HEADER BIOSYNTHETIC PROTEIN 21-APR-08 3CWI TITLE CRYSTAL STRUCTURE OF THIAMINE BIOSYNTHESIS PROTEIN (THIS) TITLE 2 FROM GEOBACTER METALLIREDUCENS. NORTHEAST STRUCTURAL TITLE 3 GENOMICS CONSORTIUM TARGET GMR137 COMPND MOL_ID: 1; COMPND 2 MOLECULE: THIAMINE-BIOSYNTHESIS PROTEIN THIS; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: GEOBACTER METALLIREDUCENS GS-15; SOURCE 3 ORGANISM_TAXID: 269799; SOURCE 4 STRAIN: GS-15 / DSM 7210; SOURCE 5 ATCC: 53774; SOURCE 6 GENE: THIS, GMET_1567; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)+MAGIC; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PET21 KEYWDS ALPHA-BETA PROTEIN, STRUCTURAL GENOMICS, PSI-2, PROTEIN KEYWDS 2 STRUCTURE INITIATIVE, NORTHEAST STRUCTURAL GENOMICS KEYWDS 3 CONSORTIUM, NESG, BIOSYNTHETIC PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR F.FOROUHAR,M.ABASHIDZE,J.SEETHARAMAN,L.MAO,H.JANJUA,R.XIAO, AUTHOR 2 M.MAGLAQUI,C.CICCOSANTI,E.L.FOOTE,H.WANG,J.K.EVERETT, AUTHOR 3 T.B.ACTON,G.T.MONTELIONE,L.TONG,J.F.HUNT,NORTHEAST AUTHOR 4 STRUCTURAL GENOMICS CONSORTIUM (NESG) REVDAT 2 24-FEB-09 3CWI 1 VERSN REVDAT 1 06-MAY-08 3CWI 0 JRNL AUTH F.FOROUHAR,M.ABASHIDZE,J.SEETHARAMAN,L.MAO, JRNL AUTH 2 H.JANJUA,R.XIAO,M.MAGLAQUI,C.CICCOSANTI,E.L.FOOTE, JRNL AUTH 3 H.WANG,J.K.EVERETT,T.B.ACTON,G.T.MONTELIONE,L.TONG, JRNL AUTH 4 J.F.HUNT JRNL TITL CRYSTAL STRUCTURE OF THIAMINE BIOSYNTHESIS PROTEIN JRNL TITL 2 (THIS) FROM GEOBACTER METALLIREDUCENS. JRNL REF TO BE PUBLISHED JRNL REFN REMARK 1 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.2 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) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.97 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 856078.580 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 90.7 REMARK 3 NUMBER OF REFLECTIONS : 10382 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) : 0.226 REMARK 3 FREE R VALUE : 0.258 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.200 REMARK 3 FREE R VALUE TEST SET COUNT : 1060 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.008 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 10 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.97 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 69.40 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 702 REMARK 3 BIN R VALUE (WORKING SET) : 0.2190 REMARK 3 BIN FREE R VALUE : 0.2400 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 11.60 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 92 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.025 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 513 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 45 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 16.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 32.00 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 4.20000 REMARK 3 B22 (A**2) : 4.20000 REMARK 3 B33 (A**2) : -8.40000 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) : 0.23 REMARK 3 ESD FROM SIGMAA (A) : 0.05 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) : 0.18 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : 1.10 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 25.60 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.59 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : OVERALL 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 : 0.45 REMARK 3 BSOL : 59.01 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 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE FRIEDEL PAIRS WERE USED IN REMARK 3 PHASING REMARK 4 REMARK 4 3CWI COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 24-APR-08. REMARK 100 THE RCSB ID CODE IS RCSB047297. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-APR-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X4C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97908 REMARK 200 MONOCHROMATOR : SI 111 CHANNEL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MAR CCD 165 MM REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11436 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 14.500 REMARK 200 R MERGE (I) : 0.07800 REMARK 200 R SYM (I) : 0.06300 REMARK 200 FOR THE DATA SET : 40.7400 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.97 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8 REMARK 200 DATA REDUNDANCY IN SHELL : 10.80 REMARK 200 R MERGE FOR SHELL (I) : 0.37000 REMARK 200 R SYM FOR SHELL (I) : 0.32800 REMARK 200 FOR SHELL : 4.540 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: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.52 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.18 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PROTEIN SOLUTION: 10 MM TRIS-HCL PH REMARK 280 7.5, 100 MM NACL, 5 MM DTT. RESERVOIR SOLUTION: 100 MM SODIUM REMARK 280 ACETATE PH 5.0, 18% PEG 8000, 200 MM MAGNESIUM CHLORIDE, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 291K 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 44.76850 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 20.48250 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 20.48250 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 67.15275 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 20.48250 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 20.48250 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 22.38425 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 20.48250 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 20.48250 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 67.15275 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 20.48250 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 20.48250 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 22.38425 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 44.76850 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: AUTHORS STATE THAT THE MONOMERIC ASSEMBLY OF THE REMARK 300 BIOLOGICAL UNIT THAT IS SHOWN IN REMARK 350 IS PUTATIVE 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 LYS A 70 REMARK 465 LEU A 71 REMARK 465 GLU A 72 REMARK 465 HIS A 73 REMARK 465 HIS A 74 REMARK 465 HIS A 75 REMARK 465 HIS A 76 REMARK 465 HIS A 77 REMARK 465 HIS A 78 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 117 O HOH A 117 7556 2.05 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: GMR137 RELATED DB: TARGETDB DBREF 3CWI A 1 70 UNP Q39VC5 Q39VC5_GEOMG 1 70 SEQADV 3CWI LEU A 71 UNP Q39VC5 EXPRESSION TAG SEQADV 3CWI GLU A 72 UNP Q39VC5 EXPRESSION TAG SEQADV 3CWI HIS A 73 UNP Q39VC5 EXPRESSION TAG SEQADV 3CWI HIS A 74 UNP Q39VC5 EXPRESSION TAG SEQADV 3CWI HIS A 75 UNP Q39VC5 EXPRESSION TAG SEQADV 3CWI HIS A 76 UNP Q39VC5 EXPRESSION TAG SEQADV 3CWI HIS A 77 UNP Q39VC5 EXPRESSION TAG SEQADV 3CWI HIS A 78 UNP Q39VC5 EXPRESSION TAG SEQRES 1 A 78 MSE ASN LEU THR VAL ASN GLY LYS PRO SER THR VAL ASP SEQRES 2 A 78 GLY ALA GLU SER LEU ASN VAL THR GLU LEU LEU SER ALA SEQRES 3 A 78 LEU LYS VAL ALA GLN ALA GLU TYR VAL THR VAL GLU LEU SEQRES 4 A 78 ASN GLY GLU VAL LEU GLU ARG GLU ALA PHE ASP ALA THR SEQRES 5 A 78 THR VAL LYS ASP GLY ASP ALA VAL GLU PHE LEU TYR PHE SEQRES 6 A 78 MSE GLY GLY GLY LYS LEU GLU HIS HIS HIS HIS HIS HIS MODRES 3CWI MSE A 1 MET SELENOMETHIONINE MODRES 3CWI MSE A 66 MET SELENOMETHIONINE HET MSE A 1 8 HET MSE A 66 8 HETNAM MSE SELENOMETHIONINE FORMUL 1 MSE 2(C5 H11 N O2 SE) FORMUL 2 HOH *45(H2 O) HELIX 1 1 VAL A 20 LEU A 27 1 8 HELIX 2 2 GLN A 31 VAL A 35 5 5 HELIX 3 3 GLU A 45 PHE A 49 5 5 SHEET 1 A 5 LYS A 8 THR A 11 0 SHEET 2 A 5 ASN A 2 VAL A 5 -1 N VAL A 5 O LYS A 8 SHEET 3 A 5 ALA A 59 LEU A 63 1 O VAL A 60 N THR A 4 SHEET 4 A 5 THR A 36 LEU A 39 -1 N THR A 36 O LEU A 63 SHEET 5 A 5 GLU A 42 VAL A 43 -1 O GLU A 42 N LEU A 39 SHEET 1 B 2 SER A 17 ASN A 19 0 SHEET 2 B 2 THR A 53 LYS A 55 -1 O VAL A 54 N LEU A 18 LINK C MSE A 1 N ASN A 2 1555 1555 1.33 LINK C PHE A 65 N MSE A 66 1555 1555 1.33 LINK C MSE A 66 N GLY A 67 1555 1555 1.33 CRYST1 40.965 40.965 89.537 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 0.024411 0.000000 0.000000 0.00000 SCALE2 0.000000 0.024411 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011169 0.00000 HETATM 1 N MSE A 1 27.129 17.327 45.961 1.00 35.75 N HETATM 2 CA MSE A 1 26.660 17.430 44.546 1.00 31.81 C HETATM 3 C MSE A 1 27.150 16.224 43.749 1.00 22.97 C HETATM 4 O MSE A 1 28.193 15.652 44.059 1.00 26.42 O HETATM 5 CB MSE A 1 27.190 18.720 43.906 1.00 35.29 C HETATM 6 CG MSE A 1 28.706 18.788 43.806 1.00 34.31 C HETATM 7 SE MSE A 1 29.341 20.290 42.743 1.00 54.83 SE HETATM 8 CE MSE A 1 29.303 19.468 40.997 1.00 46.95 C