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- PDB-2jr2: Solution NMR structure of homodimer CPS_2611 from Colwellia psych... -

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Basic information

Entry
Database: PDB / ID: 2jr2
TitleSolution NMR structure of homodimer CPS_2611 from Colwellia psychrerythraea. Northeast Structural Genomics Consortium target CsR4.
ComponentsUPF0352 protein CPS_2611
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / dimer / all alpha helix / homodimer / PSI / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homologyUncharacterised protein family UPF0352 / YejL-like superfamily / Protein of unknown function (DUF1414) / YejL-like / YejL-like / Orthogonal Bundle / Mainly Alpha / UPF0352 protein CPS_2611
Function and homology information
Biological speciesColwellia psychrerythraea (bacteria)
MethodSOLUTION NMR / simulated annealing, CNS water refinement
Model detailshomodimer, all alpha helix
AuthorsRamelot, T.A. / Cort, J.R. / Wang, H. / Nwosu, C. / Cunningham, K. / Owens, L. / Ma, L.-C. / Xiao, R. / Liu, J. / Baran, M.C. ...Ramelot, T.A. / Cort, J.R. / Wang, H. / Nwosu, C. / Cunningham, K. / Owens, L. / Ma, L.-C. / Xiao, R. / Liu, J. / Baran, M.C. / Swapna, G. / Acton, T.B. / Rost, B. / Montelione, G.T. / Kennedy, M.A. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Solution NMR structure of homodimer CPS_2611 from Colwellia psychrerythraea.
Authors: Ramelot, T.A. / Cort, J.R. / Montelione, G.A. / Kennedy, M.A.
History
DepositionJun 19, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 3, 2007Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.4Feb 19, 2020Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.5Jun 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 1.6Dec 20, 2023Group: Data collection / Other
Category: chem_comp_atom / chem_comp_bond / pdbx_database_status
Item: _pdbx_database_status.deposit_site
Revision 1.7May 8, 2024Group: Database references / Category: 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: UPF0352 protein CPS_2611
B: UPF0352 protein CPS_2611


Theoretical massNumber of molelcules
Total (without water)17,2102
Polymers17,2102
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 / 20all calculated structures submitted
RepresentativeModel #1closest to the average

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Components

#1: Protein UPF0352 protein CPS_2611


Mass: 8604.974 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Colwellia psychrerythraea (bacteria) / Strain: 34H / Gene: CPS_2611 / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pMGK / References: UniProt: Q481E4

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR / Details: homodimer, all helix
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D 1H-15N NOESY
1413D 1H-13C NOESY aliph
1513D HN(CA)CB
1622D 1H-13C HSQC
1734D 1H-13C NOESY
1813D HBHA(CO)NH
1913D HNHA
11013D CBCA(CO)NH
11113D HNCA
11213D HN(CO)CA
11313D HNCO
11413D C(CO)NH
11513D (H)CCH-COSY
11613D (H)CCH-TOCSY
11732D 1H-13C HSQC
11832D 1H-15N HSQC
11943D edited filtered 1H-13C NOESY
12013D 1H-13C NOESY arom

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM [U-13C; U-15N] protein, 100 mM sodium chloride, 20 mM ammonium acetate, 5 mM DTT, 0.02 % sodium azide, 5 mM calcium chloride, 95% H2O/5% D2O95% H2O/5% D2O
21.1 mM [U-5% 13C; U-100% 15N] protein, 100 mM sodium chloride, 5 mM calcium chloride, 20 mM ammonium acetate, 5 mM DTT, 0.02 % sodium azide, 95% H2O/5% D2O95% H2O/5% D2O
31 mM [U-13C; U-15N] protein, 100 mM sodium chloride, 5 mM calcium chloride, 20 mM ammonium acetate, 5 mM DTT, 0.02 % sodium azide, 100% D2O100% D2O
40.5 mM [U-13C; U-15N] protein, 100 mM sodium chloride, 5 mM calcium chloride, 20 mM ammonium acetate, 5 mM DTT, 0.02 % sodium azide, 0.5 mM protein, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMprotein[U-13C; U-15N]1
100 mMsodium chloride1
20 mMammonium acetate1
5 mMDTT1
0.02 %sodium azide1
5 mMcalcium chloride1
1.1 mMprotein[U-5% 13C; U-100% 15N]2
100 mMsodium chloride2
5 mMcalcium chloride2
20 mMammonium acetate2
5 mMDTT2
0.02 %sodium azide2
1. mMprotein[U-13C; U-15N]3
100 mMsodium chloride3
5 mMcalcium chloride3
20 mMammonium acetate3
5 mMDTT3
0.02 %sodium azide3
.5 mMprotein-1[U-13C; U-15N]4
100 mMsodium chloride4
5 mMcalcium chloride4
20 mMammonium acetate4
5 mMDTT4
0.02 %sodium azide4
0.5 mMprotein-24
Sample conditionsIonic strength: 0.1 / pH: 5.5 / Pressure: ambient / Temperature: 293 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipelinux9Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
VNMR6.1CVariancollection
AutoStructure2.1.1Huang, Tejero, Powers and Montelionedata analysis
X-PLOR NIH2.15.0Schwieters, Kuszewski, Tjandra and Clorestructure solution
CNS1.1Brunger, Adams, Clore, Gros, Nilges and Readrefinement
Sparky3.1Goddarddata analysis
PSVS1.3Bhattacharya and Montelionestructure validation
AutoAssignZimmerman, Moseley, Kulikowski and Montelionechemical shift assignment
RefinementMethod: simulated annealing, CNS water refinement / Software ordinal: 1 / Details: Xplor-NIH, CNS 1.1
NMR constraintsNOE constraints total: 1386 / NOE intraresidue total count: 0 / NOE long range total count: 464 / NOE medium range total count: 704 / NOE sequential total count: 218 / Hydrogen bond constraints total count: 3 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 106 / Protein psi angle constraints total count: 106
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 20 / Conformers submitted total number: 20 / Maximum lower distance constraint violation: 0.02 Å / Maximum torsion angle constraint violation: 0.04 ° / Maximum upper distance constraint violation: 0.04 Å
NMR ensemble rmsDistance rms dev: 0.001 Å

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