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- PDB-2kn9: Solution structure of zinc-substituted rubredoxin B (Rv3250c) fro... -

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Basic information

Entry
Database: PDB / ID: 2kn9
TitleSolution structure of zinc-substituted rubredoxin B (Rv3250c) from Mycobacterium tuberculosis. Seattle Structural Genomics Center for Infectious Disease target MytuD.01635.a
ComponentsRubredoxin
KeywordsELECTRON TRANSPORT / tuberculosis / metalloprotein / rubredoxin / SSGCID / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / Iron / Metal-binding / Transport
Function / homology
Function and homology information


: / iron ion binding
Similarity search - Function
Rubredoxin, iron-binding site / Rubredoxin signature. / Rubrerythrin, domain 2 - #10 / Rubredoxin domain / Rubredoxin / Rubredoxin-like domain / Rubredoxin-like domain profile. / Rubrerythrin, domain 2 / Single Sheet / Mainly Beta
Similarity search - Domain/homology
Biological speciesMycobacterium tuberculosis (bacteria)
MethodSOLUTION NMR / torsion angle dynamics
Model detailsclosest to the average, model 1
AuthorsBuchko, G.W. / Hewitt, S.N. / Napuli, A.J. / Van Voorhis, W.C. / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2011
Title: Solution-state NMR structure and biophysical characterization of zinc-substituted rubredoxin B (Rv3250c) from Mycobacterium tuberculosis.
Authors: Buchko, G.W. / Hewitt, S.N. / Napuli, A.J. / Van Voorhis, W.C. / Myler, P.J.
History
DepositionAug 20, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Sep 15, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 21, 2011Group: Database references
Revision 1.3May 1, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / struct_ref_seq_dif / struct_site
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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Rubredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,1572
Polymers9,0921
Non-polymers651
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 / 100target function
RepresentativeModel #1closest to the average

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Components

#1: Protein Rubredoxin /


Mass: 9091.978 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: MT3348, rubB, Rv3250c / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O05893
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn

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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 HN(CA)CB
1413D HN(COCA)CB
1513D C(CO)NH
1613D HNCO
1713D 1H-15N NOESY
1813D 1H-13C NOESY
192Deuterium exchange

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Sample preparation

Details
Solution-IDContents
1100 mM sodium chloride, 1 mM DTT, 20 mM TRIS, 1-2 mM [U-98% 13C; U-98% 15N] Rv3250c, 90% H2O/10% D2O
2100 mM sodium chloride, 1 mM DTT, 20 mM TRIS, 1-2 mM [U-98% 13C; U-98% 15N] Rv3250c, 100% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
100 mMsodium chloride-11
1 mMDTT-21
20 mMTRIS-31
mMRv3250c-4[U-98% 13C; U-98% 15N]1-21
100 mMsodium chloride-52
1 mMDTT-62
20 mMTRIS-72
mMRv3250c-8[U-98% 13C; U-98% 15N]1-22
Sample conditionsIonic strength: 0.12 / pH: 7.1 / Pressure: ambient / Temperature: 293 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA7501
Varian INOVAVarianINOVA6002

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
Felix2007Accelrys Software Inc.processing
Sparky3.115Goddarddata analysis
PSVSBhattacharya and Montelionedata analysis
CNS1.1Brunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
Details: Structure determination was performed iteratively using CYANA (AUTO NoesyAssign). A total of 20 structures out of 100 with lowest target function from the final set of CYANA calculations ...Details: Structure determination was performed iteratively using CYANA (AUTO NoesyAssign). A total of 20 structures out of 100 with lowest target function from the final set of CYANA calculations were taken and refined by restrained molecular dynamics in explicit water (CNS). ZN-SG (2.20 - 2.40) and SG-SG (3.4 - 4.4) restraints were added only to the final set of CYANA calculations on the basis of calculations without the restraints and other physical data. At the explicit water refinement stage, 5% was added to the upper bound restraint.
NMR constraintsNOE constraints total: 892 / NOE intraresidue total count: 204 / NOE long range total count: 286 / NOE medium range total count: 157 / NOE sequential total count: 245 / Protein phi angle constraints total count: 37 / Protein psi angle constraints total count: 37
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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