HEADER STRUCTURAL GENOMICS, UNKNOWN FUNCTION 23-JUL-14 4QY7 TITLE CRYSTAL STRUCTURE OF A YOBA PROTEIN (BSU18810) FROM BACILLUS SUBTILIS TITLE 2 SUBSP. SUBTILIS STR. 168 AT 1.55 A RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: UNCHARACTERIZED PROTEIN YOBA; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS SUBTILIS SUBSP. SUBTILIS STR. 168; SOURCE 3 ORGANISM_TAXID: 224308; SOURCE 4 STRAIN: 168; SOURCE 5 GENE: YOBA, BSU18810; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: PB1; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: SPEEDET KEYWDS PF11518 FAMILY PROTEIN, DUF3221, OB-FOLD, STRUCTURAL GENOMICS, JOINT KEYWDS 2 CENTER FOR STRUCTURAL GENOMICS, JCSG, PROTEIN STRUCTURE INITIATIVE, KEYWDS 3 PSI-BIOLOGY, UNKNOWN FUNCTION EXPDTA X-RAY DIFFRACTION AUTHOR JOINT CENTER FOR STRUCTURAL GENOMICS (JCSG) REVDAT 4 01-FEB-23 4QY7 1 REMARK SEQADV LINK REVDAT 3 22-NOV-17 4QY7 1 REMARK REVDAT 2 24-DEC-14 4QY7 1 TITLE REVDAT 1 20-AUG-14 4QY7 0 JRNL AUTH JOINT CENTER FOR STRUCTURAL GENOMICS (JCSG) JRNL TITL CRYSTAL STRUCTURE OF A HYPOTHETICAL PROTEIN (YOBA) FROM JRNL TITL 2 BACILLUS SUBTILIS SUBSP. SUBTILIS STR. 168 AT 1.55 A JRNL TITL 3 RESOLUTION JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.55 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : BUSTER-TNT 2.10.0 REMARK 3 AUTHORS : BRICOGNE,BLANC,BRANDL,FLENSBURG,KELLER, REMARK 3 : PACIOREK,ROVERSI,SMART,VONRHEIN,WOMACK, REMARK 3 : MATTHEWS,TEN EYCK,TRONRUD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.55 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.75 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 12850 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) : 0.192 REMARK 3 R VALUE (WORKING SET) : 0.190 REMARK 3 FREE R VALUE : 0.223 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.880 REMARK 3 FREE R VALUE TEST SET COUNT : 627 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 1.55 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 1.70 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.24 REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 2969 REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.2085 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2811 REMARK 3 BIN R VALUE (WORKING SET) : 0.2077 REMARK 3 BIN FREE R VALUE : 0.2232 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.32 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 158 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 730 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 7 REMARK 3 SOLVENT ATOMS : 89 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 21.03 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.83 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.75430 REMARK 3 B22 (A**2) : -0.89360 REMARK 3 B33 (A**2) : 2.64790 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) : 0.232 REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : NULL REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : NULL REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : NULL REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : NULL REMARK 3 REMARK 3 REFERENCES: BLOW, D. (2002) ACTA CRYST D58, 792-797 REMARK 3 CRUICKSHANK, D.W.J. (1999) ACTA CRYST D55, 583-601 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.957 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.939 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 1645 ; 2.000 ; HARMONIC REMARK 3 BOND ANGLES : 3011 ; 2.000 ; HARMONIC REMARK 3 TORSION ANGLES : 486 ; 2.000 ; SINUSOIDAL REMARK 3 TRIGONAL CARBON PLANES : 26 ; 2.000 ; HARMONIC REMARK 3 GENERAL PLANES : 243 ; 5.000 ; HARMONIC REMARK 3 ISOTROPIC THERMAL FACTORS : 1645 ; 20.000 ; HARMONIC REMARK 3 BAD NON-BONDED CONTACTS : 0 ; 5.000 ; SEMIHARMONIC REMARK 3 IMPROPER TORSIONS : NULL ; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES : NULL ; NULL ; NULL REMARK 3 CHIRAL IMPROPER TORSION : 110 ; 5.000 ; SEMIHARMONIC REMARK 3 SUM OF OCCUPANCIES : NULL ; NULL ; NULL REMARK 3 UTILITY DISTANCES : NULL ; NULL ; NULL REMARK 3 UTILITY ANGLES : NULL ; NULL ; NULL REMARK 3 UTILITY TORSION : NULL ; NULL ; NULL REMARK 3 IDEAL-DIST CONTACT TERM : 1872 ; 4.000 ; SEMIHARMONIC REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 1.08 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 3.87 REMARK 3 OTHER TORSION ANGLES (DEGREES) : 2.96 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: A 0 A 120 REMARK 3 ORIGIN FOR THE GROUP (A): 7.7967 7.1928 8.7526 REMARK 3 T TENSOR REMARK 3 T11: -0.0511 T22: -0.0311 REMARK 3 T33: -0.0591 T12: -0.0216 REMARK 3 T13: -0.0052 T23: 0.0031 REMARK 3 L TENSOR REMARK 3 L11: 1.3475 L22: 1.4624 REMARK 3 L33: 2.5841 L12: -0.6103 REMARK 3 L13: 0.1497 L23: 0.4900 REMARK 3 S TENSOR REMARK 3 S11: 0.0620 S12: 0.0001 S13: 0.0116 REMARK 3 S21: -0.0663 S22: 0.0031 S23: 0.0131 REMARK 3 S31: 0.0350 S32: -0.1071 S33: -0.0651 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: 1. ZERO OCCUPANCY HYDROGENS WERE REMARK 3 INCLUDED DURING REFINEMENT TO IMPROVE THE ANTI-BUMPING REMARK 3 RESTRAINTS. 2. ATOM RECORDS CONTAIN SUM OF TLS AND RESIDUAL B REMARK 3 FACTORS. 3. ANISOU RECORDS CONTAIN SUM OF TLS AND RESIDUAL U REMARK 3 FACTORS. 4. A MET-INHIBITION PROTOCOL WAS USED FOR REMARK 3 SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE REMARK 3 OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO REMARK 3 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET REMARK 3 INCORPORATION. 5. MAD PHASE RESTRAINTS WERE USED DURING REMARK 3 REFINEMENT. 6. NONAETHYLENE GLYCOL (2PE) MOLECULE FROM THE REMARK 3 CRYSTALLIZATION SOLUTION ARE MODELED. REMARK 4 REMARK 4 4QY7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 25-JUL-14. REMARK 100 THE DEPOSITION ID IS D_1000086662. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-JUN-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL14-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.95369,0.97937,0.97922 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL SI(111) REMARK 200 OPTICS : VERTICAL FOCUSING MIRROR; DOUBLE REMARK 200 CRYSTAL SI(111) MONOCHROMATOR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 325 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE JANUARY 10, 2014 REMARK 200 BUILT=20140307 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12907 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.550 REMARK 200 RESOLUTION RANGE LOW (A) : 27.746 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.3 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.03100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.8300 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.55 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.61 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.5 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.52100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: SHELX, SHARP, SHELXD REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.15 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.99 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 5.00% POLYETHYLENE GLYCOL 3000, 40.00% REMARK 280 POLYETHYLENE GLYCOL 400, 0.1M MES PH 6.0, NANODROP, VAPOR REMARK 280 DIFFUSION, SITTING 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 13.77800 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 40.62250 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 18.99400 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 40.62250 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 13.77800 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 18.99400 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: CRYSTAL PACKING ANALYSIS SUGGESTS THE ASSIGNMENT OF A REMARK 300 MONOMER AS THE SIGNIFICANT OLIGOMERIZATION STATE. 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 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 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 ASP A 29 CG OD1 OD2 REMARK 470 GLU A 30 CG CD OE1 OE2 REMARK 470 LYS A 32 CG CD CE NZ REMARK 470 ASP A 53 CG OD1 OD2 REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 2PE A 200 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 2PE A 200 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: JCSG-418978 RELATED DB: TARGETTRACK REMARK 999 REMARK 999 SEQUENCE REMARK 999 THIS CONSTRUCT WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG REMARK 999 MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING REMARK 999 ONLY A GLYCINE (0) FOLLOWED BY RESIDUES 29-120 OF THE TARGET REMARK 999 SEQUENCE. DBREF 4QY7 A 29 120 UNP O31835 YOBA_BACSU 29 120 SEQADV 4QY7 GLY A 0 UNP O31835 EXPRESSION TAG SEQRES 1 A 93 GLY ASP GLU THR LYS MSE GLN SER LEU VAL GLY TYR VAL SEQRES 2 A 93 VAL LEU LYS ASP ASN GLU ARG ALA ILE LEU ILE THR ASP SEQRES 3 A 93 THR LYS ALA PRO GLY LYS GLU ASP TYR ASN LEU SER GLU SEQRES 4 A 93 GLY GLN LEU MSE ASN LYS PHE LYS ASN ASN ILE VAL ILE SEQRES 5 A 93 VAL GLY LEU SER GLU ILE ASP ASN THR ASP ASP LEU LYS SEQRES 6 A 93 ARG GLY GLU LYS ILE LYS VAL TRP PHE HIS THR ARG LYS SEQRES 7 A 93 GLU SER ASN PRO PRO SER ALA THR ILE GLN LYS TYR GLU SEQRES 8 A 93 LEU LEU MODRES 4QY7 MSE A 33 MET SELENOMETHIONINE MODRES 4QY7 MSE A 70 MET SELENOMETHIONINE HET MSE A 33 8 HET MSE A 70 13 HET 2PE A 200 7 HETNAM MSE SELENOMETHIONINE HETNAM 2PE NONAETHYLENE GLYCOL FORMUL 1 MSE 2(C5 H11 N O2 SE) FORMUL 2 2PE C18 H38 O10 FORMUL 3 HOH *89(H2 O) HELIX 1 1 GLY A 58 LEU A 64 5 7 HELIX 2 2 SER A 65 PHE A 73 1 9 SHEET 1 A 6 SER A 111 THR A 113 0 SHEET 2 A 6 ILE A 77 GLY A 81 1 N GLY A 81 O ALA A 112 SHEET 3 A 6 ARG A 47 ILE A 51 -1 N LEU A 50 O VAL A 78 SHEET 4 A 6 GLN A 34 LYS A 43 -1 N VAL A 41 O ILE A 49 SHEET 5 A 6 LYS A 96 PHE A 101 -1 O ILE A 97 N GLY A 38 SHEET 6 A 6 LYS A 116 LEU A 120 -1 O LEU A 120 N LYS A 96 LINK C LYS A 32 N MSE A 33 1555 1555 1.35 LINK C MSE A 33 N GLN A 34 1555 1555 1.33 LINK C LEU A 69 N MSE A 70 1555 1555 1.38 LINK C MSE A 70 N ASN A 71 1555 1555 1.34 CISPEP 1 ASN A 108 PRO A 109 0 0.33 SITE 1 AC1 4 TRP A 100 LYS A 116 GLU A 118 HOH A 387 CRYST1 27.556 37.988 81.245 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 0.036290 0.000000 0.000000 0.00000 SCALE2 0.000000 0.026324 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012308 0.00000