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- PDB-2jvm: Solution NMR structure of Rhodobacter sphaeroides protein RHOS4_2... -

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Basic information

Entry
Database: PDB / ID: 2jvm
TitleSolution NMR structure of Rhodobacter sphaeroides protein RHOS4_26430. Northeast Structural Genomics Consortium target RhR95
ComponentsUncharacterized protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / alpha+beta / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homologyq5lls5 like domains / HSP40/DNAj peptide-binding domain / Zinc finger, CHCC-type / Zinc-finger domain / Sandwich / Mainly Beta / Zinc finger CHCC-type domain-containing protein
Function and homology information
Biological speciesRhodobacter sphaeroides 2.4.1 (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsEletsky, A. / Sukumaran, D. / Zhang, Q. / Parish, D. / Xu, D. / Wang, H. / Janjua, H. / Owens, L. / Xiao, R. / Liu, J. ...Eletsky, A. / Sukumaran, D. / Zhang, Q. / Parish, D. / Xu, D. / Wang, H. / Janjua, H. / Owens, L. / Xiao, R. / Liu, J. / Baran, M.C. / Swapna, G.V.T. / Acton, T.B. / Rost, B. / Montelione, G.T. / Szyperski, T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Solution NMR Structure of Rhodobacter sphaeroides protein RHOS4_26430.
Authors: Eletsky, A. / Sukumaran, D. / Zhang, Q. / Parish, D. / Xu, D. / Wang, H. / Janjua, H. / Owens, L. / Xiao, R. / Liu, J. / Baran, M.C. / Swapna, G.V.T. / Acton, T.B. / Rost, B. / Montelione, G.T. / Szyperski, T.
History
DepositionSep 21, 2007Deposition site: BMRB / Processing site: RCSB
Revision 1.0Oct 16, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)9,1751
Polymers9,1751
Non-polymers00
Water00
1


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

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Components

#1: Protein Uncharacterized protein


Mass: 9175.360 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodobacter sphaeroides 2.4.1 (bacteria)
Species: Rhodobacter sphaeroides / Strain: 2.4.1, NCIB 8253, DSM 158 / Gene: RSP_1027, RHOS4_26430 / Plasmid: pET21-23C / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: Q3IZ23

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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 aliphatic
1313D HNCO
141(4,3)D GFT CABCA(CO)NHN
151(4,3)D GFT HNNCABCA
161(4,3)D GFT HABCABCA(CO)NHN
171(4,3)D GFT (H)CCH-COSY aliphatic
181(4,3)D GFT (H)CCH-COSY aromatic
1912D 1H-15N long-range HSQC
11022D 1H-13C ct-HSQC 28ms
11113D 1H-15N/13C NOESY
11212D 1H-13C HSQC aromatic
11312D 1H-13C ct-HSQC aliphatic
11412D 1H-13C ct-HSQC aromatic
11513D (H)CCH-TOCSY
11622D 1H-13C ct-HSQC 56ms

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Sample preparation

Details
Solution-IDContentsSolvent system
10.7 mM [U-100% 13C; U-100% 15N] rhr95_protein, 5 mM calcium chloride, 100 mM sodium chloride, 20 mM ammonium acetate, 10 mM DTT, 0.02 % sodium azide, 95% H2O/5% D2O95% H2O/5% D2O
20.7 mM [U-5% 13C; U-100% 15N] rhr95_protein, 5 mM calcium chloride, 100 mM sodium chloride, 20 mM ammonium acetate, 10 mM DTT, 0.02 % sodium azide, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.7 mMrhr95_protein[U-100% 13C; U-100% 15N]1
5 mMcalcium chloride1
100 mMsodium chloride1
20 mMammonium acetate1
10 mMDTT1
0.02 %sodium azide1
0.7 mMrhr95_protein[U-5% 13C; U-100% 15N]2
5 mMcalcium chloride2
100 mMsodium chloride2
20 mMammonium acetate2
10 mMDTT2
0.02 %sodium azide2
Sample conditionsIonic strength: 135 / pH: 5.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 750 MHz

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Processing

NMR software
NameVersionDeveloperClassification
VnmrJ2.1BVariancollection
PROSA6.0.2Guntertprocessing
CARA1.8.4Kellerdata analysis
CARA1.8.4Kellerpeak picking
CARA1.8.4Kellerchemical shift assignment
AutoAssign1.15.1Zimmerman, Moseley, Kulikowski and Montelionechemical shift assignment
AutoStructure2.1.1Huang, Tejero, Powers and Montelionestructure solution
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
CNS1.1Brunger, Adams, Clore, Gros, Nilges and Readgeometry optimization
PSVSBhattacharya and Montelionestructure validation
XEASY1.3.12Bartels et al.data analysis
CYANA2.1Guntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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