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- PDB-1gpx: C85S GAPDX, NMR, 20 STRUCTURES -

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Basic information

Entry
Database: PDB / ID: 1gpx
TitleC85S GAPDX, NMR, 20 STRUCTURES
ComponentsPUTIDAREDOXIN
KeywordsELECTRON TRANSPORT / GAPDX C85S / 20 STRUCTURES ALIGNED AND SA
Function / homology
Function and homology information


P450-containing electron transport chain / 2 iron, 2 sulfur cluster binding / metal ion binding
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
GALLIUM (III) ION / Putidaredoxin
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodSOLUTION NMR / DG, SIMULATED ANNEALING
AuthorsPochapsky, T.C. / Kuti, M. / Kazanis, S.
Citation
Journal: J.Biomol.NMR / Year: 1998
Title: The solution structure of a gallium-substituted putidaredoxin mutant: GaPdx C85S.
Authors: Pochapsky, T.C. / Kuti, M. / Kazanis, S.
#1: Journal: J.Biomol.NMR / Year: 1997
Title: Structural Features of the Metal Binding Site and Dynamics of Gallium Putidaredoxin, a Diamagnetic Derivative of a Cys4Fe2S2 Ferredoxin
Authors: Kazanis, S. / Pochapsky, T.C.
#2: Journal: J.Am.Chem.Soc. / Year: 1995
Title: Conversion of a Fe2S2 Ferredoxin Into a Ga+3 Rubredoxin
Authors: Kazanis, S. / Pochapsky, T.C. / Barnhart, T.M. / Penner-Hahn, J.E. / Mirza, U.A. / Chait, B.T.
History
DepositionJun 10, 1998Processing site: BNL
Revision 1.0Jan 27, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / pdbx_struct_assembly ...pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Mar 14, 2018Group: Database references / Category: struct_ref_seq_dif / Item: _struct_ref_seq_dif.details
Revision 1.5May 1, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_ref_seq_dif.details / _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

Downloads & links

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Assembly

Deposited unit
A: PUTIDAREDOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,4832
Polymers11,4131
Non-polymers701
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100LEAST RESTRAINT VIOLATION
Representative

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Components

#1: Protein PUTIDAREDOXIN / C85S GAPDX


Mass: 11412.846 Da / Num. of mol.: 1 / Mutation: C85S
Source method: isolated from a genetically manipulated source
Details: COORDINATION OF GA+3 BY SG OF CYS 39, CYS 45, CYS 48 AND CYS 86
Source: (gene. exp.) Pseudomonas putida (bacteria) / Description: FROM P. PUTIDA CAMPHOR HYDROXYLASE SYSTEM / Gene: CAMB / Plasmid: PKM536 / Production host: Escherichia coli (E. coli) / References: UniProt: P00259
#2: Chemical ChemComp-GA / GALLIUM (III) ION


Mass: 69.723 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ga

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111HOMO
121HETERONUCLEAR NMR 2D
1313D
NMR detailsText: TRIPLE-RESONANCE 13C,15N NMR SPECTROSCOPY

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Sample preparation

DetailsContents: 90/10 H2O/D2O
Sample conditionsIonic strength: 0.01M / pH: 7.4 / Pressure: 1 ATMOSPHERE / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AMX500BrukerAMX5005001
Bruker DRX600BrukerDRX6006002

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Processing

Software
NameVersionClassification
X-PLOR3.85model building
X-PLOR3.85refinement
X-PLOR3.85phasing
NMR software
NameVersionDeveloperClassification
X-PLOR3.85BRUNGERrefinement
X-PLOR3.85structure solution
RefinementMethod: DG, SIMULATED ANNEALING / Software ordinal: 1 / Details: REFINEMENT DETAILS IN PRIMARY REFERENCE
NMR ensembleConformer selection criteria: LEAST RESTRAINT VIOLATION / Conformers calculated total number: 100 / Conformers submitted total number: 20

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