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- PDB-1off: 2Fe-2S Ferredoxin from Synechocystis sp. PCC 6803 -

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Basic information

Entry
Database: PDB / ID: 1off
Title2Fe-2S Ferredoxin from Synechocystis sp. PCC 6803
ComponentsFERREDOXIN I
KeywordsELECTRON TRANSPORT / FERREDOXIN / ELECTRON TRANSFER / IRON-SULPHUR / 2FE-2S / METAL-BINDING
Function / homology
Function and homology information


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-1
Similarity search - Component
Biological speciesSYNECHOCYSTIS SP. (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsVan Den heuvel, R.H.H. / Mattevi, A.
CitationJournal: J.Mol.Biol. / Year: 2003
Title: The Active Conformation of Glutamate Synthase and its Binding to Ferredoxin
Authors: Van Den Heuvel, R.H.H. / Svergun, D.I. / Petoukhov, M.V. / Coda, A. / Curti, B. / Ravasio, S. / Vanoni, M.A. / Mattevi, A.
History
DepositionApr 14, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 11, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FERREDOXIN I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,5442
Polymers10,3681
Non-polymers1761
Water2,072115
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)38.788, 38.788, 111.751
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein FERREDOXIN I / FERREDOXIN


Mass: 10368.233 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SYNECHOCYSTIS SP. (bacteria) / Strain: PCC6803 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P27320
#2: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe2S2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 115 / Source method: isolated from a natural source / Formula: H2O
Compound detailsFERREDOXINS ARE IRON-SULFUR PROTEINS THAT ARE INVOLVED IN THE TRANSFER OF ELECTRONS IN A WIDE ...FERREDOXINS ARE IRON-SULFUR PROTEINS THAT ARE INVOLVED IN THE TRANSFER OF ELECTRONS IN A WIDE VARIETY OF METABOLIC REACTIONS

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.34 Å3/Da / Density % sol: 49 %
Crystal growpH: 6.5 / Details: pH 6.50
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
112 mg/mlprotein1drop
225 mMHEPES-KOH1drop
3100 mM1droppH7.5NaCl
4100 mMMES-KOH1reservoir
53.6 Mammonium sulfate1reservoir
61 %(v/v)MPD1reservoirpH6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. obs: 8723 / % possible obs: 98.5 % / Redundancy: 7.7 % / Rmerge(I) obs: 0.055
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 7.9 % / Rmerge(I) obs: 0.317 / % possible all: 97.2
Reflection
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 33.5 Å / Num. measured all: 161518 / Rmerge(I) obs: 0.055
Reflection shell
*PLUS
% possible obs: 97.2 % / Rmerge(I) obs: 0.317 / Mean I/σ(I) obs: 7.7

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Processing

Software
NameClassification
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1CZP

1czp


Resolution: 1.8→33.52 Å / SU B: 2.689 / SU ML: 0.083 / Cross valid method: THROUGHOUT / ESU R: 0.129 / ESU R Free: 0.125
RfactorNum. reflection% reflectionSelection details
Rfree0.21619 412 4.7 %RANDOM
Rwork0.17351 ---
obs0.17553 8282 98.52 %-
Displacement parametersBiso mean: 22.385 Å2
Baniso -1Baniso -2Baniso -3
1-0.26 Å20.13 Å20 Å2
2--0.26 Å20 Å2
3----0.39 Å2
Refinement stepCycle: LAST / Resolution: 1.8→33.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms700 0 4 115 819
Refinement
*PLUS
Highest resolution: 1.8 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.216 / Rfactor Rwork: 0.176
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONbond_d0.014
X-RAY DIFFRACTIONangle_d
X-RAY DIFFRACTIONangle_deg1.63

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