HEADER STRUCTURAL GENOMICS, UNKNOWN FUNCTION 18-JUN-09 2KKE TITLE SOLUTION NMR STRUCTURE OF A DIMERIC PROTEIN OF UNKNOWN FUNCTION FROM TITLE 2 METHANOBACTERIUM THERMOAUTOTROPHICUM, NORTHEAST STRUCTURAL GENOMICS TITLE 3 CONSORTIUM TARGET TR5 COMPND MOL_ID: 1; COMPND 2 MOLECULE: UNCHARACTERIZED PROTEIN; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: METHANOTHERMOBACTER THERMAUTOTROPHICUS STR. SOURCE 3 DELTA H; SOURCE 4 ORGANISM_TAXID: 187420; SOURCE 5 GENE: MTH467, MTH_467; 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: PET15B KEYWDS PROTEIN NMR, NORTHEAST STRUCTURAL GENOMICS CONSORTIUM (NESG), TARGET KEYWDS 2 TR5, PSI-2, PROTEIN STRUCTURE INITIATIVE, METHANOTHERMOBACTER KEYWDS 3 THERMAUTOTROPHICUS, O26567_METTH, STRUCTURAL GENOMICS, NORTHEAST KEYWDS 4 STRUCTURAL GENOMICS CONSORTIUM, NESG, UNKNOWN FUNCTION EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR G.V.T.SWAPNA,X.GUNSALUS,L.HUANG,K.XIAO,J.K.EVERETT,T.B.ACTON, AUTHOR 2 G.T.MONTELIONE,NORTHEAST STRUCTURAL GENOMICS CONSORTIUM (NESG) REVDAT 3 14-JUN-23 2KKE 1 REMARK REVDAT 2 26-FEB-20 2KKE 1 REMARK REVDAT 1 14-JUL-09 2KKE 0 JRNL AUTH G.V.T.SWAPNA,X.GUNSALUS,L.HUANG,K.XIAO,J.K.EVERETT, JRNL AUTH 2 T.B.ACTON,G.T.MONTELIONE JRNL TITL NMR SOLUTION STRUCTURE OF A PUTATIVE UNCHARACTERIZED PROTEIN JRNL TITL 2 FROM METHANOBACTERIUM THERMOAUTOTROPHICUM, NORTHEAST JRNL TITL 3 STRUCTURAL GENOMICS CONSORTIUM TARGET:TR5 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AUTOASSIGN 2.2.1, CNS 2.0.6 REMARK 3 AUTHORS : ZIMMERMAN, MOSELEY, KULIKOWSKI AND MONTELIONE REMARK 3 (AUTOASSIGN), BRUNGER, ADAMS, CLORE, GROS, NILGES REMARK 3 AND READ (CNS) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: INITIAL NOESY ASSIGNMENTS FOR THE REMARK 3 MONOMER WERE MADE USING AUTOSTRUCTURE AND THE SOLUTION STRUCTURE REMARK 3 OF THE DIMER WAS OBTAINED USING CYANA-2.1. CONSTRAINTS FOR THE REMARK 3 DIMER INTERFACE WERE OBTAINED FROM THE X-FILTERED NOESY DATA AND REMARK 3 SLOW EXCHANGING AMIDES FROM H/D EXCHANGE. 100 STRUCTURES WERE REMARK 3 CALCULATED AND 20 BEST CONFORMERS WERE THEN REFINED IN A SHELL REMARK 3 OF WATER USING CNS. INITIAL DIHEDRAL ANGLE CONSTRAINTS WERE REMARK 3 OBTAINED FROM TALOS. FINAL STRUCTURE QUALITY FACTORS DETERMINED REMARK 3 USING PSVS SOFTWARE: ORDERED RESIDUES ARE DEFINED AS (10-53,212- REMARK 3 236,238-251). (A)RMSD(ORDERED RESIDUES) ALL BACKBONE ATOMS: 0.7A; REMARK 3 ALL HEAVY ATOMS: 1.0A. (B) RAMCHANDRAN STATISTICS FOR ALL REMARK 3 ORDERED RESIDUES: MOST FAVOURED REGION: 93.1%; ADDITIONALLY REMARK 3 ALLOWED REGION: 6.6%; GENEROUSLY ALLOWED REGION 0.1% AND REMARK 3 DISALLOWED REGION: 0.2%. (C) PROCHECK SCORES FOR ALL ORDERED REMARK 3 RESIDUES (RAW/Z) PHI-PSI -0.11/-0.12; ALL: -0.07/-0.41; (D) REMARK 3 MOLPROBITY CLASH SCORE (RAW/Z): 16.97/-1.39. (E) RPF SCORES FOR REMARK 3 THE GOODNESS OF FIT TO NOESY DATA: RECALL :0.913; PRECISION: REMARK 3 0.849; F-MEASURE:0.88; FINAL DP SCORE :0.703 REMARK 4 REMARK 4 2KKE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-JUN-09. REMARK 100 THE DEPOSITION ID IS D_1000101229. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 303 REMARK 210 PH : 6.5 REMARK 210 IONIC STRENGTH : 300 MM NACL REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 0.4 MM [U-100% 13C; U-100% 15N] REMARK 210 TR5, 95% H2O/5% D2O; 0.95 MM [U- REMARK 210 10% 13C; U-100% 15N] TR5, 95% REMARK 210 H2O/5% D2O; 0.4 MM [U-10% 13C; U- REMARK 210 100% 15N] + UNLABELED TR5 REMARK 210 PROTEIN TR5, 95% H2O/5% 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 HBHA(CO)NH; 3D HCCH-TOCSY; 3D REMARK 210 HNCO; 3D 1H-13C NOESY; 3D 1H-15N REMARK 210 NOESY; 3D- X-FILTERED NOESY; 2D REMARK 210 HNOE REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 500 MHZ REMARK 210 SPECTROMETER MODEL : INOVA; UNITY REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CYANA 2.1, CNS 2.0.6 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: THE STRUCTURE WAS DETERMINED USING TRIPLE RESONANCE NMR REMARK 210 SPECTROSCOPY. AUTOMATED BACKBONE ASSIGNMENTS WERE MADE USING REMARK 210 AUTOASSIGN SOFTWARE. SIDECHAIN ASSIGNMENTS WERE COMPLETED REMARK 210 MANUALLY. THE OLIGOMERIC STATE WAS CONFIRMED TO BE A DIMER FROM REMARK 210 SEDIMENTATION-EQUILIBRIUM ANALYSIS (KD =0.3UM) AND STATIC LIGHT REMARK 210 SCATTERING EXPERIMENT THAT REPORTED 90% OF THE PROTEIN IN A REMARK 210 DIMER WITH A MOLECULAR WEIGHT OF 15.03KD. 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 LYS A 11 18.96 -142.40 REMARK 500 1 ARG B 205 81.20 64.75 REMARK 500 1 LEU B 210 -65.19 -148.36 REMARK 500 1 LYS B 211 35.93 -97.74 REMARK 500 2 ARG B 205 85.04 64.94 REMARK 500 2 LEU B 210 -64.60 -150.20 REMARK 500 2 LYS B 211 32.53 -83.96 REMARK 500 2 ASP B 212 21.30 -77.50 REMARK 500 3 PRO A 6 154.16 -43.60 REMARK 500 3 ARG B 205 82.97 61.62 REMARK 500 3 PRO B 206 -79.10 -63.72 REMARK 500 3 LEU B 210 -76.77 -132.96 REMARK 500 3 THR B 236 98.34 -69.94 REMARK 500 3 ASN B 248 37.48 -79.96 REMARK 500 3 HIS B 249 -40.91 -144.34 REMARK 500 4 PRO A 6 154.46 -44.63 REMARK 500 4 LYS A 11 32.08 -97.22 REMARK 500 4 ARG A 31 -28.76 -147.56 REMARK 500 4 ASP A 52 -51.39 174.75 REMARK 500 4 LEU B 210 -70.95 -142.53 REMARK 500 5 ARG B 204 166.92 70.12 REMARK 500 5 ALA B 234 20.87 -74.77 REMARK 500 5 ASP B 252 -53.42 -133.29 REMARK 500 6 ARG B 204 -164.49 -113.66 REMARK 500 6 LEU B 210 -101.59 -123.71 REMARK 500 6 SER B 230 48.88 -76.45 REMARK 500 6 ARG B 231 -31.05 177.96 REMARK 500 6 ASP B 252 -82.95 -88.28 REMARK 500 7 ARG B 204 -169.21 -107.25 REMARK 500 7 LEU B 210 -86.83 -102.84 REMARK 500 7 MET B 238 -81.07 48.09 REMARK 500 7 ASP B 252 -67.98 -126.52 REMARK 500 8 ARG A 4 -161.02 -120.33 REMARK 500 8 LYS B 211 23.92 -145.44 REMARK 500 8 ASP B 252 -71.35 -115.72 REMARK 500 9 ASP A 12 -80.35 -60.91 REMARK 500 9 LEU B 210 -72.77 -102.88 REMARK 500 9 SER B 237 -174.95 72.09 REMARK 500 9 MET B 238 -70.51 -83.40 REMARK 500 9 ASP B 252 -75.43 -108.44 REMARK 500 10 LEU B 210 -84.60 -117.82 REMARK 500 10 ASP B 252 -75.06 -127.07 REMARK 500 11 LEU A 10 -76.63 -106.50 REMARK 500 11 ASP A 52 -84.60 -83.48 REMARK 500 11 MET B 238 -80.54 46.52 REMARK 500 12 LYS A 11 23.07 -157.21 REMARK 500 12 ASN A 48 21.21 -72.49 REMARK 500 12 ASP B 212 -55.40 -168.15 REMARK 500 13 PRO A 6 -167.70 -68.57 REMARK 500 13 VAL B 202 4.98 -66.93 REMARK 500 REMARK 500 THIS ENTRY HAS 88 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 16357 RELATED DB: BMRB REMARK 900 RELATED ID: TR5 RELATED DB: TARGETDB REMARK 999 REMARK 999 SEQUENCE REMARK 999 NMR ANALYSIS SHOWED THAT THE RESIDUE AT 53 AND 253 IS A GLU AND NOT REMARK 999 AN ASP. THE DATABASE HAS TO BE CORRECTED FOR THIS. GLU IS CORRECT. DBREF 2KKE A 1 53 UNP O26567 O26567_METTH 1 53 DBREF 2KKE B 201 253 UNP O26567 O26567_METTH 1 53 SEQADV 2KKE GLU A 53 UNP O26567 ASP 53 SEE REMARK 999 SEQADV 2KKE GLU B 253 UNP O26567 ASP 53 SEE REMARK 999 SEQRES 1 A 53 MET VAL GLY ARG ARG PRO GLY GLY GLY LEU LYS ASP THR SEQRES 2 A 53 LYS PRO VAL VAL VAL ARG LEU TYR PRO ASP GLU ILE GLU SEQRES 3 A 53 ALA LEU LYS SER ARG VAL PRO ALA ASN THR SER MET SER SEQRES 4 A 53 ALA TYR ILE ARG ARG ILE ILE LEU ASN HIS LEU GLU ASP SEQRES 5 A 53 GLU SEQRES 1 B 53 MET VAL GLY ARG ARG PRO GLY GLY GLY LEU LYS ASP THR SEQRES 2 B 53 LYS PRO VAL VAL VAL ARG LEU TYR PRO ASP GLU ILE GLU SEQRES 3 B 53 ALA LEU LYS SER ARG VAL PRO ALA ASN THR SER MET SER SEQRES 4 B 53 ALA TYR ILE ARG ARG ILE ILE LEU ASN HIS LEU GLU ASP SEQRES 5 B 53 GLU HELIX 1 1 TYR A 21 SER A 30 1 10 HELIX 2 2 SER A 37 ASP A 52 1 16 HELIX 3 3 TYR B 221 LYS B 229 1 9 HELIX 4 4 SER B 237 GLU B 251 1 15 SHEET 1 A 2 LYS A 14 LEU A 20 0 SHEET 2 A 2 LYS B 214 LEU B 220 -1 O LYS B 214 N LEU A 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 MODEL 1