HEADER STRUCTURAL GENOMICS, UNKNOWN FUNCTION 10-OCT-08 3EUR TITLE CRYSTAL STRUCTURE OF THE C-TERMINAL DOMAIN OF UNCHARACTERIZED PROTEIN TITLE 2 FROM BACTEROIDES FRAGILIS NCTC 9343 COMPND MOL_ID: 1; COMPND 2 MOLECULE: UNCHARACTERIZED PROTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACTEROIDES FRAGILIS; SOURCE 3 ORGANISM_TAXID: 272559; SOURCE 4 STRAIN: NCTC 9343; SOURCE 5 GENE: BF1587; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21DE(3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PMCSG19 KEYWDS PSI2, MCSG, CONSERVED PROTEIN, STRUCTURAL GENOMICS, PROTEIN STRUCTURE KEYWDS 2 INITIATIVE, MIDWEST CENTER FOR STRUCTURAL GENOMICS, UNKNOWN FUNCTION EXPDTA X-RAY DIFFRACTION AUTHOR B.NOCEK,C.TESAR,G.COBB,A.JOACHIMIAK,MIDWEST CENTER FOR STRUCTURAL AUTHOR 2 GENOMICS (MCSG) REVDAT 4 16-OCT-24 3EUR 1 REMARK REVDAT 3 27-DEC-23 3EUR 1 SEQADV LINK REVDAT 2 13-JUL-11 3EUR 1 VERSN REVDAT 1 02-DEC-08 3EUR 0 JRNL AUTH B.NOCEK,C.TESAR,G.COBB,A.JOACHIMIAK JRNL TITL CRYSTAL STRUCTURE OF THE C-TERMINAL DOMAIN OF JRNL TITL 2 UNCHARACTERIZED PROTEIN FROM BACTEROIDES FRAGILIS NCTC 9343 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 49.33 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 91.1 REMARK 3 NUMBER OF REFLECTIONS : 31061 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 + TEST SET) : 0.140 REMARK 3 R VALUE (WORKING SET) : 0.139 REMARK 3 FREE R VALUE : 0.170 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1646 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.33 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1263 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 50.94 REMARK 3 BIN R VALUE (WORKING SET) : 0.1760 REMARK 3 BIN FREE R VALUE SET COUNT : 70 REMARK 3 BIN FREE R VALUE : 0.2200 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1128 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 230 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 12.08 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.17000 REMARK 3 B22 (A**2) : 0.29000 REMARK 3 B33 (A**2) : -0.46000 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 OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.053 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.050 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.023 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.152 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.972 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.963 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1232 ; 0.019 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 830 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1687 ; 1.711 ; 1.978 REMARK 3 BOND ANGLES OTHERS (DEGREES): 2063 ; 1.019 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 163 ; 6.242 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 57 ;41.543 ;25.965 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 232 ;12.804 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 3 ;14.410 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 190 ; 0.120 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1388 ; 0.009 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 233 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 746 ; 1.856 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 297 ; 0.869 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1217 ; 2.858 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 486 ; 3.709 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 462 ; 5.331 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): 2062 ; 1.650 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 236 ;10.178 ; 3.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 2027 ; 4.678 ; 3.000 REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 3EUR COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-OCT-08. REMARK 100 THE DEPOSITION ID IS D_1000049791. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-SEP-08 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-BM REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9794 REMARK 200 MONOCHROMATOR : SI CRYSTAL 111 REMARK 200 OPTICS : MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : SBC-3 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 32763 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.300 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 91.2 REMARK 200 DATA REDUNDANCY : 8.000 REMARK 200 R MERGE (I) : 0.04300 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 44.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.33 REMARK 200 COMPLETENESS FOR SHELL (%) : 50.0 REMARK 200 DATA REDUNDANCY IN SHELL : 4.00 REMARK 200 R MERGE FOR SHELL (I) : 0.15000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 5.140 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: HKL-3000, MLPHARE, SHELX, PHENIX, REFMAC REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.74 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.19 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M POTASSIUM SODIUM TARTRATE REMARK 280 TETRAHYDRATE 20% PEG 3350, PH 7.5, VAPOR DIFFUSION, SITTING DROP, REMARK 280 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 16.57250 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 49.34600 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 21.71400 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 49.34600 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 16.57250 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 21.71400 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 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 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 SER A -2 REMARK 465 ASN A -1 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 ASP A 73 -169.88 -103.69 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: APC61442.2 RELATED DB: TARGETDB DBREF 3EUR A 1 139 UNP Q5LF10 Q5LF10_BACFN 171 309 SEQADV 3EUR SER A -2 UNP Q5LF10 EXPRESSION TAG SEQADV 3EUR ASN A -1 UNP Q5LF10 EXPRESSION TAG SEQADV 3EUR ALA A 0 UNP Q5LF10 EXPRESSION TAG SEQRES 1 A 142 SER ASN ALA LYS ASN ARG LEU GLY THR LYS ALA LEU ASN SEQRES 2 A 142 PHE THR TYR THR LEU ASP SER GLY VAL LYS GLY THR LEU SEQRES 3 A 142 TYR GLN PHE PRO ALA GLU TYR THR LEU LEU PHE ILE ASN SEQRES 4 A 142 ASN PRO GLY CYS HIS ALA CYS ALA GLU MSE ILE GLU GLY SEQRES 5 A 142 LEU LYS ALA SER PRO VAL ILE ASN GLY PHE THR ALA ALA SEQRES 6 A 142 LYS LYS LEU LYS VAL LEU SER ILE TYR PRO ASP GLU GLU SEQRES 7 A 142 LEU ASP GLU TRP LYS LYS HIS ARG ASN ASP PHE ALA LYS SEQRES 8 A 142 GLU TRP THR ASN GLY TYR ASP LYS GLU LEU VAL ILE LYS SEQRES 9 A 142 ASN LYS ASN LEU TYR ASP LEU ARG ALA ILE PRO THR LEU SEQRES 10 A 142 TYR LEU LEU ASP LYS ASN LYS THR VAL LEU LEU LYS ASP SEQRES 11 A 142 ALA THR LEU GLN LYS VAL GLU GLN TYR LEU ALA GLU MODRES 3EUR MSE A 46 MET SELENOMETHIONINE HET MSE A 46 16 HETNAM MSE SELENOMETHIONINE FORMUL 1 MSE C5 H11 N O2 SE FORMUL 2 HOH *230(H2 O) HELIX 1 1 CYS A 40 SER A 53 1 14 HELIX 2 2 SER A 53 ALA A 62 1 10 HELIX 3 3 GLU A 75 ARG A 83 1 9 HELIX 4 4 ASN A 84 PHE A 86 5 3 HELIX 5 5 LEU A 98 LYS A 103 1 6 HELIX 6 6 THR A 129 GLU A 139 1 11 SHEET 1 A 7 LYS A 20 THR A 22 0 SHEET 2 A 7 THR A 12 LEU A 15 -1 N TYR A 13 O GLY A 21 SHEET 3 A 7 THR A 91 TYR A 94 -1 O TYR A 94 N THR A 14 SHEET 4 A 7 LEU A 65 TYR A 71 1 N SER A 69 O THR A 91 SHEET 5 A 7 TYR A 30 ILE A 35 1 N PHE A 34 O LEU A 68 SHEET 6 A 7 THR A 113 LEU A 117 -1 O LEU A 117 N THR A 31 SHEET 7 A 7 VAL A 123 ALA A 128 -1 O LEU A 124 N LEU A 116 LINK C GLU A 45 N AMSE A 46 1555 1555 1.33 LINK C GLU A 45 N BMSE A 46 1555 1555 1.33 LINK C AMSE A 46 N ILE A 47 1555 1555 1.34 LINK C BMSE A 46 N ILE A 47 1555 1555 1.33 CISPEP 1 ILE A 111 PRO A 112 0 5.09 CISPEP 2 ILE A 111 PRO A 112 0 10.35 CRYST1 33.145 43.428 98.692 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 0.030170 0.000000 0.000000 0.00000 SCALE2 0.000000 0.023027 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010133 0.00000