PDB Short entry for 2K5P HEADER BIOSYNTHETIC PROTEIN 30-JUN-08 2K5P TITLE NMR SOLUTION STRUCTURE OF A THIAMINE BIOSYNTHESIS PROTEIN FROM TITLE 2 GEOBACTER METALLIREDUCENS: NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TITLE 3 TARGET GMR137 COMPND MOL_ID: 1; COMPND 2 MOLECULE: THIAMINE-BIOSYNTHESIS PROTEIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: THIS PROTEIN; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: GEOBACTER METALLIREDUCENS GS-15; SOURCE 3 ORGANISM_TAXID: 269799; SOURCE 4 GENE: GMET_1567; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)+MAGIC; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET 21-23C KEYWDS NESG, GMR137, GEOBACTER METALLIREDUCENS, THIAMINE BIOSYNTHESIS, KEYWDS 2 STRUCTURAL GENOMICS, PSI-2, PROTEIN STRUCTURE INITIATIVE, NORTHEAST KEYWDS 3 STRUCTURAL GENOMICS CONSORTIUM, BIOSYNTHETIC PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR R.MANI,H.WANG,M.JIANG,M.MAGLIAQUI,R.XIAO,R.NAIR,M.C.BARAN, AUTHOR 2 S.V.T.GURLA,T.B.ACTON,B.ROST,G.T.MONTELIONE,NORTHEAST STRUCTURAL AUTHOR 3 GENOMICS CONSORTIUM (NESG) REVDAT 4 14-JUN-23 2K5P 1 REMARK REVDAT 3 19-FEB-20 2K5P 1 REMARK SEQADV REVDAT 2 24-FEB-09 2K5P 1 VERSN REVDAT 1 26-AUG-08 2K5P 0 JRNL AUTH R.MANI,H.WANG,M.JIANG,M.MAGLIAQUI,R.XIAO,R.NAIR,M.C.BARAN, JRNL AUTH 2 S.V.T.GURLA,T.B.ACTON,B.ROST,G.T.MONTELIONE JRNL TITL NMR SOLUTION STRUCTURE OF A THIAMINE BIOSYNTHESIS PROTEIN JRNL TITL 2 FROM GEOBACTER METALLIREDUCENS: NORTHEAST STRUCTURAL JRNL TITL 3 GENOMICS CONSORTIUM TARGET GMR137 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 2.0.6 REMARK 3 AUTHORS : BRUNGER, ADAMS, CLORE, GROS, NILGES AND READ REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURE WAS OBTAINED USING TRIPLE REMARK 3 RESONANCE NMR SPECTROSCOPY. GFT-NMR EXPERIMENTS WERE USED FOR REMARK 3 BACKBONE RESONANCE ASSIGNMENTS AND CONVENTIONAL 3D TOCSY AND REMARK 3 COSY EXPERIMENTS WERE USED TO OBTAIN SIDECHAIN RESONANCE REMARK 3 ASSIGNMENTS. AUTOMATED NOESY ASSIGNMENTS WERE MADE USING REMARK 3 AUTOSTRUCTURE AND CYANA-2.1. DIHEDRAL ANGLE CONSTRAINTS WERE REMARK 3 OBTAINED FROM TALOS. THE STRUCTURE CALCULATION WAS DONE REMARK 3 EXCLUDING 5 HIS FROM 8-RESIDUE C-TERMINAL TAG (LEHHHHHH). REMARK 3 COMPLETENESS OF ASSIGNMENTS EXCLUDING 5-HIS: BACKBONE - 100%, REMARK 3 SIDECHAIN (ALIPHATIC) - 99% SIDECHAIN (AROMATIC) - 96%. THE REMARK 3 ASSIGNMENTS WERE VALIDATED USING AVS SOFTWARE. FINAL STRUCTURE REMARK 3 QUALITY FACTROS (EXCLUDING 5 HIS) DETERMINED USING PSVS-V1.3: REMARK 3 ORDERED RESIDUES ARE DEFIEND AS: 1-13, 18-29, 32-63. (A) RMSD REMARK 3 (ORDERED RESIDUES) ALL BACKBONE ATOMS: 0.7A AND HEAVY ATOMS: REMARK 3 1.2A. (B) RAMACHANDRAN STATISTICS FOR ORDERED RESIDUES: MOST REMARK 3 FAVORED REGION: 82.8%, ADDITIONALLY ALLOWED REGIONS: 17.0% REMARK 3 GENEROUSLY ALLOWED REGION: 0.1%, DISALLOWED REGIONS: 0.1%. (C) REMARK 3 PROCHECK SCORES FOR ORDERED RESIDUES (RAW/Z-): PHI/PSI -0.58/- REMARK 3 1.97, ALL -0.48/-2.84, (D) MOLPROBITY CLASHSCORES (RAW/Z-) 17.03/ REMARK 3 -1.40, (E) RPF SCORES FOR THE GOODNESS OF THE FIT TO NOESY DATA: REMARK 3 RECALL - 0.99, PRECISION - 0.942, F-MEASURE - 0.966 AND FINAL DP REMARK 3 SCORE - 0.88. (F) NUMBER OF CLOSE CONTACTS FOR 20 MODELS: 6, RMS REMARK 3 DEVIATION FOR BOND ANGLES - 0.6DEG, RMS DEVIATION FOR BOND REMARK 3 LENGTHS - 0.009A. REMARK 4 REMARK 4 2K5P COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 01-JUL-08. REMARK 100 THE DEPOSITION ID IS D_1000100708. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 293; 293 REMARK 210 PH : 6.5; 6.5 REMARK 210 IONIC STRENGTH : 5 MM CACL2, 100MM NACL; 5 MM REMARK 210 CACL2, 100MM NACL REMARK 210 PRESSURE : AMBIENT; AMBIENT REMARK 210 SAMPLE CONTENTS : 1.06 MM [U-100% 13C; U-100% 15N] REMARK 210 GMR137, THIS PROTEIN, 90% H2O/10% REMARK 210 D2O; 1.26 MM [U-10% 13C; U-99% REMARK 210 15N] GMR137, THIS PROTEIN, 90% REMARK 210 H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC; REMARK 210 (4,3)D GFT-HNNCABCA; (4,3)D GFT- REMARK 210 CABCA(CO)NHN; (4,3)D GFT- REMARK 210 HABCAB(CO)NHN; 3D CBCA(CO)NH; 3D REMARK 210 HBHA(CO)NH; 3D HNCO; 3D HCCH- REMARK 210 TOCSY; 3D-CCH-TOCSY; 3D 1H-15N REMARK 210 NOESY; 3D 1H-13C ALIPH NOESY; 3D REMARK 210 1H-13C AROM NOESY; 3D HCCH-COSY REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ; 600 MHZ; 500 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE; INOVA REMARK 210 SPECTROMETER MANUFACTURER : BRUKER; VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : AUTOSTRUCTURE 2.2.1, CYANA 2.1, REMARK 210 AUTOASSIGN 2.4.0 REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 140 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. 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 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 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 1 ALA A 15 92.53 62.84 REMARK 500 1 SER A 17 114.14 61.63 REMARK 500 1 LYS A 28 82.52 67.02 REMARK 500 1 ASN A 40 18.87 56.47 REMARK 500 1 MET A 66 167.16 69.20 REMARK 500 1 LYS A 70 103.73 -167.05 REMARK 500 1 HIS A 73 -47.76 -141.46 REMARK 500 1 HIS A 74 121.33 65.60 REMARK 500 1 HIS A 75 43.50 -81.59 REMARK 500 2 PRO A 9 96.15 -60.85 REMARK 500 2 SER A 17 143.64 64.51 REMARK 500 2 ALA A 30 36.38 -79.03 REMARK 500 2 VAL A 35 89.00 -68.27 REMARK 500 2 ASP A 56 93.35 -68.11 REMARK 500 2 HIS A 74 19.92 58.88 REMARK 500 3 SER A 17 112.38 -164.32 REMARK 500 3 LYS A 28 76.49 65.78 REMARK 500 3 LYS A 55 -167.43 -112.00 REMARK 500 3 HIS A 74 93.70 -56.19 REMARK 500 3 HIS A 75 -168.68 -76.95 REMARK 500 4 LYS A 28 89.02 57.49 REMARK 500 4 VAL A 35 94.21 -58.70 REMARK 500 4 ASP A 56 105.61 -58.65 REMARK 500 4 TYR A 64 -37.08 73.91 REMARK 500 5 LYS A 28 81.65 63.10 REMARK 500 5 GLU A 33 -32.45 -140.86 REMARK 500 5 LYS A 70 94.77 -67.47 REMARK 500 5 HIS A 74 86.54 -63.42 REMARK 500 5 HIS A 75 162.22 72.84 REMARK 500 5 HIS A 77 -160.00 -120.77 REMARK 500 6 SER A 17 71.19 53.48 REMARK 500 6 LYS A 28 86.81 57.51 REMARK 500 6 TYR A 64 -19.72 70.96 REMARK 500 7 ALA A 32 -62.16 -146.05 REMARK 500 7 TYR A 64 -3.28 68.05 REMARK 500 7 LYS A 70 104.25 -51.09 REMARK 500 7 GLU A 72 92.21 62.95 REMARK 500 8 ALA A 15 105.74 -59.84 REMARK 500 8 LYS A 28 88.97 69.25 REMARK 500 8 TYR A 64 -3.28 67.06 REMARK 500 8 MET A 66 103.81 72.63 REMARK 500 8 HIS A 74 87.32 -62.86 REMARK 500 8 HIS A 76 128.21 65.63 REMARK 500 9 ASP A 13 174.50 59.71 REMARK 500 9 LYS A 28 74.04 66.77 REMARK 500 9 TYR A 64 34.66 -78.51 REMARK 500 9 PHE A 65 149.50 66.41 REMARK 500 9 LYS A 70 158.33 66.44 REMARK 500 9 HIS A 73 -54.30 -170.99 REMARK 500 9 HIS A 74 66.58 -179.97 REMARK 500 REMARK 500 THIS ENTRY HAS 113 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: GMR137 RELATED DB: TARGETDB REMARK 900 RELATED ID: 15844 RELATED DB: BMRB DBREF 2K5P A 1 70 UNP Q39VC5 Q39VC5_GEOMG 1 70 SEQADV 2K5P LEU A 71 UNP Q39VC5 EXPRESSION TAG SEQADV 2K5P GLU A 72 UNP Q39VC5 EXPRESSION TAG SEQADV 2K5P HIS A 73 UNP Q39VC5 EXPRESSION TAG SEQADV 2K5P HIS A 74 UNP Q39VC5 EXPRESSION TAG SEQADV 2K5P HIS A 75 UNP Q39VC5 EXPRESSION TAG SEQADV 2K5P HIS A 76 UNP Q39VC5 EXPRESSION TAG SEQADV 2K5P HIS A 77 UNP Q39VC5 EXPRESSION TAG SEQADV 2K5P HIS A 78 UNP Q39VC5 EXPRESSION TAG SEQRES 1 A 78 MET 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 MET GLY GLY GLY LYS LEU GLU HIS HIS HIS HIS HIS HIS HELIX 1 1 VAL A 20 LYS A 28 1 9 HELIX 2 2 GLU A 47 THR A 52 1 6 SHEET 1 A 2 ASN A 2 VAL A 5 0 SHEET 2 A 2 LYS A 8 THR A 11 -1 O SER A 10 N LEU A 3 SHEET 1 B 2 LEU A 18 ASN A 19 0 SHEET 2 B 2 THR A 53 VAL A 54 -1 O VAL A 54 N LEU A 18 SHEET 1 C 3 GLU A 42 VAL A 43 0 SHEET 2 C 3 VAL A 37 LEU A 39 -1 N LEU A 39 O GLU A 42 SHEET 3 C 3 VAL A 60 PHE A 62 -1 O GLU A 61 N GLU A 38 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 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 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000