HEADER STRUCTURAL GENOMICS, UNKNOWN FUNCTION 02-AUG-07 2QTI TITLE CRYSTAL STRUCTURE OF THE UPF0352 PROTEIN SO_2176 FROM SHEWANELLA TITLE 2 ONEIDENSIS. NESG TARGET SOR77. COMPND MOL_ID: 1; COMPND 2 MOLECULE: UPF0352 PROTEIN SO_2176; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SHEWANELLA ONEIDENSIS; SOURCE 3 ORGANISM_TAXID: 211586; SOURCE 4 STRAIN: MR-1; SOURCE 5 GENE: SO_2176; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)+MAGIC; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET21 KEYWDS Y2176_SHEON, UPF0352, SO_2176, PF07208, NESG, SOR77, STRUCTURAL KEYWDS 2 GENOMICS, PSI-2, PROTEIN STRUCTURE INITIATIVE, NORTHEAST STRUCTURAL KEYWDS 3 GENOMICS CONSORTIUM, UNKNOWN FUNCTION EXPDTA X-RAY DIFFRACTION AUTHOR S.M.VOROBIEV,M.SU,J.SEETHARAMAN,A.P.KUZIN,D.WANG,K.CUNNINGHAM, AUTHOR 2 L.OWENS,M.MAGLAQUI,Y.FANG,R.XIAO,T.B.ACTON,G.T.MONTELIONE,L.TONG, AUTHOR 3 J.F.HUNT,NORTHEAST STRUCTURAL GENOMICS CONSORTIUM (NESG) REVDAT 4 25-OCT-17 2QTI 1 REMARK REVDAT 3 13-JUL-11 2QTI 1 VERSN REVDAT 2 24-FEB-09 2QTI 1 VERSN REVDAT 1 21-AUG-07 2QTI 0 JRNL AUTH S.M.VOROBIEV,M.SU,J.SEETHARAMAN,A.P.KUZIN,D.WANG, JRNL AUTH 2 K.CUNNINGHAM,L.OWENS,M.MAGLAQUI,Y.FANG,R.XIAO,T.B.ACTON, JRNL AUTH 3 G.T.MONTELIONE,L.TONG,J.F.HUNT JRNL TITL CRYSTAL STRUCTURE OF THE UPF0352 PROTEIN SO_2176 FROM JRNL TITL 2 SHEWANELLA ONEIDENSIS. JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.30 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) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.32 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 74338.720 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 91.0 REMARK 3 NUMBER OF REFLECTIONS : 6260 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) : 0.223 REMARK 3 FREE R VALUE : 0.232 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.800 REMARK 3 FREE R VALUE TEST SET COUNT : 615 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) : 2.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.44 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 76.40 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 774 REMARK 3 BIN R VALUE (WORKING SET) : 0.2110 REMARK 3 BIN FREE R VALUE : 0.2060 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 10.70 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 93 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 : 498 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 19 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 24.90 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 44.30 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.28000 REMARK 3 B22 (A**2) : -1.28000 REMARK 3 B33 (A**2) : 2.56000 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) : 0.28 REMARK 3 ESD FROM SIGMAA (A) : 0.13 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) : 0.31 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.17 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : 1.000 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 16.60 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.720 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 : 0.40 REMARK 3 BSOL : 60.16 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 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : ION.TOP REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE FRIEDEL PAIRS WERE USED FOR PHASING REMARK 4 REMARK 4 2QTI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-AUG-07. REMARK 100 THE DEPOSITION ID IS D_1000044035. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-JUL-07 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.0 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) : 0.97913 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7182 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 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 (%) : 99.9 REMARK 200 DATA REDUNDANCY : 12.70 REMARK 200 R MERGE (I) : 0.08000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 41.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.38 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.4 REMARK 200 DATA REDUNDANCY IN SHELL : 8.00 REMARK 200 R MERGE FOR SHELL (I) : 0.52700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.470 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SNB, RESOLVE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.38 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.21 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 40% PEG 1000, 0.1M AMMONIUM PHOSPHATE, REMARK 280 0.1M SODIUM CITRATE PH 4.0, MICROBATCH UNDER OIL, TEMPERATURE REMARK 280 291.0K 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 31.26400 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 25.28800 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 25.28800 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 46.89600 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 25.28800 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 25.28800 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 15.63200 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 25.28800 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 25.28800 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 46.89600 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 25.28800 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 25.28800 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 15.63200 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 31.26400 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: DIMER BY GEL FILTRATION. THE SECOND PART OF THE BIOLOGICAL REMARK 300 ASSEMBLY IS GENERATED BY Y, X, -Z+1 SYMMETRY OPERATOR. 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 REMARK 350 TOTAL BURIED SURFACE AREA: 4180 ANGSTROM**2 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 62.52800 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 MSE A 1 REMARK 465 ALA A 2 REMARK 465 ILE A 3 REMARK 465 GLN A 4 REMARK 465 SER A 5 REMARK 465 LYS A 6 REMARK 465 TYR A 7 REMARK 465 HIS A 75 REMARK 465 HIS A 76 REMARK 465 HIS A 77 REMARK 465 HIS A 78 REMARK 465 HIS A 79 REMARK 465 HIS A 80 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 ASN A 9 CG OD1 ND2 REMARK 470 GLN A 11 CG CD OE1 NE2 REMARK 470 GLU A 74 CG CD OE1 OE2 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 SER A 51 -39.19 -39.98 REMARK 500 LEU A 73 49.62 -87.27 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: SOR77 RELATED DB: TARGETDB REMARK 900 RELATED ID: 2OTA RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF UPF0352 PROTEIN CPS_2611 FROM COLWELLIA REMARK 900 PSYCHRERYTHRAEA. NESG TARGET CSR4 (HOMOLOG PROTEIN) REMARK 900 RELATED ID: 2JR2 RELATED DB: PDB REMARK 900 SOLUTION NMR STRUCTURE OF HOMODIMER CPS_2611 FROM COLWELLIA REMARK 900 PSYCHRERYTHRAEA. NESG TARGET CSR4 (HOMOLOG PROTEIN) DBREF 2QTI A 1 72 UNP Q8EF26 Y2176_SHEON 1 72 SEQADV 2QTI LEU A 73 UNP Q8EF26 EXPRESSION TAG SEQADV 2QTI GLU A 74 UNP Q8EF26 EXPRESSION TAG SEQADV 2QTI HIS A 75 UNP Q8EF26 EXPRESSION TAG SEQADV 2QTI HIS A 76 UNP Q8EF26 EXPRESSION TAG SEQADV 2QTI HIS A 77 UNP Q8EF26 EXPRESSION TAG SEQADV 2QTI HIS A 78 UNP Q8EF26 EXPRESSION TAG SEQADV 2QTI HIS A 79 UNP Q8EF26 EXPRESSION TAG SEQADV 2QTI HIS A 80 UNP Q8EF26 EXPRESSION TAG SEQRES 1 A 80 MSE ALA ILE GLN SER LYS TYR SER ASN THR GLN VAL GLU SEQRES 2 A 80 SER LEU ILE ALA GLU ILE LEU VAL VAL LEU GLU LYS HIS SEQRES 3 A 80 LYS ALA PRO THR ASP LEU SER LEU MSE ALA LEU GLY ASN SEQRES 4 A 80 CYS VAL THR HIS LEU LEU GLU ARG LYS VAL PRO SER GLU SEQRES 5 A 80 SER ARG GLN ALA VAL ALA GLU GLN PHE ALA LYS ALA LEU SEQRES 6 A 80 ALA GLN SER VAL LYS SER ASN LEU GLU HIS HIS HIS HIS SEQRES 7 A 80 HIS HIS MODRES 2QTI MSE A 35 MET SELENOMETHIONINE HET MSE A 35 8 HETNAM MSE SELENOMETHIONINE FORMUL 1 MSE C5 H11 N O2 SE FORMUL 2 HOH *19(H2 O) HELIX 1 1 SER A 8 LYS A 27 1 20 HELIX 2 2 PRO A 29 VAL A 49 1 21 HELIX 3 3 PRO A 50 LEU A 73 1 24 LINK C LEU A 34 N MSE A 35 1555 1555 1.32 LINK C MSE A 35 N ALA A 36 1555 1555 1.33 CRYST1 50.576 50.576 62.528 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 0.019772 0.000000 0.000000 0.00000 SCALE2 0.000000 0.019772 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015993 0.00000