HEADER STRUCTURAL GENOMICS, UNKNOWN FUNCTION 26-SEP-07 2JVW TITLE SOLUTION NMR STRUCTURE OF UNCHARACTERIZED PROTEIN Q5E7H1 FROM VIBRIO TITLE 2 FISCHERI. NORTHEAST STRUCTURAL GENOMICS TARGET VFR117 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: VIBRIO FISCHERI; SOURCE 3 ORGANISM_TAXID: 312309; SOURCE 4 STRAIN: ES114; SOURCE 5 ATCC: 700601; SOURCE 6 GENE: VF0530; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)MGK; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: VFR117-21.1 KEYWDS SOLUTION NMR STRUCTURE, ALPHA HELICAL PROTEIN, STRUCTURAL GENOMICS, KEYWDS 2 UNKNOWN FUNCTION, PSI-2, PROTEIN STRUCTURE INITIATIVE, NORTHEAST KEYWDS 3 STRUCTURAL GENOMICS CONSORTIUM, NESG EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR J.M.ARAMINI,P.ROSSI,D.WANG,C.NWOSU,L.A.OWENS,R.XIAO,J.LIU,M.C.BARAN, AUTHOR 2 G.V.T.SWAPNA,T.B.ACTON,B.ROST,G.T.MONTELIONE,NORTHEAST STRUCTURAL AUTHOR 3 GENOMICS CONSORTIUM (NESG) REVDAT 8 08-MAY-24 2JVW 1 REMARK REVDAT 7 14-JUN-23 2JVW 1 DBREF REVDAT 6 19-FEB-20 2JVW 1 REMARK SEQADV REVDAT 5 21-SEP-11 2JVW 1 JRNL REVDAT 4 03-AUG-11 2JVW 1 JRNL REVDAT 3 13-JUL-11 2JVW 1 VERSN REVDAT 2 24-FEB-09 2JVW 1 VERSN REVDAT 1 16-OCT-07 2JVW 0 JRNL AUTH J.M.ARAMINI,P.ROSSI,M.FISCHER,R.XIAO,T.B.ACTON, JRNL AUTH 2 G.T.MONTELIONE JRNL TITL SOLUTION NMR STRUCTURE OF VF0530 FROM VIBRIO FISCHERI JRNL TITL 2 REVEALS A NUCLEIC ACID-BINDING FUNCTION. JRNL REF PROTEINS V. 79 2988 2011 JRNL REFN ISSN 0887-3585 JRNL PMID 21905121 JRNL DOI 10.1002/PROT.23121 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : TOPSPIN 1.3, CNS 1.1 REMARK 3 AUTHORS : BRUKER BIOSPIN (TOPSPIN), BRUNGER, ADAMS, CLORE, REMARK 3 GROS, NILGES AND READ (CNS) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE FINAL STRUCTURES ARE BASED ON A REMARK 3 TOTAL OF 1424 CONFORMATIONALLY-RESTRICTING NOE-DERIVED DISTANCE REMARK 3 CONSTRAINTS, 88 DIHEDRAL ANGLE CONSTRAINTS, AND 46 HYDROGEN BOND REMARK 3 CONSTRAINTS (19.2 CONSTRAINTS PER RESIDUE, 3.3 LONG RANGE REMARK 3 CONSTRAINTS PER RESIDUE, COMPUTED FOR RESIDUES 1 TO 82 BY PSVS REMARK 3 1.3). STRUCTURE DETERMINATION WAS PERFORMED ITERATIVELY USING REMARK 3 CYANA 2.1. THE 20 STRUCTURES OUT OF 100 WITH THE LOWEST TARGET REMARK 3 FUNCTION WERE FURTHER REFINED BY RESTRAINED MOLECULAR DYNAMICS/ REMARK 3 ENERGY MINIMIZATION IN EXPLICIT WATER (CNS) WITH PARAM19. REMARK 4 REMARK 4 2JVW COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-OCT-07. REMARK 100 THE DEPOSITION ID IS D_1000100356. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 293 REMARK 210 PH : 4.5 REMARK 210 IONIC STRENGTH : 0.1 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.95 MM [U-100% 13C; U-100% 15N] REMARK 210 VFR117, 20 MM AMMONIUM ACETATE, REMARK 210 100 MM SODIUM CHLORIDE, 5 MM REMARK 210 CALCIUM CHLORIDE, 10 MM DTT, REMARK 210 0.02 % SODIUM AZIDE, 95% H2O/5% REMARK 210 D2O; 1.08 MM [U-5% 13C; U-100% REMARK 210 15N] VFR117, 20 MM AMMONIUM REMARK 210 ACETATE, 100 MM SODIUM CHLORIDE, REMARK 210 5 MM CALCIUM CHLORIDE, 10 MM DTT, REMARK 210 0.02 % SODIUM AZIDE, 95% H2O/5% REMARK 210 D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC; REMARK 210 3D HNCO; 3D HN(CA)CO; 3D HN(COCA) REMARK 210 CB; 3D HNCACB; 3D HBHA(CO)NH; 3D REMARK 210 HCCH-COSY; 3D HCCH-TOCSY; 3D CCH- REMARK 210 TOCSY; 3D CCH-TOCSY AROMATIC; 3D REMARK 210 SIMULTANEOUS CN-NOESY; 3D HNHA; REMARK 210 2D 1H-13C HSQC STEREOSPECIFIC REMARK 210 LEU/VAL METHYL REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : AUTOASSIGN 2.4.0, CYANA 2.1, REMARK 210 NMRPIPE 2.3, AUTOSTRUCTURE 2.1.1, REMARK 210 PSVS 1.3, PDBSTAT 5.0, SPARKY REMARK 210 3.110 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 PROTEIN IS MONOMERIC BY GEL FILTRATION CHROMATOGRAPHY REMARK 210 AND STATIC LIGHT SCATTERING. THE STRUCTURE WAS DETERMINED USING REMARK 210 TRIPLE RESONANCE NMR SPECTROSCOPY. AUTOMATED BACKBONE REMARK 210 ASSIGNMENTS WERE MADE USING AUTOASSIGN, AND THE SIDE CHAIN REMARK 210 ASSIGNMENTS WERE COMPLETED MANUALLY. AUTOMATIC NOESY ASSIGNMENTS REMARK 210 WERE DETERMINED USING CYANA 2.1. DIHEDRAL ANGLE CONSTRAINTS WERE REMARK 210 OBTAINED FROM TALOS. HYDROGEN BOND CONSTRAINTS WERE DETERMINED REMARK 210 USING BOTH AUTOSTRUCTURE AND CYANA, AND WERE APPLIED ONLY IN THE REMARK 210 FINAL REFINEMENT STAGE (CNS) OF THE STRUCTURE DETERMINATION. REMARK 210 COMPLETENESS OF NMR ASSIGNMENTS (EXCLUDING C-TERMINAL HHHHHH): REMARK 210 BACKBONE, 98.8%, SIDE CHAIN, 95.3%, AROMATICS, 100%, REMARK 210 STEREOSPECIFIC METHYL, 100%, STEREOSPECIFIC SIDE CHAIN NH2: 100% REMARK 210 . FINAL STRUCTURE QUALITY FACTORS (FOR RESIDUES 1 TO 82, PSVS REMARK 210 1.3), WHERE ORDERED RESIDUES [S(PHI) + S(PSI) > 1.8] COMPRISE: REMARK 210 15-37,42-43,46-75: (A) RMSD (ORDERED RESIDUES): BB, 0.5, HEAVY REMARK 210 ATOM, 1.1. (B) RAMACHANDRAN STATISTICS FOR ORDERED RESIDUES: REMARK 210 MOST FAVORED, 93.9, ADDITIONALLY ALLOWED, 6.1%, GENEROUSLY REMARK 210 ALLOWED, 0.0%, DISALLOWED, 0.0%. (C) PROCHECK SCORES FOR ORDERED REMARK 210 RESIDUES (RAW/Z-): PHI-PSI, 0.17/0.98, ALL, 0.19/1.12. (D) REMARK 210 MOLPROBITY CLASH SCORE (RAW/Z-): 14.65/-0.99. (E) RPF SCORES FOR REMARK 210 GOODNESS OF FIT TO NOESY DATA (RESIDUES 1-82): RECALL, 0.989, REMARK 210 PRECISION, 0.945, F-MEASURE, 0.967, DP-SCORE, 0.810. (F) NUMBER REMARK 210 OF CLOSE CONTACTS PER 20 MODELS: 2. THE C-TERMINAL HIS TAG REMARK 210 RESIDUES OF THE PROTEIN (HHHHHH) WERE NOT INCLUDED IN THE REMARK 210 STRUCTURE CALCULATIONS AND HAVE BEEN OMITTED FROM THIS REMARK 210 DEPOSITION. COORDINATES FOR THE FOLLOWING RESIDUES ARE NOT WELL REMARK 210 DETERMINED [S(PHI) + S(PSI) < 1.8]: 1-14,38-41,44-45,76-82. 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 83 REMARK 465 HIS A 84 REMARK 465 HIS A 85 REMARK 465 HIS A 86 REMARK 465 HIS A 87 REMARK 465 HIS A 88 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 THR A 6 49.60 -83.62 REMARK 500 1 TYR A 28 -68.53 -121.34 REMARK 500 1 CYS A 41 -59.07 -134.07 REMARK 500 1 ASP A 45 71.13 54.51 REMARK 500 1 PRO A 46 93.21 -53.69 REMARK 500 1 GLU A 77 106.39 -57.02 REMARK 500 1 GLN A 80 -166.45 -76.55 REMARK 500 2 ASN A 38 79.14 -69.90 REMARK 500 2 CYS A 41 -32.74 -142.02 REMARK 500 2 LYS A 43 -67.96 -100.17 REMARK 500 2 PRO A 46 80.08 -68.10 REMARK 500 3 LEU A 12 54.17 -144.95 REMARK 500 3 ASP A 45 73.68 59.56 REMARK 500 3 LYS A 57 -59.89 -125.61 REMARK 500 3 LYS A 76 105.34 -55.94 REMARK 500 4 ASN A 9 139.52 72.85 REMARK 500 4 HIS A 13 85.87 -67.18 REMARK 500 4 TYR A 28 -70.95 -93.67 REMARK 500 4 LEU A 81 -166.41 -72.28 REMARK 500 5 ASN A 10 128.17 63.53 REMARK 500 5 TYR A 28 -70.53 -89.57 REMARK 500 5 CYS A 41 -53.85 -151.41 REMARK 500 5 ASP A 45 69.99 68.05 REMARK 500 6 ALA A 2 99.71 -66.68 REMARK 500 6 LEU A 12 -30.41 -137.79 REMARK 500 6 HIS A 13 82.16 -61.80 REMARK 500 6 TYR A 28 -57.71 -128.67 REMARK 500 6 ASN A 38 43.25 -75.43 REMARK 500 6 ASP A 45 73.89 60.22 REMARK 500 6 GLU A 77 102.27 -59.98 REMARK 500 6 ASN A 79 -174.01 -173.51 REMARK 500 6 LEU A 81 92.00 57.58 REMARK 500 7 TYR A 28 -70.77 -86.42 REMARK 500 7 CYS A 41 -69.17 -145.26 REMARK 500 8 ILE A 4 90.68 -61.57 REMARK 500 8 LEU A 12 42.79 -86.85 REMARK 500 8 HIS A 27 -62.76 -94.15 REMARK 500 8 ASP A 45 73.28 61.60 REMARK 500 8 PRO A 46 99.73 -66.37 REMARK 500 8 LYS A 76 85.66 -57.79 REMARK 500 9 ALA A 2 -69.47 69.90 REMARK 500 9 TYR A 28 -70.52 -98.89 REMARK 500 9 PRO A 46 42.76 -76.97 REMARK 500 9 ASP A 59 -75.99 -80.66 REMARK 500 10 THR A 6 -63.95 70.19 REMARK 500 10 HIS A 13 139.82 68.68 REMARK 500 10 TYR A 28 -70.69 -84.33 REMARK 500 10 ASP A 45 76.33 62.33 REMARK 500 11 ASN A 9 117.34 -164.32 REMARK 500 11 TYR A 28 -62.46 -98.94 REMARK 500 REMARK 500 THIS ENTRY HAS 91 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: VFR117 RELATED DB: TARGETDB REMARK 900 RELATED ID: 15491 RELATED DB: BMRB DBREF 2JVW A 1 80 UNP Q5E7H1 Q5E7H1_VIBF1 1 80 SEQADV 2JVW LEU A 81 UNP Q5E7H1 EXPRESSION TAG SEQADV 2JVW GLU A 82 UNP Q5E7H1 EXPRESSION TAG SEQADV 2JVW HIS A 83 UNP Q5E7H1 EXPRESSION TAG SEQADV 2JVW HIS A 84 UNP Q5E7H1 EXPRESSION TAG SEQADV 2JVW HIS A 85 UNP Q5E7H1 EXPRESSION TAG SEQADV 2JVW HIS A 86 UNP Q5E7H1 EXPRESSION TAG SEQADV 2JVW HIS A 87 UNP Q5E7H1 EXPRESSION TAG SEQADV 2JVW HIS A 88 UNP Q5E7H1 EXPRESSION TAG SEQRES 1 A 88 MET ALA LEU ILE MET THR GLN GLN ASN ASN PRO LEU HIS SEQRES 2 A 88 GLY ILE THR LEU GLN LYS LEU LEU THR GLU LEU VAL GLU SEQRES 3 A 88 HIS TYR GLY TRP GLU GLU LEU SER TYR MET VAL ASN ILE SEQRES 4 A 88 ASN CYS PHE LYS LYS ASP PRO SER ILE LYS SER SER LEU SEQRES 5 A 88 LYS PHE LEU ARG LYS THR ASP TRP ALA ARG GLU ARG VAL SEQRES 6 A 88 GLU ASN ILE TYR LEU LYS LEU GLN ARG HIS LYS GLU ARG SEQRES 7 A 88 ASN GLN LEU GLU HIS HIS HIS HIS HIS HIS HELIX 1 1 THR A 16 TYR A 28 1 13 HELIX 2 2 GLY A 29 VAL A 37 1 9 HELIX 3 3 SER A 47 THR A 58 1 12 HELIX 4 4 THR A 58 ARG A 74 1 17 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