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- PDB-2kkd: NMR Structure of Ni Substitued Desulfovibrio vulgaris Rubredoxin -

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Basic information

Entry
Database: PDB / ID: 2kkd
TitleNMR Structure of Ni Substitued Desulfovibrio vulgaris Rubredoxin
ComponentsRubredoxin
KeywordsELECTRON TRANSPORT / [Fe-4S] / iron / metal-binding / Cytoplasm / Transport
Function / homology
Function and homology information


alkane catabolic process / electron transfer activity / iron ion binding / cytoplasm
Similarity search - Function
Rubredoxin / 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
NICKEL (II) ION / Rubredoxin
Similarity search - Component
Biological speciesDesulfovibrio vulgaris str. Hildenborough (bacteria)
MethodSOLUTION NMR / torsion angle dynamics
Model detailsclosest to the average, model 6
AuthorsNunes, S.G. / Volkman, B.F. / Moura, J.J.G. / Moura, I. / Macedo, A.L. / Markley, J.L. / Duarte, I.C.
CitationJournal: J.Biol.Inorg.Chem. / Year: 2010
Title: An NMR structural study of nickel-substituted rubredoxin
Authors: Goodfellow, B.J. / Duarte, I.C. / Macedo, A.L. / Volkman, B.F. / Nunes, S.G. / Moura, I. / Markley, J.L. / Moura, J.J.
History
DepositionJun 18, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Dec 22, 2009Provider: repository / Type: Initial release
SupersessionJan 26, 2010ID: 2QKZ
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3May 22, 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: Rubredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,6372
Polymers5,5781
Non-polymers591
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)15 / 400target function
RepresentativeModel #1closest to the average

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Components

#1: Protein Rubredoxin / Rd


Mass: 5578.174 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Desulfovibrio vulgaris str. Hildenborough (bacteria)
Strain: Hidenborough/ATCC 29579/NCIMB 8303 / Gene: rub, DVU_3184 / Production host: Escherichia coli (E. coli) / References: UniProt: P00269
#2: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 1H-15N NOESY
1213D 1H-15N TOCSY
1312D 1H-15N HSQC
1422D 1H-1H NOESY
1522D 1H-1H TOCSY
1622D NOESY with fast recycle
1731D NOE difference with super-WEFT
1832D NOESY with fast recycle
1932D 1H-1H NOESY
11032D 1H-1H TOCSY

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Sample preparation

Details
Solution-IDContentsSolvent system
150 mM sodium phosphate-1, 90% H2O/10% D2O90% H2O/10% D2O
250 mM sodium phosphate-2, 90% H2O/10% D2O90% H2O/10% D2O
32 mM sodium azide-3, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
50 mMsodium phosphate-11
50 mMsodium phosphate-22
2 mMsodium azide-33
Sample conditionsIonic strength: 0.05 / pH: 7.2 / Pressure: ambient / Temperature: 296 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX5001
Bruker DRXBrukerDRX6002

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Processing

NMR softwareName: CYANA / Developer: Guntert P. / Classification: refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1 / Details: structure refinement used pseudocontact shifts
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 400 / Conformers submitted total number: 15

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