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- PDB-2jvd: Solution NMR structure of the folded N-terminal fragment of UPF02... -

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Basic information

Entry
Database: PDB / ID: 2jvd
TitleSolution NMR structure of the folded N-terminal fragment of UPF0291 protein ynzC from Bacillus subtilis. Northeast Structural Genomics target SR384-1-46
ComponentsUPF0291 protein ynzC
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / solution NMR structure / construct optimization / Cytoplasm / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homologyProtein of unknown function DUF896 / Bacterial protein of unknown function (DUF896) / Helix hairpin bin / Helix Hairpins / Orthogonal Bundle / Mainly Alpha / cytoplasm / UPF0291 protein YnzC
Function and homology information
Biological speciesBacillus subtilis (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsAramini, J.M. / Sharma, S. / Huang, Y.J. / Zhao, L. / Owens, L.A. / Stokes, K. / Jiang, M. / Xiao, R. / Baran, M.C. / Swapna, G.V.T. ...Aramini, J.M. / Sharma, S. / Huang, Y.J. / Zhao, L. / Owens, L.A. / Stokes, K. / Jiang, M. / Xiao, R. / Baran, M.C. / Swapna, G.V.T. / Acton, T.B. / Montelione, G.T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: Proteins / Year: 2008
Title: Solution NMR structure of the SOS response protein YnzC from Bacillus subtilis.
Authors: Aramini, J.M. / Sharma, S. / Huang, Y.J. / Swapna, G.V. / Ho, C.K. / Shetty, K. / Cunningham, K. / Ma, L.C. / Zhao, L. / Owens, L.A. / Jiang, M. / Xiao, R. / Liu, J. / Baran, M.C. / Acton, T. ...Authors: Aramini, J.M. / Sharma, S. / Huang, Y.J. / Swapna, G.V. / Ho, C.K. / Shetty, K. / Cunningham, K. / Ma, L.C. / Zhao, L. / Owens, L.A. / Jiang, M. / Xiao, R. / Liu, J. / Baran, M.C. / Acton, T.B. / Rost, B. / Montelione, G.T.
History
DepositionSep 18, 2007Deposition site: BMRB / Processing site: RCSB
Revision 1.0Oct 2, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 19, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / 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 1.3Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.4May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: UPF0291 protein ynzC


Theoretical massNumber of molelcules
Total (without water)6,2901
Polymers6,2901
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein UPF0291 protein ynzC


Mass: 6290.241 Da / Num. of mol.: 1 / Fragment: Residues 1-46
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: 168 / Gene: ynzC, BSU17880 / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)MGK / References: UniProt: O31818

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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(CA)CB
1613D HN(COCA)CB
1713D HBHA(CO)NH
1813D (H)CCH-COSY
1913D CCH-TOCSY
11013D simultaneous CN-NOESY
11113D HNHA
11222D 1H-13C HSQC stereospecific Leu/Val methyl
NMR detailsText: THE PROTEIN IS MONOMERIC BY STATIC LIGHT SCATTERING. THE STRUCTURE WAS DETERMINED USING TRIPLE RESONANCE NMR SPECTROSCOPY. AUTOMATED BACKBONE ASSIGNMENTS WERE MADE USING AUTOASSIGN, AND THE ...Text: THE PROTEIN IS MONOMERIC BY 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, 96.9%, AROMATICS, 100%, STEREOSPECIFIC METHYL, 100%, STEREOSPECIFIC SIDE CHAIN NH2: 100%. FINAL STRUCTURE QUALITY FACTORS (FOR RESIDUES 1 TO 48, PSVS 1.3), WHERE ORDERED RESIDUES [S(PHI) + S(PSI) > 1.8] COMPRISE: 2-38: (A) RMSD (ORDERED RESIDUES): BB, 0.4, HEAVY ATOM, 0.9. (B) RAMACHANDRAN STATISTICS FOR ORDERED RESIDUES: MOST FAVORED, 98.6%, ADDITIONALLY ALLOWED, 1.4%, GENEROUSLY ALLOWED, 0.0%, DISALLOWED, 0.0%. (C) PROCHECK SCORES FOR ORDERED RESIDUES (RAW/Z-): PHI-PSI, 0.53/2.40, ALL, 0.50/2.96. (D) MOLPROBITY CLASH SCORE (RAW/Z-): 15.44/-1.12. (E) RPF SCORES FOR GOODNESS OF FIT TO NOESY DATA (RESIDUES 1-48): RECALL, 0.988, PRECISION, 0.944, F-MEASURE, 0.966, DP-SCORE, 0.822. (F) NUMBER OF CLOSE CONTACTS PER 20 MODELS: NONE. 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]: 1,39-48.

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Sample preparation

Details
Solution-IDContentsSolvent system
11.36 mM [U-100% 13C; U-100% 15N] SR384-1-46, 20 mM MES, 100 mM sodium chloride, 10 mM DTT, 5 mM calcium chloride, 0.02 % sodium azide, 95% H2O/5% D2O95% H2O/5% D2O
21.1 mM [U-5% 13C; U-100% 15N] SR384-1-46, 20 mM MES, 100 mM sodium chloride, 10 mM DTT, 5 mM calcium chloride, 0.02 % sodium azide, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.36 mMSR384-1-46[U-100% 13C; U-100% 15N]1
20 mMMES1
100 mMsodium chloride1
10 mMDTT1
5 mMcalcium chloride1
0.02 %sodium azide1
1.1 mMSR384-1-46[U-5% 13C; U-100% 15N]2
20 mMMES2
100 mMsodium chloride2
10 mMDTT2
5 mMcalcium chloride2
0.02 %sodium azide2
Sample conditionsIonic strength: 100 / pH: 6.5 / Pressure: ambient / Temperature: 293 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
Varian INOVAVarianINOVA6002

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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 Montelionedata analysis
AutoStructure2.1.1Huang, Tejero, Powers and Montelionerpf calculation
PSVS1.3Bhattacharya and Montelionestructure validation
PdbStat5Tejero and Montelionepdb analysis
ProcheckLaskowski, MacArthur, Smith, Jones, Hutchinson, Morris, Mossstructure validation
MolProbityRichardsonstructure validation
Sparky3.11Goddardpeak picking
Sparky3.11Goddarddata analysis
VNMR6.1CVariancollection
CYANA2.1Guntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: THE FINAL STRUCTURES ARE BASED ON A TOTAL OF 1022 CONFORMATIONALLY-RESTRICTING NOE-DERIVED DISTANCE CONSTRAINTS, 68 DIHEDRAL ANGLE CONSTRAINTS, AND 48 HYDROGEN BOND CONSTRAINTS (25.9 ...Details: THE FINAL STRUCTURES ARE BASED ON A TOTAL OF 1022 CONFORMATIONALLY-RESTRICTING NOE-DERIVED DISTANCE CONSTRAINTS, 68 DIHEDRAL ANGLE CONSTRAINTS, AND 48 HYDROGEN BOND CONSTRAINTS (25.9 CONSTRAINTS PER RESIDUE, 4.4 LONG RANGE CONSTRAINTS PER RESIDUE, COMPUTED FOR RESIDUES 1 TO 48 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: 1040 / NOE intraresidue total count: 328 / NOE long range total count: 196 / NOE medium range total count: 315 / NOE sequential total count: 201 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 66 / Protein psi angle constraints total count: 66
NMR representativeSelection criteria: lowest energy
NMR ensembleAverage torsion angle constraint violation: 0 °
Conformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20 / Maximum torsion angle constraint violation: 0 ° / Maximum upper distance constraint violation: 0.31 Å / Torsion angle constraint violation method: PDBStat
NMR ensemble rmsDistance rms dev: 0 Å

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