HEADER STRUCTURAL GENOMICS, UNKNOWN FUNCTION 23-OCT-06 2NN4 TITLE CRYSTAL STRUCTURE OF BACILLUS SUBTILIS YQGQ, PFAM DUF910 COMPND MOL_ID: 1; COMPND 2 MOLECULE: HYPOTHETICAL PROTEIN YQGQ; COMPND 3 CHAIN: A, B, C; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS SUBTILIS; SOURCE 3 ORGANISM_TAXID: 1423; SOURCE 4 GENE: YQGQ; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)-CODON+RIL; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PSGX4 (BS) KEYWDS NOVEL FOLD, PFAM:DUF910, 10278A, STRUCTURAL GENOMICS, PSI-2, PROTEIN KEYWDS 2 STRUCTURE INITIATIVE, NEW YORK SGX RESEARCH CENTER FOR STRUCTURAL KEYWDS 3 GENOMICS, NYSGXRC, UNKNOWN FUNCTION EXPDTA X-RAY DIFFRACTION AUTHOR L.DAMODHARAN,S.ESWARAMOORTHY,S.K.BURLEY,S.SWAMINATHAN,NEW YORK SGX AUTHOR 2 RESEARCH CENTER FOR STRUCTURAL GENOMICS (NYSGXRC) REVDAT 5 27-DEC-23 2NN4 1 REMARK REVDAT 4 03-FEB-21 2NN4 1 AUTHOR JRNL SEQADV REVDAT 3 24-OCT-12 2NN4 1 JRNL VERSN REVDAT 2 24-FEB-09 2NN4 1 VERSN REVDAT 1 31-OCT-06 2NN4 0 JRNL AUTH D.LAKSHMINARASIMHAN,S.ESWARAMOORTHY,S.K.BURLEY,S.SWAMINATHAN JRNL TITL STRUCTURE OF YQGQ PROTEIN FROM BACILLUS SUBTILIS, A JRNL TITL 2 CONSERVED HYPOTHETICAL PROTEIN. JRNL REF ACTA CRYSTALLOGR.,SECT.F V. 66 8 2010 JRNL REFN ESSN 1744-3091 JRNL PMID 20057058 JRNL DOI 10.1107/S1744309109047009 REMARK 2 REMARK 2 RESOLUTION. 2.10 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) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.59 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 127065.320 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 93.6 REMARK 3 NUMBER OF REFLECTIONS : 11871 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) : 0.247 REMARK 3 FREE R VALUE : 0.280 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 8.100 REMARK 3 FREE R VALUE TEST SET COUNT : 959 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.009 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) : 2.10 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.23 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 75.60 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1447 REMARK 3 BIN R VALUE (WORKING SET) : 0.3140 REMARK 3 BIN FREE R VALUE : 0.3690 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 8.10 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 128 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.033 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1590 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 47 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 17.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 38.10 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 3.42000 REMARK 3 B22 (A**2) : -6.56000 REMARK 3 B33 (A**2) : 3.15000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 6.15000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.31 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) : 0.38 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.34 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.017 REMARK 3 BOND ANGLES (DEGREES) : 1.800 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 17.60 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.930 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) : 1.550 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.490 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.440 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.850 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.39 REMARK 3 BSOL : 51.13 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 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE MISSING RESIDUES LISTED IN REMARK REMARK 3 465 ARE DUE TO LACK OF ELECTRON DENSITY. REMARK 4 REMARK 4 2NN4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 25-OCT-06. REMARK 100 THE DEPOSITION ID IS D_1000040064. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-OCT-06 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.2 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X25 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9801 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12344 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.5 REMARK 200 DATA REDUNDANCY : 6.500 REMARK 200 R MERGE (I) : 0.08000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.18 REMARK 200 COMPLETENESS FOR SHELL (%) : 84.7 REMARK 200 DATA REDUNDANCY IN SHELL : 3.90 REMARK 200 R MERGE FOR SHELL (I) : 0.37000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SOLVE, SHARP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.71 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.07 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.066M SODIUM DI-HYDROGEN PHOPHATE, REMARK 280 3.385M DI-POTASSIUM HYDROGEN PHOSPHATE, PH 8.2, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 278K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 20.62500 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3 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 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B 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 REMARK 350 BIOMOLECULE: 3 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: C 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 0 REMARK 465 LYS A 63 REMARK 465 ASN A 64 REMARK 465 GLY A 65 REMARK 465 ARG A 66 REMARK 465 ASP A 67 REMARK 465 PHE A 68 REMARK 465 TYR A 69 REMARK 465 LYS A 70 REMARK 465 GLY A 71 REMARK 465 SER B 0 REMARK 465 LYS B 63 REMARK 465 ASN B 64 REMARK 465 GLY B 65 REMARK 465 ARG B 66 REMARK 465 ASP B 67 REMARK 465 PHE B 68 REMARK 465 TYR B 69 REMARK 465 LYS B 70 REMARK 465 GLY B 71 REMARK 465 SER C 0 REMARK 465 LYS C 63 REMARK 465 ASN C 64 REMARK 465 GLY C 65 REMARK 465 ARG C 66 REMARK 465 ASP C 67 REMARK 465 PHE C 68 REMARK 465 TYR C 69 REMARK 465 LYS C 70 REMARK 465 GLY C 71 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 ASN C 2 28.00 -162.14 REMARK 500 HIS C 16 -133.74 58.86 REMARK 500 ILE C 17 82.86 74.90 REMARK 500 VAL C 18 -101.81 -50.07 REMARK 500 TYR C 19 87.81 78.48 REMARK 500 ASP C 22 108.32 -160.86 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: NYSGXRC-10278A RELATED DB: TARGETDB DBREF 2NN4 A 2 71 UNP P54494 YQGQ_BACSU 2 71 DBREF 2NN4 B 2 71 UNP P54494 YQGQ_BACSU 2 71 DBREF 2NN4 C 2 71 UNP P54494 YQGQ_BACSU 2 71 SEQADV 2NN4 SER A 0 UNP P54494 CLONING ARTIFACT SEQADV 2NN4 LEU A 1 UNP P54494 CLONING ARTIFACT SEQADV 2NN4 SER B 0 UNP P54494 CLONING ARTIFACT SEQADV 2NN4 LEU B 1 UNP P54494 CLONING ARTIFACT SEQADV 2NN4 SER C 0 UNP P54494 CLONING ARTIFACT SEQADV 2NN4 LEU C 1 UNP P54494 CLONING ARTIFACT SEQRES 1 A 72 SER LEU ASN THR PHE TYR ASP VAL GLN GLN LEU LEU LYS SEQRES 2 A 72 THR PHE GLY HIS ILE VAL TYR PHE GLY ASP ARG GLU LEU SEQRES 3 A 72 GLU ILE GLU PHE MET LEU ASP GLU LEU LYS GLU LEU TYR SEQRES 4 A 72 MET ASN HIS MET ILE GLU LYS GLU GLN TRP ALA ARG ALA SEQRES 5 A 72 ALA ALA VAL LEU ARG LYS GLU LEU GLU GLN THR LYS ASN SEQRES 6 A 72 GLY ARG ASP PHE TYR LYS GLY SEQRES 1 B 72 SER LEU ASN THR PHE TYR ASP VAL GLN GLN LEU LEU LYS SEQRES 2 B 72 THR PHE GLY HIS ILE VAL TYR PHE GLY ASP ARG GLU LEU SEQRES 3 B 72 GLU ILE GLU PHE MET LEU ASP GLU LEU LYS GLU LEU TYR SEQRES 4 B 72 MET ASN HIS MET ILE GLU LYS GLU GLN TRP ALA ARG ALA SEQRES 5 B 72 ALA ALA VAL LEU ARG LYS GLU LEU GLU GLN THR LYS ASN SEQRES 6 B 72 GLY ARG ASP PHE TYR LYS GLY SEQRES 1 C 72 SER LEU ASN THR PHE TYR ASP VAL GLN GLN LEU LEU LYS SEQRES 2 C 72 THR PHE GLY HIS ILE VAL TYR PHE GLY ASP ARG GLU LEU SEQRES 3 C 72 GLU ILE GLU PHE MET LEU ASP GLU LEU LYS GLU LEU TYR SEQRES 4 C 72 MET ASN HIS MET ILE GLU LYS GLU GLN TRP ALA ARG ALA SEQRES 5 C 72 ALA ALA VAL LEU ARG LYS GLU LEU GLU GLN THR LYS ASN SEQRES 6 C 72 GLY ARG ASP PHE TYR LYS GLY FORMUL 4 HOH *47(H2 O) HELIX 1 1 THR A 3 THR A 13 1 11 HELIX 2 2 ASP A 22 ASN A 40 1 19 HELIX 3 3 GLU A 44 THR A 62 1 19 HELIX 4 4 THR B 3 LYS B 12 1 10 HELIX 5 5 THR B 13 GLY B 15 5 3 HELIX 6 6 ASP B 22 ASN B 40 1 19 HELIX 7 7 GLU B 44 THR B 62 1 19 HELIX 8 8 THR C 3 THR C 13 1 11 HELIX 9 9 ASP C 22 ASN C 40 1 19 HELIX 10 10 GLU C 44 THR C 62 1 19 CRYST1 51.850 41.250 55.180 90.00 113.39 90.00 P 1 21 1 6 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 0.019285 0.000000 0.008342 0.00000 SCALE2 0.000000 0.024244 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019747 0.00000