HEADER STRUCTURAL GENOMICS, UNKNOWN FUNCTION 03-DEC-10 3PU6 TITLE THE CRYSTAL STRUCTURE OF AN UNCHARACTERIZED PROTEIN FROM WOLINELLA TITLE 2 SUCCINOGENES 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: WOLINELLA SUCCINOGENES; SOURCE 3 ORGANISM_TAXID: 844; SOURCE 4 GENE: WS1834; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3) - CODON+RIL (P) -STRATAGENE; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: BC-PSGX3 KEYWDS STRUCTURAL GENOMICS, PSI-2, PROTEIN STRUCTURE INITIATIVE, NEW YORK KEYWDS 2 SGX RESEARCH CENTER FOR STRUCTURAL GENOMICS, NYSGXRC, PSI, UNKNOWN KEYWDS 3 FUNCTION EXPDTA X-RAY DIFFRACTION AUTHOR Z.ZHANG,S.K.BURLEY,S.SWAMINATHAN,NEW YORK SGX RESEARCH CENTER FOR AUTHOR 2 STRUCTURAL GENOMICS (NYSGXRC) REVDAT 2 10-FEB-21 3PU6 1 AUTHOR JRNL SEQADV LINK REVDAT 1 19-JAN-11 3PU6 0 JRNL AUTH Z.ZHANG,S.K.BURLEY,S.SWAMINATHAN JRNL TITL THE CRYSTAL STRUCTURE OF AN UNCHARACTERIZED PROTEIN FROM JRNL TITL 2 WOLINELLA SUCCINOGENES JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.37 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.080 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 5005 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.227 REMARK 3 R VALUE (WORKING SET) : 0.224 REMARK 3 FREE R VALUE : 0.275 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.600 REMARK 3 FREE R VALUE TEST SET COUNT : 230 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 40.3767 - 3.2755 1.00 2471 110 0.2135 0.2519 REMARK 3 2 3.2755 - 2.6000 0.99 2304 120 0.2466 0.3220 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : 0.38 REMARK 3 B_SOL : 54.54 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.490 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 29.100 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 47.45 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -12.72660 REMARK 3 B22 (A**2) : 23.05070 REMARK 3 B33 (A**2) : -10.32410 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 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.010 1078 REMARK 3 ANGLE : 1.179 1453 REMARK 3 CHIRALITY : 0.067 170 REMARK 3 PLANARITY : 0.005 183 REMARK 3 DIHEDRAL : 17.018 391 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3PU6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 16-DEC-10. REMARK 100 THE DEPOSITION ID IS D_1000062815. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-DEC-10 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 : NSLS REMARK 200 BEAMLINE : X29A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9791 REMARK 200 MONOCHROMATOR : SI 111 CHANNEL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 5065 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.600 REMARK 200 RESOLUTION RANGE LOW (A) : 66.680 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 7.300 REMARK 200 R MERGE (I) : 0.06900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.74 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.6 REMARK 200 DATA REDUNDANCY IN SHELL : 7.30 REMARK 200 R MERGE FOR SHELL (I) : 0.27300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 13.60 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SOLVE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.29 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.17 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M SODIUM FORMATE, 20% W/V PEG REMARK 280 3350, PH 7.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 291K 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 22.60100 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 33.33800 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 25.36400 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 33.33800 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 22.60100 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 25.36400 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 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 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 SER A 0 REMARK 465 PHE A 66 REMARK 465 LYS A 67 REMARK 465 GLU A 68 REMARK 465 GLY A 69 REMARK 465 SER A 85 REMARK 465 THR A 86 REMARK 465 HIS A 87 REMARK 465 ASN A 88 REMARK 465 LEU A 89 REMARK 465 GLU A 148 REMARK 465 GLY A 149 REMARK 465 HIS A 150 REMARK 465 HIS A 151 REMARK 465 HIS A 152 REMARK 465 HIS A 153 REMARK 465 HIS A 154 REMARK 465 HIS A 155 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 GLU A 70 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 ASP A 15 3.33 -67.98 REMARK 500 TYR A 39 -120.60 41.21 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: NYSGXRC-11294B RELATED DB: TARGETDB DBREF 3PU6 A 2 147 UNP Q7MR08 Q7MR08_WOLSU 2 147 SEQADV 3PU6 MSE A -1 UNP Q7MR08 EXPRESSION TAG SEQADV 3PU6 SER A 0 UNP Q7MR08 EXPRESSION TAG SEQADV 3PU6 LEU A 1 UNP Q7MR08 EXPRESSION TAG SEQADV 3PU6 GLU A 148 UNP Q7MR08 EXPRESSION TAG SEQADV 3PU6 GLY A 149 UNP Q7MR08 EXPRESSION TAG SEQADV 3PU6 HIS A 150 UNP Q7MR08 EXPRESSION TAG SEQADV 3PU6 HIS A 151 UNP Q7MR08 EXPRESSION TAG SEQADV 3PU6 HIS A 152 UNP Q7MR08 EXPRESSION TAG SEQADV 3PU6 HIS A 153 UNP Q7MR08 EXPRESSION TAG SEQADV 3PU6 HIS A 154 UNP Q7MR08 EXPRESSION TAG SEQADV 3PU6 HIS A 155 UNP Q7MR08 EXPRESSION TAG SEQRES 1 A 157 MSE SER LEU LYS LYS VAL LEU LEU CYS VAL GLY ASN GLU SEQRES 2 A 157 LEU ARG GLY ASP ASP GLY VAL ALA ILE ALA LEU GLY ARG SEQRES 3 A 157 LEU VAL GLU GLU GLN MSE PRO GLU TRP SER VAL PHE PHE SEQRES 4 A 157 GLY TYR ASP THR PRO GLU SER GLU PHE GLY LYS LEU ARG SEQRES 5 A 157 GLU LEU ALA PRO ASP VAL ILE VAL VAL ALA ASP ALA MSE SEQRES 6 A 157 SER GLY PHE LYS GLU GLY GLU ILE GLU PHE LEU ASP LEU SEQRES 7 A 157 SER ASP GLU ARG THR TYR LEU TYR SER THR HIS ASN LEU SEQRES 8 A 157 PRO THR PRO ILE LEU ILE SER TYR LEU ARG GLY ILE CYS SEQRES 9 A 157 SER LYS THR ILE PHE LEU GLY ILE SER VAL LEU LEU GLU SEQRES 10 A 157 ASN VAL LEU HIS PHE SER GLU GLY LEU SER GLN GLY ALA SEQRES 11 A 157 SER ASP SER ALA PHE VAL ALA LEU GLY ARG ILE LYS GLU SEQRES 12 A 157 LEU ASP GLY MSE LEU LYS GLU GLY HIS HIS HIS HIS HIS SEQRES 13 A 157 HIS MODRES 3PU6 MSE A 30 MET SELENOMETHIONINE MODRES 3PU6 MSE A 63 MET SELENOMETHIONINE MODRES 3PU6 MSE A 145 MET SELENOMETHIONINE HET MSE A 30 8 HET MSE A 63 8 HET MSE A 145 8 HETNAM MSE SELENOMETHIONINE FORMUL 1 MSE 3(C5 H11 N O2 SE) FORMUL 2 HOH *11(H2 O) HELIX 1 1 ARG A 13 ASP A 16 5 4 HELIX 2 2 GLY A 17 MSE A 30 1 14 HELIX 3 3 THR A 41 SER A 44 5 4 HELIX 4 4 GLU A 45 ALA A 53 1 9 HELIX 5 5 ASP A 78 TYR A 84 1 7 HELIX 6 6 THR A 91 CYS A 102 1 12 HELIX 7 7 GLU A 115 LEU A 118 5 4 HELIX 8 8 SER A 125 LEU A 146 1 22 SHEET 1 A 5 TRP A 33 TYR A 39 0 SHEET 2 A 5 LYS A 3 VAL A 8 1 N CYS A 7 O GLY A 38 SHEET 3 A 5 VAL A 56 GLY A 65 1 O VAL A 56 N VAL A 4 SHEET 4 A 5 LYS A 104 LEU A 113 1 O ILE A 106 N ILE A 57 SHEET 5 A 5 ILE A 71 ASP A 75 -1 N LEU A 74 O PHE A 107 LINK C GLN A 29 N MSE A 30 1555 1555 1.33 LINK C MSE A 30 N PRO A 31 1555 1555 1.34 LINK C ALA A 62 N MSE A 63 1555 1555 1.33 LINK C MSE A 63 N SER A 64 1555 1555 1.33 LINK C GLY A 144 N MSE A 145 1555 1555 1.32 LINK C MSE A 145 N LEU A 146 1555 1555 1.33 CRYST1 45.202 50.728 66.676 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 0.022123 0.000000 0.000000 0.00000 SCALE2 0.000000 0.019713 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014998 0.00000