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 <I/SIGMA(I)> 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 <I/SIGMA(I)> 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
(ATOM LINES ARE NOT SHOWN.)
END
