HEADER STRUCTURAL GENOMICS, UNKNOWN FUNCTION 01-JUL-04 1TWU TITLE 2.0 A CRYSTAL STRUCTURE OF A YYCE PROTEIN OF UNKNOWN FUNCTION FROM TITLE 2 BACILLUS SUBTILIS, PUTATIVE GLYOXALASE/FOSFOMYCIN RESISTANCE PROTEIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: HYPOTHETICAL PROTEIN YYCE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS SUBTILIS; SOURCE 3 ORGANISM_TAXID: 1423; SOURCE 4 STRAIN: 168; SOURCE 5 GENE: YYCE OR BSU40430; 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: PDM68 KEYWDS STRUCTURAL GENOMICS, PROTEIN STRUCTURE INITIATIVE, MCSG, DUPLICATION KEYWDS 2 OF THE ALPHA-BETA SANDWICHS. BACILLUS SUBTILIS, PSI, MIDWEST CENTER KEYWDS 3 FOR STRUCTURAL GENOMICS, UNKNOWN FUNCTION EXPDTA X-RAY DIFFRACTION AUTHOR R.ZHANG,P.QUARTEY,F.COLLART,A.JOACHIMIAK,MIDWEST CENTER FOR AUTHOR 2 STRUCTURAL GENOMICS (MCSG) REVDAT 4 13-JUL-11 1TWU 1 VERSN REVDAT 3 24-FEB-09 1TWU 1 VERSN REVDAT 2 18-JAN-05 1TWU 1 AUTHOR KEYWDS REMARK REVDAT 1 17-AUG-04 1TWU 0 JRNL AUTH R.ZHANG,P.QUARTEY,F.COLLART,A.JOACHIMIAK JRNL TITL 2.0 A CRYSTAL STRUCTURE OF A HYPOTHETICAL PROTEIN YYCE FROM JRNL TITL 2 BACILLUS SUBTILIS JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.55 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 269090.610 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 92.0 REMARK 3 NUMBER OF REFLECTIONS : 24172 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) : 0.207 REMARK 3 FREE R VALUE : 0.233 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 1155 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.007 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) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.13 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 73.60 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 3080 REMARK 3 BIN R VALUE (WORKING SET) : 0.2980 REMARK 3 BIN FREE R VALUE : 0.3300 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.80 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 154 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.027 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1089 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 79 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 16.40 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 33.90 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 5.58000 REMARK 3 B22 (A**2) : 5.58000 REMARK 3 B33 (A**2) : -11.15000 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) : 0.26 REMARK 3 ESD FROM SIGMAA (A) : 0.29 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) : 0.24 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : 1.40 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 24.70 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.80 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 : 0.36 REMARK 3 BSOL : 52.12 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 1TWU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-JUL-04. REMARK 100 THE RCSB ID CODE IS RCSB022982. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-JUN-04 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 19-BM REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9795 REMARK 200 MONOCHROMATOR : SI 111 CHANNEL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : SBC-3 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : SBCCOLLECT REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25357 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 4.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.5 REMARK 200 DATA REDUNDANCY : 5.200 REMARK 200 R MERGE (I) : 0.06200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 23.7000 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) : 2.07 REMARK 200 COMPLETENESS FOR SHELL (%) : 75.6 REMARK 200 DATA REDUNDANCY IN SHELL : 3.60 REMARK 200 R MERGE FOR SHELL (I) : 0.28700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD 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 (%): 60.27 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.21 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: VAPOR DIFFUSION, SITTING DROP REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 56.10400 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 29.88650 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 29.88650 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 84.15600 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 29.88650 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 29.88650 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 28.05200 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 29.88650 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 29.88650 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 84.15600 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 29.88650 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 29.88650 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 28.05200 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 56.10400 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 EXISTS AS DIMER.THE SECOND PART OF THE REMARK 300 BIOLOGICAL ASSEMBLY IS GENERATED BY THE TWO FOLD AXIS:-X,-Y,-Z 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,PQS REMARK 350 TOTAL BURIED SURFACE AREA: 5000 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11940 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -31.0 KCAL/MOL 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 350 BIOMT1 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 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 MET A 1 REMARK 465 GLY A 2 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 HIS A 56 -155.15 -113.35 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: APC1848 RELATED DB: TARGETDB DBREF 1TWU A 1 139 UNP P37479 YYCE_BACSU 1 139 SEQRES 1 A 139 MET GLY LYS ARG PHE SER SER PHE GLN ALA ALA GLN ILE SEQRES 2 A 139 ARG ILE ALA ARG PRO THR GLY GLN LEU ASP GLU ILE ILE SEQRES 3 A 139 ARG PHE TYR GLU GLU GLY LEU CYS LEU LYS ARG ILE GLY SEQRES 4 A 139 GLU PHE SER GLN HIS ASN GLY TYR ASP GLY VAL MET PHE SEQRES 5 A 139 GLY LEU PRO HIS ALA ASP TYR HIS LEU GLU PHE THR GLN SEQRES 6 A 139 TYR GLU GLY GLY SER THR ALA PRO VAL PRO HIS PRO ASP SEQRES 7 A 139 SER LEU LEU VAL PHE TYR VAL PRO ASN ALA VAL GLU LEU SEQRES 8 A 139 ALA ALA ILE THR SER LYS LEU LYS HIS MET GLY TYR GLN SEQRES 9 A 139 GLU VAL GLU SER GLU ASN PRO TYR TRP SER ASN GLY GLY SEQRES 10 A 139 VAL THR ILE GLU ASP PRO ASP GLY TRP ARG ILE VAL PHE SEQRES 11 A 139 MET ASN SER LYS GLY ILE SER GLY LYS FORMUL 2 HOH *79(H2 O) HELIX 1 1 GLN A 21 GLU A 30 1 10 HELIX 2 2 ASN A 87 MET A 101 1 15 HELIX 3 3 ASN A 110 ASN A 115 1 6 SHEET 1 A 4 ILE A 13 PRO A 18 0 SHEET 2 A 4 TYR A 59 TYR A 66 1 O GLU A 62 N ARG A 17 SHEET 3 A 4 TYR A 47 GLY A 53 -1 N PHE A 52 O LEU A 61 SHEET 4 A 4 ARG A 37 HIS A 44 -1 N GLY A 39 O MET A 51 SHEET 1 B 4 LEU A 80 TYR A 84 0 SHEET 2 B 4 ARG A 127 MET A 131 1 O VAL A 129 N PHE A 83 SHEET 3 B 4 GLY A 117 GLU A 121 -1 N ILE A 120 O ILE A 128 SHEET 4 B 4 GLU A 105 VAL A 106 -1 N VAL A 106 O THR A 119 CISPEP 1 LEU A 54 PRO A 55 0 -0.01 CRYST1 59.773 59.773 112.208 90.00 90.00 90.00 P 43 21 2 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 0.016730 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016730 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008912 0.00000 MASTER 269 0 0 3 8 0 0 6 0 0 0 11 END