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- PDB-2m4y: Rubredoxin type protein from Mycobacterium ulcerans -

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Basic information

Entry
Database: PDB / ID: 2m4y
TitleRubredoxin type protein from Mycobacterium ulcerans
ComponentsRubredoxin
KeywordsELECTRON TRANSPORT / rubredoxin / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Function / homology
Function and homology information


: / 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 ulcerans (bacteria)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsBarnwal, R. / Varani, G. / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To be Published
Title: Structure of Rubredoxin type protein from Mycobacterium ulcerans
Authors: Barnwal, R. / Varani, G.
History
DepositionFeb 11, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0Mar 13, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 10, 2014Group: Database references
Revision 1.2Sep 17, 2014Group: Database references
Revision 1.3May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Rubredoxin


Theoretical massNumber of molelcules
Total (without water)6,4621
Polymers6,4621
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)10 / 100target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Rubredoxin


Mass: 6462.183 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium ulcerans (bacteria) / Strain: Agy99 / Gene: rubA, MUL_2595 / Plasmid: pET28a-AVA / Production host: Escherichia coli (E. coli) / References: UniProt: A0PRF8

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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 CBCA(CO)NH
1413D HNCO
1513D HN(CA)CB
1613D (H)CCH-TOCSY
1713D 1H-15N NOESY
1813D 1H-13C NOESY

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Sample preparation

DetailsContents: 1.2 mM [U-98% 15N] rubredoxin type protein, 1.4 mM [U-95% 13C; U-95% 15N] rubredoxin type protein, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.2 mMrubredoxin type protein-1[U-98% 15N]1
1.4 mMrubredoxin type protein-2[U-95% 13C; U-95% 15N]1
Sample conditionspH: 7 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AMXBrukerAMX5001
Bruker AvanceBrukerAVANCE6002

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Processing

NMR software
NameDeveloperClassification
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
TopSpinBruker Biospincollection
TopSpinBruker Biospinprocessing
CCPNMRCCPNdata analysis
CCPNMRCCPNchemical shift assignment
CCPNMRCCPNpeak picking
CYANAGuntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 10

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