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- PDB-2jvw: Solution NMR structure of uncharacterized protein Q5E7H1 from Vib... -

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Basic information

Entry
Database: PDB / ID: 2jvw
TitleSolution NMR structure of uncharacterized protein Q5E7H1 from Vibrio fischeri. Northeast Structural Genomics target VfR117
ComponentsUncharacterized protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / solution NMR structure / alpha helical protein / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homologyDNA-binding protein VF530-like / DNA-binding protein VF530 / SAP domain / Transcription Termination Factor Rho, Rna-binding Domain; Chain A, Domain 1 / SAP domain superfamily / double-stranded DNA binding / Orthogonal Bundle / Mainly Alpha / DNA-binding protein VF_0530
Function and homology information
Biological speciesVibrio fischeri (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsAramini, J.M. / Rossi, P. / Wang, D. / Nwosu, C. / Owens, L.A. / Xiao, R. / Liu, J. / Baran, M.C. / Swapna, G.V.T. / Acton, T.B. ...Aramini, J.M. / Rossi, P. / Wang, D. / Nwosu, C. / Owens, L.A. / Xiao, R. / Liu, J. / Baran, M.C. / Swapna, G.V.T. / Acton, T.B. / Rost, B. / Montelione, G.T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: Proteins / Year: 2011
Title: Solution NMR structure of VF0530 from Vibrio fischeri reveals a nucleic acid-binding function.
Authors: Aramini, J.M. / Rossi, P. / Fischer, M. / Xiao, R. / Acton, T.B. / Montelione, G.T.
History
DepositionSep 26, 2007Deposition site: BMRB / Processing site: RCSB
Revision 1.0Oct 16, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Aug 3, 2011Group: Database references
Revision 1.3Sep 21, 2011Group: Database references
Revision 1.4Feb 19, 2020Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name ..._pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.5Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status / struct_ref
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _struct_ref.pdbx_seq_one_letter_code

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)10,7461
Polymers10,7461
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Uncharacterized protein


Mass: 10746.398 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio fischeri (bacteria) / Species: Aliivibrio fischeri / Strain: ES114 / Gene: VF0530 / Plasmid: VfR117-21.1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)MGK / References: UniProt: Q5E7H1

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D HNCO
1413D HN(CA)CO
1513D HN(COCA)CB
1613D HN(CA)CB
1713D HBHA(CO)NH
1813D (H)CCH-COSY
1913D (H)CCH-TOCSY
11013D CCH-TOCSY
11113D CCH-TOCSY aromatic
11213D simultaneous CN-NOESY
11313D HNHA
11422D 1H-13C HSQC stereospecific Leu/Val methyl
NMR detailsText: THE PROTEIN IS MONOMERIC BY GEL FILTRATION CHROMATOGRAPHY AND STATIC LIGHT SCATTERING. THE STRUCTURE WAS DETERMINED USING TRIPLE RESONANCE NMR SPECTROSCOPY. AUTOMATED BACKBONE ASSIGNMENTS WERE ...Text: THE PROTEIN IS MONOMERIC BY GEL FILTRATION CHROMATOGRAPHY AND STATIC LIGHT SCATTERING. THE STRUCTURE WAS DETERMINED USING TRIPLE RESONANCE NMR SPECTROSCOPY. AUTOMATED BACKBONE ASSIGNMENTS WERE MADE USING AUTOASSIGN, AND THE SIDE CHAIN ASSIGNMENTS WERE COMPLETED MANUALLY. AUTOMATIC NOESY ASSIGNMENTS WERE DETERMINED USING CYANA 2.1. DIHEDRAL ANGLE CONSTRAINTS WERE OBTAINED FROM TALOS. HYDROGEN BOND CONSTRAINTS WERE DETERMINED USING BOTH AUTOSTRUCTURE AND CYANA, AND WERE APPLIED ONLY IN THE FINAL REFINEMENT STAGE (CNS) OF THE STRUCTURE DETERMINATION. COMPLETENESS OF NMR ASSIGNMENTS (EXCLUDING C-TERMINAL HHHHHH): BACKBONE, 98.8%, SIDE CHAIN, 95.3%, AROMATICS, 100%, STEREOSPECIFIC METHYL, 100%, STEREOSPECIFIC SIDE CHAIN NH2: 100%. FINAL STRUCTURE QUALITY FACTORS (FOR RESIDUES 1 TO 82, PSVS 1.3), WHERE ORDERED RESIDUES [S(PHI) + S(PSI) > 1.8] COMPRISE: 15-37,42-43,46-75: (A) RMSD (ORDERED RESIDUES): BB, 0.5, HEAVY ATOM, 1.1. (B) RAMACHANDRAN STATISTICS FOR ORDERED RESIDUES: MOST FAVORED, 93.9, ADDITIONALLY ALLOWED, 6.1%, GENEROUSLY ALLOWED, 0.0%, DISALLOWED, 0.0%. (C) PROCHECK SCORES FOR ORDERED RESIDUES (RAW/Z-): PHI-PSI, 0.17/0.98, ALL, 0.19/1.12. (D) MOLPROBITY CLASH SCORE (RAW/Z-): 14.65/-0.99. (E) RPF SCORES FOR GOODNESS OF FIT TO NOESY DATA (RESIDUES 1-82): RECALL, 0.989, PRECISION, 0.945, F-MEASURE, 0.967, DP-SCORE, 0.810. (F) NUMBER OF CLOSE CONTACTS PER 20 MODELS: 2. THE C-TERMINAL HIS TAG RESIDUES OF THE PROTEIN (HHHHHH) WERE NOT INCLUDED IN THE STRUCTURE CALCULATIONS AND HAVE BEEN OMITTED FROM THIS DEPOSITION. COORDINATES FOR THE FOLLOWING RESIDUES ARE NOT WELL DETERMINED [S(PHI) + S(PSI) < 1.8]: 1-14,38-41,44-45,76-82.

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Sample preparation

Details
Solution-IDContentsSolvent system
10.95 mM [U-100% 13C; U-100% 15N] VfR117, 20 mM ammonium acetate, 100 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 0.02 % sodium azide, 95% H2O/5% D2O95% H2O/5% D2O
21.08 mM [U-5% 13C; U-100% 15N] VfR117, 20 mM ammonium acetate, 100 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 0.02 % sodium azide, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.95 mMVfR117[U-100% 13C; U-100% 15N]1
20 mMammonium acetate1
100 mMsodium chloride1
5 mMcalcium chloride1
10 mMDTT1
0.02 %sodium azide1
1.08 mMVfR117[U-5% 13C; U-100% 15N]2
20 mMammonium acetate2
100 mMsodium chloride2
5 mMcalcium chloride2
10 mMDTT2
0.02 %sodium azide2
Sample conditionsIonic strength: 0.1 / pH: 4.5 / Pressure: ambient / Temperature: 293 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
Bruker AvanceBrukerAVANCE6002

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin1.3Bruker Biospincollection
AutoAssign2.4.0Zimmerman, Moseley, Kulikowski and Montelionechemical shift assignment
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
NMRPipe2.3Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
AutoStructure2.1.1Huang, Tejero, Powers and Montelionerpf analysis
PSVS1.3Bhattacharya and Montelionestructure validation
PdbStat5Tejero and Montelionepdb analysis
Sparky3.11Goddarddata analysis
Sparky3.11Goddardpeak picking
CNS1.1Brunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: THE FINAL STRUCTURES ARE BASED ON A TOTAL OF 1424 CONFORMATIONALLY-RESTRICTING NOE-DERIVED DISTANCE CONSTRAINTS, 88 DIHEDRAL ANGLE CONSTRAINTS, AND 46 HYDROGEN BOND CONSTRAINTS (19.2 ...Details: THE FINAL STRUCTURES ARE BASED ON A TOTAL OF 1424 CONFORMATIONALLY-RESTRICTING NOE-DERIVED DISTANCE CONSTRAINTS, 88 DIHEDRAL ANGLE CONSTRAINTS, AND 46 HYDROGEN BOND CONSTRAINTS (19.2 CONSTRAINTS PER RESIDUE, 3.3 LONG RANGE CONSTRAINTS PER RESIDUE, COMPUTED FOR RESIDUES 1 TO 82 BY PSVS 1.3). STRUCTURE DETERMINATION WAS PERFORMED ITERATIVELY USING CYANA 2.1. THE 20 STRUCTURES OUT OF 100 WITH THE LOWEST TARGET FUNCTION WERE FURTHER REFINED BY RESTRAINED MOLECULAR DYNAMICS/ENERGY MINIMIZATION IN EXPLICIT WATER (CNS) WITH PARAM19.
NMR constraintsNOE constraints total: 1424 / NOE intraresidue total count: 489 / NOE long range total count: 270 / NOE medium range total count: 285 / NOE sequential total count: 380
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20 / Maximum lower distance constraint violation: 0 Å / Maximum torsion angle constraint violation: 1.2 ° / Maximum upper distance constraint violation: 0.32 Å / Torsion angle constraint violation method: PDBStat
NMR ensemble rmsDistance rms dev: 0.01 Å

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