLART,A.JOACHIMIAK JRNL TITL 1.9A CRYSTAL STRUCTURE OF AN ACETYLTRANSFERASE FROM BACILLUS JRNL TITL 2 CEREUS ATCC 14579 JRNL REF TO BE PUBLISHED 2005 JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.90 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 : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 26.80 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 293105.610 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 89.7 REMARK 3 NUMBER OF REFLECTIONS : 43982 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) : 0.202 REMARK 3 FREE R VALUE : 0.254 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2181 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.005 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) : 1.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.02 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 76.10 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 5899 REMARK 3 BIN R VALUE (WORKING SET) : 0.2900 REMARK 3 BIN FREE R VALUE : 0.2920 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.60 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 287 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.017 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2324 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 250 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 12.20 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.20 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.43000 REMARK 3 B22 (A**2) : -3.79000 REMARK 3 B33 (A**2) : 3.35000 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) : 0.26 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) : 0.28 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.18 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : 1.200 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 22.90 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.750 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 : 0.34 REMARK 3 BSOL : 48.78 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 : ION.PARAM REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1Y9W COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 17-DEC-04. REMARK 100 THE DEPOSITION ID IS D_1000031299. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-FEB-04 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 19-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9795,0.9797,0.94656 REMARK 200 MONOCHROMATOR : SI 111 CHANNEL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : SBC-2 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : SBCCOLLECT REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 45795 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.4 REMARK 200 DATA REDUNDANCY : 4.500 REMARK 200 R MERGE (I) : 0.07400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 30.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.97 REMARK 200 COMPLETENESS FOR SHELL (%) : 85.2 REMARK 200 DATA REDUNDANCY IN SHELL : 3.60 REMARK 200 R MERGE FOR SHELL (I) : 0.55800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.180 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.51 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.05M MGCL2, 0.1M HEPES, 30% PEG REMARK 280 MME550, PH 7.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K 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 27.51600 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 44.59650 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 32.67200 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 44.59650 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 27.51600 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 32.67200 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 300 REMARK: THIS PROTEIN EXISTED AS DIMER, THE MOL.A AND MOL.B REMARK 300 REPRESENT THE DIMER IN THE ASSYMMETRIC UNIT. 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: 5920 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14740 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -34.0 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 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 TYR A 2 10.76 -144.51 REMARK 500 TYR A 60 158.90 177.75 REMARK 500 PHE A 61 19.46 57.39 REMARK 500 HIS A 127 117.84 -160.60 REMARK 500 ALA B 109 62.23 64.39 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: BC2806 RELATED DB: TARGETDB DBREF 1Y9W A 1 140 UNP Q81CG1 Q81CG1_BACCR 1 140 DBREF 1Y9W B 1 140 UNP Q81CG1 Q81CG1_BACCR 1 140 SEQRES 1 A 140 MET TYR MET LYS HIS ILE GLU ASN GLY THR ARG ILE GLU SEQRES 2 A 140 GLY GLU TYR ILE LYS ASN LYS VAL ILE GLN TYR ASN MET SEQRES 3 A 140 SER ILE LEU THR ASP GLU VAL LYS GLN PRO MET GLU GLU SEQRES 4 A 140 VAL SER LEU VAL VAL LYS ASN GLU GLU GLY LYS ILE PHE SEQRES 5 A 140 GLY GLY VAL THR GLY THR MET TYR PHE TYR HIS LEU HIS SEQRES 6 A 140 ILE ASP PHE LEU TRP VAL ASP GLU SER VAL ARG HIS ASP SEQRES 7 A 140 GLY TYR GLY SER GLN LEU LEU HIS GLU ILE GLU GLY ILE SEQRES 8 A 140 ALA LYS GLU LYS GLY CYS ARG LEU ILE LEU LEU ASP SER SEQRES 9 A 140 PHE SER PHE GLN ALA PRO GLU PHE TYR LYS LYS HIS GLY SEQRES 10 A 140 TYR ARG GLU TYR GLY VAL VAL GLU ASP HIS PRO LYS GLY SEQRES 11 A 140 HIS SER GLN HIS PHE PHE GLU LYS ARG LEU SEQRES 1 B 140 MET TYR MET LYS HIS ILE GLU ASN GLY THR ARG ILE GLU SEQRES 2 B 140 GLY GLU TYR ILE LYS ASN LYS VAL ILE GLN TYR ASN MET SEQRES 3 B 140 SER ILE LEU THR ASP GLU VAL LYS GLN PRO MET GLU GLU SEQRES 4 B 140 VAL SER LEU VAL VAL LYS ASN GLU GLU GLY LYS ILE PHE SEQRES 5 B 140 GLY GLY VAL THR GLY THR MET TYR PHE TYR HIS LEU HIS SEQRES 6 B 140 ILE ASP PHE LEU TRP VAL ASP GLU SER VAL ARG HIS ASP SEQRES 7 B 140 GLY TYR GLY SER GLN LEU LEU HIS GLU ILE GLU GLY ILE SEQRES 8 B 140 ALA LYS GLU LYS GLY CYS ARG LEU ILE LEU LEU ASP SER SEQRES 9 B 140 PHE SER PHE GLN ALA PRO GLU PHE TYR LYS LYS HIS GLY SEQRES 10 B 140 TYR ARG GLU TYR GLY VAL VAL GLU ASP HIS PRO LYS GLY SEQRES 11 B 140 HIS SER GLN HIS PHE PHE GLU LYS ARG LEU FORMUL 3 HOH *250(H2 O) HELIX 1 1 THR A 10 ILE A 28 1 19 HELIX 2 2 LEU A 29 LYS A 34 5 6 HELIX 3 3 GLU A 73 ARG A 76 5 4 HELIX 4 4 GLY A 79 LYS A 95 1 17 HELIX 5 5 ALA A 109 HIS A 116 1 8 HELIX 6 6 THR B 10 LEU B 29 1 20 HELIX 7 7 THR B 30 LYS B 34 5 5 HELIX 8 8 GLU B 73 ARG B 76 5 4 HELIX 9 9 GLY B 79 LYS B 95 1 17 HELIX 10 10 ALA B 109 HIS B 116 1 8 SHEET 1 A 7 HIS A 5 ASN A 8 0 SHEET 2 A 7 GLU B 38 LYS B 45 -1 O VAL B 43 N GLU A 7 SHEET 3 A 7 ILE B 51 TYR B 60 -1 O MET B 59 N GLU B 38 SHEET 4 A 7 HIS B 63 VAL B 71 -1 O TRP B 70 N GLY B 54 SHEET 5 A 7 LEU B 99 PHE B 105 1 O LEU B 101 N LEU B 64 SHEET 6 A 7 GLN B 133 ARG B 139 -1 O PHE B 136 N LEU B 102 SHEET 7 A 7 ARG B 119 VAL B 124 -1 N ARG B 119 O GLU B 137 SHEET 1 B 7 ARG A 119 VAL A 124 0 SHEET 2 B 7 GLN A 133 ARG A 139 -1 O GLU A 137 N ARG A 119 SHEET 3 B 7 LEU A 99 PHE A 105 -1 N LEU A 102 O PHE A 136 SHEET 4 B 7 HIS A 63 VAL A 71 1 N LEU A 64 O LEU A 101 SHEET 5 B 7 ILE A 51 TYR A 60 -1 N GLY A 54 O TRP A 70 SHEET 6 B 7 GLU A 38 LYS A 45 -1 N GLU A 38 O MET A 59 SHEET 7 B 7 HIS B 5 ASN B 8 -1 O GLU B 7 N VAL A 43 CISPEP 1 HIS A 127 PRO A 128 0 -0.66 CISPEP 2 HIS B 127 PRO B 128 0 -0.51 CRYST1 55.032 65.344 89.193 90.00 90.00 90.00 P 21 21 21 8 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 0.018171 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015304 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011212 0.00000