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- PDB-1jq4: [2Fe-2S] Domain of Methane Monooxygenase Reductase from Methyloco... -

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Basic information

Entry
Database: PDB / ID: 1jq4
Title[2Fe-2S] Domain of Methane Monooxygenase Reductase from Methylococcus capsulatus (Bath)
ComponentsMETHANE MONOOXYGENASE COMPONENT C
KeywordsOXIDOREDUCTASE / [2Fe-2S] ferredoxin
Function / homology
Function and homology information


methane monooxygenase (soluble) / : / : / 2 iron, 2 sulfur cluster binding / one-carbon metabolic process / metal ion binding
Similarity search - Function
: / Flavoprotein pyridine nucleotide cytochrome reductase-like, FAD-binding domain / Oxidoreductase FAD-binding domain / 2Fe-2S ferredoxin, iron-sulphur binding site / 2Fe-2S ferredoxin-type iron-sulfur binding region signature. / Beta-grasp domain / 2Fe-2S iron-sulfur cluster binding domain / Beta-grasp domain superfamily / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / 2Fe-2S ferredoxin-type iron-sulfur binding domain ...: / Flavoprotein pyridine nucleotide cytochrome reductase-like, FAD-binding domain / Oxidoreductase FAD-binding domain / 2Fe-2S ferredoxin, iron-sulphur binding site / 2Fe-2S ferredoxin-type iron-sulfur binding region signature. / Beta-grasp domain / 2Fe-2S iron-sulfur cluster binding domain / Beta-grasp domain superfamily / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / 2Fe-2S ferredoxin-type iron-sulfur binding domain / 2Fe-2S ferredoxin-like superfamily / Flavoprotein pyridine nucleotide cytochrome reductase / Oxidoreductase FAD/NAD(P)-binding / Oxidoreductase NAD-binding domain / FAD-binding domain, ferredoxin reductase-type / Ferredoxin-NADP reductase (FNR), nucleotide-binding domain / Ferredoxin reductase-type FAD binding domain profile. / Riboflavin synthase-like beta-barrel / Ubiquitin-like (UB roll) / Roll / Alpha Beta
Similarity search - Domain/homology
FE2/S2 (INORGANIC) CLUSTER / Methane monooxygenase component C
Similarity search - Component
Biological speciesMethylococcus capsulatus str. Bath (bacteria)
MethodSOLUTION NMR / NMR
AuthorsMueller, J. / Lugovskoy, A.A. / Wagner, G. / Lippard, S.J.
CitationJournal: Biochemistry / Year: 2002
Title: NMR structure of the [2Fe-2S] ferredoxin domain from soluble methane monooxygenase reductase and interaction with its hydroxylase.
Authors: Muller, J. / Lugovskoy, A.A. / Wagner, G. / Lippard, S.J.
History
DepositionAug 3, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 9, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 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: METHANE MONOOXYGENASE COMPONENT C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,1182
Polymers10,9421
Non-polymers1761
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 / 300target function
RepresentativeModel #9closest to the average

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Components

#1: Protein METHANE MONOOXYGENASE COMPONENT C / METHANE MONOOXYGENASE REDUCTASE


Mass: 10942.320 Da / Num. of mol.: 1 / Fragment: N-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methylococcus capsulatus str. Bath (bacteria)
Species: Methylococcus capsulatus / Strain: bath / Plasmid: pRED-Fd / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P22868, methane monooxygenase (soluble)
#2: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe2S2

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111A standard set of NMR experiments required for high resolution structure determination
1212D NOESY

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Sample preparation

DetailsContents: 0.5 mM protein; 50 mM Na phosphate pH 7.0; 1 mM DTT; 1.5 mM Na dithionite; 0.1 % NaN3; protease inhibitor
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 50 mM Na phosphate / pH: 7 / Pressure: ambient / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX6001
Bruker DRXBrukerDRX5002
Varian UNITYPLUSVarianUNITYPLUS4003
Varian UNITYVarianUNITY5004
Varian INOVAVarianINOVA5005
Varian UNITYPLUSVarianUNITYPLUS7506

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Processing

NMR software
NameVersionDeveloperClassification
Felix97MSIprocessing
DYANA1.5Guentertstructure solution
X-PLOR3.84Brungerrefinement
XEASY1.3.9Xia, Bartelsdata analysis
VNMR5.1AVariancollection
XwinNMR2.5Brukercollection
RefinementMethod: NMR / Software ordinal: 1 / Details: High-resolution NMR
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 300 / Conformers submitted total number: 10

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