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- PDB-1pdx: PUTIDAREDOXIN -

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Basic information

Entry
Database: PDB / ID: 1pdx
TitlePUTIDAREDOXIN
ComponentsPROTEIN (PUTIDAREDOXIN)
KeywordsELECTRON TRANSFER / CYTOCHROME P450CAM / FERREDOXIN / IRON-SULFUR CLUSTER
Function / homology
Function and homology information


P450-containing electron transport chain / 2 iron, 2 sulfur cluster binding / electron transfer activity / metal ion binding / cytosol
Similarity search - Function
Adrenodoxin, iron-sulphur binding site / Adrenodoxin family, iron-sulfur binding region signature. / Adrenodoxin / 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 / Ubiquitin-like (UB roll) ...Adrenodoxin, iron-sulphur binding site / Adrenodoxin family, iron-sulfur binding region signature. / Adrenodoxin / 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 / Ubiquitin-like (UB roll) / Roll / Alpha Beta
Similarity search - Domain/homology
FE2/S2 (INORGANIC) CLUSTER / Putidaredoxin
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodSOLUTION NMR / DG,SA
AuthorsPochapsky, T.C. / Jain, N.U. / Kuti, M. / Lyons, T.A. / Heymont, J.
Citation
Journal: Biochemistry / Year: 1999
Title: A refined model for the solution structure of oxidized putidaredoxin.
Authors: Pochapsky, T.C. / Jain, N.U. / Kuti, M. / Lyons, T.A. / Heymont, J.
#1: Journal: Structure / Year: 1998
Title: New aspects of electron transfer revealed by the crystal structure of a truncated bovine adrenodoxin, Adx(4-108).
Authors: Muller, A. / Muller, J.J. / Muller, Y.A. / Uhlmann, H. / Bernhardt, R. / Heinemann, U.
#2: Journal: Biochemistry / Year: 1994
Title: An NMR-derived model for the solution structure of oxidized putidaredoxin, a 2-Fe, 2-S ferredoxin from Pseudomonas.
Authors: Pochapsky, T.C. / Ye, X.M. / Ratnaswamy, G. / Lyons, T.A.
#3: Journal: Biochemistry / Year: 1994
Title: Redox-dependent 1H NMR spectral features and tertiary structural constraints on the C-terminal region of putidaredoxin.
Authors: Pochapsky, T.C. / Ratnaswamy, G. / Patera, A.
#4: Journal: Magn.Reson.Chem. / Year: 1993
Title: Characterization of hyperfine-shifted 1H resonances in oxidized and reduced putidaredoxin, an Fe2S2 ferredoxin from Pseudomonas putida
Authors: Ratnaswamy, G. / Pochapsky, T.C.
#5: Journal: Biochemistry / Year: 1992
Title: 1H NMR sequential assignments and identification of secondary structural elements in oxidized putidaredoxin, an electron-transfer protein from Pseudomonas.
Authors: Ye, X.M. / Pochapsky, T.C. / Pochapsky, S.S.
#6: Journal: Biochemistry / Year: 1991
Title: 1H NMR identification of a beta-sheet structure and description of folding topology in putidaredoxin.
Authors: Pochapsky, T.C. / Ye, X.M.
History
DepositionFeb 15, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0May 12, 1999Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_oper_list ...pdbx_struct_assembly / pdbx_struct_oper_list / struct_conf / struct_conf_type
Revision 1.4Nov 6, 2019Group: Data collection / Database references / Category: citation / pdbx_nmr_software
Item: _citation.page_last / _citation.pdbx_database_id_DOI ..._citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_nmr_software.name
Revision 1.5Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: PROTEIN (PUTIDAREDOXIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,6052
Polymers11,4291
Non-polymers1761
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)14 / 80NO NOE VIOL.>0.5 A, NO DIHEDRAL VIOLATION > 5 DEG.
Representative

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Components

#1: Protein PROTEIN (PUTIDAREDOXIN) / PDX


Mass: 11428.911 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: 2FE-2S CLUSTER LIGATED BY CYS 39, CYS 45, CYS 48 AND CYS 86
Source: (gene. exp.) Pseudomonas putida (bacteria)
Description: ORIGINALLY ISOLATED FROM P. PUTIDA GROWN WITH CAMPHOR AS SOLE CARBON SOURCE
Plasmid: PKM536 / Gene (production host): CAMB / Production host: Escherichia coli (E. coli) / Strain (production host): TB1 / References: UniProt: P00259
#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
111NOESY
121HSQC
131(H)CCH-TOCSY
141HNCA
151HSQC-NOESY
NMR detailsText: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR SPECTROSCOPY ON 13C, 15N-LABELED PUTIDAREDOXIN

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Sample preparation

Sample conditionspH: 7.4 / Pressure: 1 atm / Temperature: 290 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Bruker AMX / Manufacturer: Bruker / Model: AMX / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.1BRUNGERrefinement
Felixstructure solution
XPLORstructure solution
RefinementMethod: DG,SA / Software ordinal: 1
NMR ensembleConformer selection criteria: NO NOE VIOL.>0.5 A, NO DIHEDRAL VIOLATION > 5 DEG.
Conformers calculated total number: 80 / Conformers submitted total number: 14

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