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- PDB-1pfd: THE SOLUTION STRUCTURE OF HIGH PLANT PARSLEY [2FE-2S] FERREDOXIN,... -

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Entry
Database: PDB / ID: 1pfd
TitleTHE SOLUTION STRUCTURE OF HIGH PLANT PARSLEY [2FE-2S] FERREDOXIN, NMR, 18 STRUCTURES
ComponentsFERREDOXIN
KeywordsELECTRON TRANSPORT / [2FE-2S] FERREDOXIN / SOLUTION STRUCTURE / PARAMAGNETISM / NUCLEAR RELAXATION
Function / homology
Function and homology information


ferredoxin metabolic process / chloroplast stroma / electron transport chain / 2 iron, 2 sulfur cluster binding / electron transfer activity / metal ion binding
Similarity search - Function
Ferredoxin [2Fe-2S], plant / 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 / Ubiquitin-like (UB roll) ...Ferredoxin [2Fe-2S], plant / 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 / Ubiquitin-like (UB roll) / Roll / Alpha Beta
Similarity search - Domain/homology
FE2/S2 (INORGANIC) CLUSTER / Ferredoxin
Similarity search - Component
Biological speciesPetroselinum crispum (parsley)
MethodSOLUTION NMR / distance geometry
AuthorsIm, S.-C. / Liu, G. / Luchinat, C. / Sykes, A.G. / Bertini, I.
Citation
Journal: Eur.J.Biochem. / Year: 1998
Title: The solution structure of parsley [2Fe-2S]ferredoxin.
Authors: Im, S.C. / Liu, G. / Luchinat, C. / Sykes, A.G. / Bertini, I.
#1: Journal: Biochemistry / Year: 1996
Title: Structure of Synechococcus Elongatus [Fe2S2] Ferredoxin in Solution
Authors: Baumann, B. / Sticht, H. / Scharpf, M. / Sutter, M. / Haehnel, W. / Rosch, P.
#2: Journal: Biochemistry / Year: 1995
Title: 1H and 15N NMR Sequential Assignment, Secondary Structure, and Tertiary Fold of [2Fe-2S] Ferredoxin from Synechocystis Sp. Pcc 6803
Authors: Lelong, C. / Setif, P. / Bottin, H. / Andre, F. / Neumann, J.M.
#3: 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.
#4: Journal: Biochemistry / Year: 1990
Title: Multinuclear Magnetic Resonance Studies of the 2Fe(Dot)2Sferredoxin from Anabaena Species Strain Pcc 7120. 1. Sequence-Specific Hydrogen-1 Resonance Assignments and Secondary Structure in ...Title: Multinuclear Magnetic Resonance Studies of the 2Fe(Dot)2Sferredoxin from Anabaena Species Strain Pcc 7120. 1. Sequence-Specific Hydrogen-1 Resonance Assignments and Secondary Structure in Solution of the Oxidized Form
Authors: Oh, B.H. / Markley, J.L.
History
DepositionMay 5, 1998Processing site: BNL
Revision 1.0May 11, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_struct_assembly / 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_database_status.process_site / _pdbx_nmr_software.name / _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: FERREDOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,6722
Polymers10,4961
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)18 / 50LEAST TARGET FUNCTION
RepresentativeModel #1

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Components

#1: Protein FERREDOXIN


Mass: 10496.383 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Petroselinum crispum (parsley) / Organ: LEAVES / References: UniProt: Q7M1S1, EC: 1.7.7.2
#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
121TOCSY
131DQF-COSY
141INVERSION-RECOVER NOESY
NMR detailsText: MODEL NUMBER 1 WAS DETERMINED USING 2D NMR SPECTROSCOPY

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Sample preparation

DetailsContents: WATER
Sample conditionsIonic strength: 0.10 M / pH: 7 / Pressure: NORMAL / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE 800BrukerAVANCE 8008001
Bruker AVANCE 600BrukerAVANCE 6008002

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Processing

Software
NameClassification
DYANAmodel building
AMBERrefinement
DYANArefinement
NMR software
NameVersionDeveloperClassification
DYANA1.4GUNTERT,WUTHRICHrefinement
DYANAstructure solution
DYANAT1structure solution
Amberstructure solution
RefinementMethod: distance geometry / Software ordinal: 1
NMR ensembleConformer selection criteria: LEAST TARGET FUNCTION / Conformers calculated total number: 50 / Conformers submitted total number: 18

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