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- PDB-1put: AN NMR-DERIVED MODEL FOR THE SOLUTION STRUCTURE OF OXIDIZED PUTID... -

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Entry
Database: PDB / ID: 1put
TitleAN NMR-DERIVED MODEL FOR THE SOLUTION STRUCTURE OF OXIDIZED PUTIDAREDOXIN, A 2FE, 2-S FERREDOXIN FROM PSEUDOMONAS
ComponentsPUTIDAREDOXIN
KeywordsELECTRON TRANSPORT
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
AuthorsPochapsky, T.C. / Ye, X.M. / Ratnaswamy, G. / Lyons, T.A.
Citation
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.
#1: 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.
#2: Journal: Magn.Reson.Chem. / Year: 1994
Title: Characterization of Hyperfine-Shifted 1H Resonances in Oxidized and Reduced Putidaredoxin, an Fe2S2Ferredoxin from Pseudomonus Putida
Authors: Ratnaswamy, G. / Pochapsky, T.C.
#3: 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.
#4: 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.
#5: Journal: Biochemistry / Year: 1991
Title: Crystallization and Structure Determination to 2.5-Angstroms Resolution of the Oxidized [2Fe-2S] Ferredoxin Isolated from Anabaena 7120
Authors: Rypniewski, W.R. / Breiter, D.R. / Benning, M.M. / Wesenberg, G. / Oh, B.H. / Markley, J.L. / Rayment, I. / Holden, H.M.
History
DepositionJul 9, 1994Processing site: BNL
Revision 1.0Sep 30, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 3, 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 1.4May 1, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / 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 / _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_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

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Assembly

Deposited unit
A: PUTIDAREDOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,6042
Polymers11,4281
Non-polymers1761
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)12 / -
Representative

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Components

#1: Protein PUTIDAREDOXIN


Mass: 11427.927 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / 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

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
NMR softwareName: X-PLOR / Developer: BRUNGER / Classification: refinement
NMR ensembleConformers submitted total number: 12

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