PDB Short entry for 2K53 HEADER STRUCTURAL GENOMICS, UNKNOWN FUNCTION 24-JUN-08 2K53 TITLE NMR SOLUTION STRUCTURE OF A3DK08 PROTEIN FROM CLOSTRIDIUM TITLE 2 THERMOCELLUM: NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET CMR9 COMPND MOL_ID: 1; COMPND 2 MOLECULE: A3DK08 PROTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CLOSTRIDIUM THERMOCELLUM ATCC 27405; SOURCE 3 ORGANISM_TAXID: 203119; SOURCE 4 GENE: CTHE_3092; 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, CMR9, CLOSTRIDIUM THERMOCELLUM, A3DK08 PROTEIN, STRUCTURAL KEYWDS 2 GENOMICS, PSI-2, PROTEIN STRUCTURE INITIATIVE, NORTHEAST STRUCTURAL KEYWDS 3 GENOMICS CONSORTIUM, UNKNOWN FUNCTION EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR G.V.T.SWAPNA,W.HUANG,M.JIANG,E.L.FOOTE,R.XIAO,R.NAIR,J.EVERETT, AUTHOR 2 T.B.ACTON,B.ROST,G.T.MONTELIONE,NORTHEAST STRUCTURAL GENOMICS AUTHOR 3 CONSORTIUM (NESG) REVDAT 3 16-MAR-22 2K53 1 REMARK REVDAT 2 24-FEB-09 2K53 1 VERSN REVDAT 1 19-AUG-08 2K53 0 JRNL AUTH G.V.T.SWAPNA,W.HUANG,M.JIANG,E.L.FOOTE,R.XIAO,R.NAIR, JRNL AUTH 2 J.EVERETT,T.B.ACTON,B.ROST,G.T.MONTELIONE JRNL TITL NMR SOLUTION STRUCTURE OF A3DK08 PROTEIN FROM CLOSTRIDIUM JRNL TITL 2 THERMOCELLUM: NORTHEAST STRUCTURAL GENOMICS CONSORTIUM JRNL TITL 3 TARGET CMR9 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 DETERMINED USING REMARK 3 TRIPLE RESONANCE NMR SPECTROSCOPY. AUTOMATED BACKBONE RESONANCE REMARK 3 ASSIGNMENTS WERE MADE USING AUTOASSIGN AND THE SIDECHAIN REMARK 3 ASSIGNMENTS WERE COMPLETED MANUALLY. AUTOMATED NOESY ASSIGNMENTS REMARK 3 WERE MADE USING AUTOSTRUCTURE AND CYANA-2.1. DIHEDRAL ANGLE REMARK 3 CONSTRAINTS WERE OBTAINED FROM TALOS. THE STRUCTURE CALCULATIONS REMARK 3 WERE DONE EXCLUDING THE SIX HIS FROM THE 8-RESIDUE C-TERMINAL REMARK 3 TAG(LEHHHHHH). COMPLETENESS OF ASSIGNMENTS EXCLUDING THE HHHHHH: REMARK 3 BACKBONE:100% SIDECHAIN(ALIPHATIC): 99% SIDECHAIN (AROMATIC): 90% REMARK 3 STEREOSPECIFIC METHYL ASSIGNMENTS:100%. THE ASSIGNMENTS WERE REMARK 3 VALIDATED USING AVS SOFTWARE. FINAL STRUCTURE QUALITY REMARK 3 FACTORS(EXCLUDING THE HHHHHH) DETERMINED USING PSVS-V1.3: REMARK 3 ORDERED RESIDUES ARE DEFINED AS RESIDUES 2-28,33-34,37-69.(A) REMARK 3 RMSD (ORDERED RESIDUES)ALL BACKBONE ATOMS:0.4A, ALL HEAVY ATOMS: REMARK 3 0.7A; RMSD (ALL RESIDUES) BACKBONE: 0.7A AND HEAVY ATOMS: 1.0A. REMARK 3 (B) RAMACHANDRAN STATISTICS FOR ORDERED RESIDUES : MOST FAVOURED REMARK 3 REGIONS: 97.1%, ADDITIONALLY ALLOWED REGIONS: 2.9%.(C) PROCHECK REMARK 3 SCORES FOR ORDERED RESIDUES (RAW/Z-): PHI-PSI,0.21/1.14, ALL, REMARK 3 0.24/1.42 (D) MOLPROBITY CLASH SCORE (RAW/Z-): 17.26/-1.44. (E) REMARK 3 RPF SCORES FOR THE GOODNESS OF THE FIT TO NOESY DATA: RECALL: REMARK 3 0.984, PRECISION: 0.848, F-MEASURE: 0.911 AND FINAL DP-SCORE: REMARK 3 0.743. (F) NUMBER OF CLOSE CONTACTS FOR 20 MODELS: 6. RMS REMARK 3 DEVIATION FOR BOND ANGLES:0.6DEG. RMS DEVIATION FOR BOND LENGTHS REMARK 3 0.008A. REMARK 4 REMARK 4 2K53 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 25-JUN-08. REMARK 100 THE DEPOSITION ID IS D_1000100686. 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 : 5MM CACL2, 100MM NACL; 5MM REMARK 210 CACL2, 100MM NACL REMARK 210 PRESSURE : 1 ATM; 1 ATM REMARK 210 SAMPLE CONTENTS : 0.91 MM [U-100% 13C; U-100% 15N] REMARK 210 A3DK08 PROTEIN, 90% H2O/10% D2O; REMARK 210 1.05 MM [U-10% 13C; U-99% 15N] REMARK 210 A3DK08 PROTEIN, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC; REMARK 210 3D CBCA(CO)NH; 3D HNCACB; 3D REMARK 210 HNCO; 3D HBHA(CO)NH; 3D HCCH- REMARK 210 TOCSY; 3D 1H-13C NOESY; 3D 1H- REMARK 210 15N NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : INOVA; AVANCE REMARK 210 SPECTROMETER MANUFACTURER : VARIAN; BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CYANA 2.1, AUTOASSIGN 2.4.0, REMARK 210 AUTOSTRUCTURE 2.2.1 REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 MODELS 1-20 REMARK 465 RES C SSSEQI REMARK 465 HIS A 71 REMARK 465 HIS A 72 REMARK 465 HIS A 73 REMARK 465 HIS A 74 REMARK 465 HIS A 75 REMARK 465 HIS A 76 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 SER A 35 20.61 -69.70 REMARK 500 1 SER A 36 -46.42 -146.69 REMARK 500 2 SER A 35 1.58 -64.03 REMARK 500 2 SER A 36 -50.28 -133.50 REMARK 500 3 LEU A 31 107.78 -177.00 REMARK 500 4 CYS A 30 -164.34 -73.20 REMARK 500 5 SER A 35 76.80 -67.23 REMARK 500 5 SER A 36 -30.54 156.36 REMARK 500 5 MET A 37 -68.33 -103.60 REMARK 500 7 MET A 37 -71.66 -100.15 REMARK 500 10 SER A 35 -83.44 39.44 REMARK 500 14 SER A 36 -8.20 -57.24 REMARK 500 15 LEU A 31 106.55 -54.09 REMARK 500 16 MET A 37 -61.14 -121.74 REMARK 500 17 LEU A 31 83.30 -169.95 REMARK 500 17 MET A 37 -69.19 -125.69 REMARK 500 18 LEU A 31 36.79 -85.80 REMARK 500 18 MET A 37 -67.28 -104.93 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: CMR9 RELATED DB: TARGETDB REMARK 900 RELATED ID: 15822 RELATED DB: BMRB DBREF 2K53 A 1 68 UNP A3DK08 A3DK08_CLOTH 1 68 SEQADV 2K53 LEU A 69 UNP A3DK08 EXPRESSION TAG SEQADV 2K53 GLU A 70 UNP A3DK08 EXPRESSION TAG SEQADV 2K53 HIS A 71 UNP A3DK08 EXPRESSION TAG SEQADV 2K53 HIS A 72 UNP A3DK08 EXPRESSION TAG SEQADV 2K53 HIS A 73 UNP A3DK08 EXPRESSION TAG SEQADV 2K53 HIS A 74 UNP A3DK08 EXPRESSION TAG SEQADV 2K53 HIS A 75 UNP A3DK08 EXPRESSION TAG SEQADV 2K53 HIS A 76 UNP A3DK08 EXPRESSION TAG SEQRES 1 A 76 MET LYS ILE THR LYS ASP MET ILE ILE ALA ASP VAL LEU SEQRES 2 A 76 GLN MET ASP ARG GLY THR ALA PRO ILE PHE ILE ASN ASN SEQRES 3 A 76 GLY MET HIS CYS LEU GLY CYS PRO SER SER MET GLY GLU SEQRES 4 A 76 SER ILE GLU ASP ALA CYS ALA VAL HIS GLY ILE ASP ALA SEQRES 5 A 76 ASP LYS LEU VAL LYS GLU LEU ASN GLU TYR PHE GLU LYS SEQRES 6 A 76 LYS GLU VAL LEU GLU HIS HIS HIS HIS HIS HIS HELIX 1 1 ILE A 8 ASP A 16 1 9 HELIX 2 2 THR A 19 ASN A 26 1 8 HELIX 3 3 SER A 40 GLY A 49 1 10 HELIX 4 4 ASP A 51 GLU A 70 1 20 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