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- PDB-1s24: Rubredoxin domain II from Pseudomonas oleovorans -

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Basic information

Entry
Database: PDB / ID: 1s24
TitleRubredoxin domain II from Pseudomonas oleovorans
ComponentsRubredoxin 2
KeywordsELECTRON TRANSPORT / Rubredoxin
Function / homology
Function and homology information


alkane catabolic process / : / iron ion binding / cytoplasm
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 speciesPseudomonas oleovorans (bacteria)
MethodSOLUTION NMR / Aria protocol was used to deal with ambiguous distance restraints, some NOE assignment. Simulating annealing was used.
AuthorsPerry, A. / Tambyrajah, W. / Grossmann, J.G. / Lian, L.Y. / Scrutton, N.S.
CitationJournal: Biochemistry / Year: 2004
Title: Solution structure of the two-iron rubredoxin of Pseudomonas oleovorans determined by NMR spectroscopy and solution X-ray scattering and interactions with rubredoxin reductase.
Authors: Perry, A. / Tambyrajah, W. / Grossmann, J.G. / Lian, L.Y. / Scrutton, N.S.
History
DepositionJan 8, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 4, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / 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_nmr_software.name / _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_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 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 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,8142
Polymers9,7021
Non-polymers1121
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 / 20The submitted conformer models are the 20 structures with the lowest
RepresentativeModel #1lowest energy

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Components

#1: Protein Rubredoxin 2 / Two-iron rubredoxin


Mass: 9701.712 Da / Num. of mol.: 1 / Fragment: Rubredoxin C-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas oleovorans (bacteria) / Gene: ALKG / Production host: Escherichia coli (E. coli) / References: UniProt: P00272
#2: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cd

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111DQF-COSY
221DQF-COSY
1312D TOCSY
2412D TOCSY
3512D TOCSY
4612D TOCSY
1712D NOESY
2812D NOESY
NMR detailsText: This structure was determined using standard 2D homonuclear techniques.

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Sample preparation

DetailsContents: 10mM Rubredoxin C-terminal domain; 20 mM potassium phosphate buffer, 10mM Cd(II)
Solvent system: 90% H2O/10% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
140mM 61 atm298 K
240mM 61 atm310 K
340mM 7.61 atm298 K
440mM 7.61 atm310 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker DMX / Manufacturer: Bruker / Model: DMX / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3Brukercollection
XwinNMR3Brukerdata analysis
CNS1Nilgesprocessing
CNS1Nilgesstructure solution
CNS1Nilgesrefinement
RefinementMethod: Aria protocol was used to deal with ambiguous distance restraints, some NOE assignment. Simulating annealing was used.
Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: The submitted conformer models are the 20 structures with the lowest
Conformers calculated total number: 20 / Conformers submitted total number: 20

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