HEADER STRUCTURAL GENOMICS, UNKNOWN FUNCTION 27-JUL-03 1Q2Y TITLE CRYSTAL STRUCTURE OF THE PROTEIN YJCF FROM BACILLUS SUBTILIS: A MEMBER TITLE 2 OF THE GCN5-RELATED N-ACETYLTRANSFERASE SUPERFAMILY FOLD COMPND MOL_ID: 1; COMPND 2 MOLECULE: SIMILAR TO HYPOTHETICAL PROTEINS; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PROTEIN YJCF; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS SUBTILIS; SOURCE 3 ORGANISM_TAXID: 1423; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS GCN5-RELATED N-ACETYLTRANSFERASE SUPERFAMILY FOLD, NYSGXRC, T804, KEYWDS 2 PSI, PROTEIN STRUCTURE INITIATIVE, NEW YORK SGX RESEARCH CENTER FOR KEYWDS 3 STRUCTURAL GENOMICS, STRUCTURAL GENOMICS, UNKNOWN FUNCTION EXPDTA X-RAY DIFFRACTION AUTHOR A.A.FEDOROV,U.A.RAMAGOPAL,E.V.FEDOROV,R.THIRUMURUHAN,S.C.ALMO, AUTHOR 2 S.K.BURLEY,NEW YORK SGX RESEARCH CENTER FOR STRUCTURAL GENOMICS AUTHOR 3 (NYSGXRC) REVDAT 6 21-FEB-24 1Q2Y 1 REMARK REVDAT 5 03-FEB-21 1Q2Y 1 AUTHOR REVDAT 4 24-FEB-09 1Q2Y 1 VERSN REVDAT 3 25-JAN-05 1Q2Y 1 AUTHOR KEYWDS REMARK REVDAT 2 18-NOV-03 1Q2Y 1 KEYWDS HEADER REVDAT 1 19-AUG-03 1Q2Y 0 JRNL AUTH A.A.FEDOROV,U.A.RAMAGOPAL,E.V.FEDOROV,R.THIRUMURUHAN, JRNL AUTH 2 S.C.ALMO JRNL TITL CRYSTAL STRUCTURE OF THE PROTEIN YJCF FROM BACILLUS JRNL TITL 2 SUBTILIS: A MEMBER OF THE GCN5-RELATED N-ACETYLTRANSFERASE JRNL TITL 3 SUPERFAMILY JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.0 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 15.00 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) (%) : 93.0 REMARK 3 NUMBER OF REFLECTIONS : 9584 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) : 0.234 REMARK 3 FREE R VALUE : 0.265 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.300 REMARK 3 FREE R VALUE TEST SET COUNT : 507 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.006 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 10 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.09 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 83.00 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1170 REMARK 3 BIN R VALUE (WORKING SET) : 0.2420 REMARK 3 BIN FREE R VALUE : 0.2940 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.00 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 29 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.021 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1101 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 36 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 39.20 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 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.26 REMARK 3 ESD FROM SIGMAA (A) : 0.12 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) : 0.32 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.22 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.360 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.50 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.720 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 3.260 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 5.110 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 5.980 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 9.300 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.41 REMARK 3 BSOL : 57.83 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 : ION.PARAM REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : ION.TOP REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1Q2Y COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 28-JUL-03. REMARK 100 THE DEPOSITION ID IS D_1000019849. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-FEB-03 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X9A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0088 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9584 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 15.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.0 REMARK 200 DATA REDUNDANCY : 4.100 REMARK 200 R MERGE (I) : 0.04800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 32.6000 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) : 2.09 REMARK 200 COMPLETENESS FOR SHELL (%) : 92.1 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.15300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 7.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MIR REMARK 200 SOFTWARE USED: SOLVE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.13 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.33 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 550, AMMONIUM TARTRATE, BISTRIS , REMARK 280 PH 6.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277K 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 17.63300 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 35.77800 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 29.64150 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 35.77800 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 17.63300 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 29.64150 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: THE BIOLOGICAL ASSEMBLY IS A MONOMER 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 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 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 VAL A 24 -60.31 -90.23 REMARK 500 GLN A 27 -132.67 -81.27 REMARK 500 ASN A 28 19.11 -153.41 REMARK 500 ALA A 31 -85.58 -5.18 REMARK 500 ASP A 129 -63.73 -95.53 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: NYSGXRC-T804 RELATED DB: TARGETDB DBREF 1Q2Y A 1 140 UNP O31628 O31628_BACSU 1 140 SEQRES 1 A 140 MET LYS ALA VAL ILE ALA LYS ASN GLU GLU GLN LEU LYS SEQRES 2 A 140 ASP ALA PHE TYR VAL ARG GLU GLU VAL PHE VAL LYS GLU SEQRES 3 A 140 GLN ASN VAL PRO ALA GLU GLU GLU ILE ASP GLU LEU GLU SEQRES 4 A 140 ASN GLU SER GLU HIS ILE VAL VAL TYR ASP GLY GLU LYS SEQRES 5 A 140 PRO VAL GLY ALA GLY ARG TRP ARG MET LYS ASP GLY TYR SEQRES 6 A 140 GLY LYS LEU GLU ARG ILE CYS VAL LEU LYS SER HIS ARG SEQRES 7 A 140 SER ALA GLY VAL GLY GLY ILE ILE MET LYS ALA LEU GLU SEQRES 8 A 140 LYS ALA ALA ALA ASP GLY GLY ALA SER GLY PHE ILE LEU SEQRES 9 A 140 ASN ALA GLN THR GLN ALA VAL PRO PHE TYR LYS LYS HIS SEQRES 10 A 140 GLY TYR ARG VAL LEU SER GLU LYS GLU PHE LEU ASP ALA SEQRES 11 A 140 GLY ILE PRO HIS LEU GLN MET MET LYS ASP FORMUL 2 HOH *36(H2 O) HELIX 1 1 ASN A 8 VAL A 24 1 17 HELIX 2 2 LEU A 38 SER A 42 5 5 HELIX 3 3 LEU A 74 ARG A 78 5 5 HELIX 4 4 GLY A 81 GLY A 97 1 17 HELIX 5 5 ALA A 110 HIS A 117 1 8 SHEET 1 A 7 LYS A 2 ALA A 6 0 SHEET 2 A 7 GLU A 43 ASP A 49 -1 O TYR A 48 N LYS A 2 SHEET 3 A 7 LYS A 52 LYS A 62 -1 O VAL A 54 N VAL A 47 SHEET 4 A 7 TYR A 65 CYS A 72 -1 O LYS A 67 N ARG A 60 SHEET 5 A 7 PHE A 102 GLN A 107 1 O ILE A 103 N LEU A 68 SHEET 6 A 7 PRO A 133 LYS A 139 -1 O LYS A 139 N PHE A 102 SHEET 7 A 7 ARG A 120 VAL A 121 -1 N ARG A 120 O MET A 138 SHEET 1 B 7 LYS A 2 ALA A 6 0 SHEET 2 B 7 GLU A 43 ASP A 49 -1 O TYR A 48 N LYS A 2 SHEET 3 B 7 LYS A 52 LYS A 62 -1 O VAL A 54 N VAL A 47 SHEET 4 B 7 TYR A 65 CYS A 72 -1 O LYS A 67 N ARG A 60 SHEET 5 B 7 PHE A 102 GLN A 107 1 O ILE A 103 N LEU A 68 SHEET 6 B 7 PRO A 133 LYS A 139 -1 O LYS A 139 N PHE A 102 SHEET 7 B 7 PHE A 127 LEU A 128 -1 N PHE A 127 O HIS A 134 CRYST1 35.266 59.283 71.556 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 0.028356 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016868 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013975 0.00000