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- PDB-1siz: Crystal structure of the [Fe3S4]-ferredoxin from the hyperthermop... -

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Basic information

Entry
Database: PDB / ID: 1siz
TitleCrystal structure of the [Fe3S4]-ferredoxin from the hyperthermophilic archaeon Pyrococcus furiosus
ComponentsFerredoxin
KeywordsELECTRON TRANSPORT / thermostability / iron-sulfur clusters / dimer
Function / homology
Function and homology information


3 iron, 4 sulfur cluster binding / 4 iron, 4 sulfur cluster binding / electron transfer activity / iron ion binding
Similarity search - Function
4Fe-4S single cluster domain of Ferredoxin I / 3Fe-4S ferredoxin / Alpha-Beta Plaits - #20 / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
COBALT (III) ION / FE3-S4 CLUSTER / Ferredoxin
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsNielsen, M.S. / Harris, P. / Christensen, H.E.M.
CitationJournal: Biochemistry / Year: 2004
Title: The 1.5 A Resolution Crystal Structure of [Fe3S4]-Ferredoxin from the Hyperthermophilic Archaeon Pyrococcus furiosus
Authors: Nielsen, M.S. / Harris, P. / Ooi, B.L. / Christensen, H.E.M.
History
DepositionMar 2, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 25, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_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: Ferredoxin
C: Ferredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,1698
Polymers14,3422
Non-polymers8276
Water82946
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.447, 51.637, 54.549
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is either the dimer in the asymmetric unit or a monomer

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Components

#1: Protein Ferredoxin /


Mass: 7171.001 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Gene: FDXA, PF1909 / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / References: UniProt: P29603
#2: Chemical
ChemComp-3CO / COBALT (III) ION / Cobalt


Mass: 58.933 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Co
#3: Chemical ChemComp-F3S / FE3-S4 CLUSTER / Iron–sulfur cluster


Mass: 295.795 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe3S4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 46 / Source method: isolated from a natural source / Formula: H2O

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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: 2.33 Å3/Da / Density % sol: 47.18 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG 400, hexammine cobalt(III)-ions, HEPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9999 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 17, 2003
RadiationMonochromator: Silicium / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 2.25→35 Å / Num. obs: 6508 / % possible obs: 94.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 28.06 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 4.8
Reflection shellResolution: 2.25→2.37 Å / Rmerge(I) obs: 0.22 / % possible all: 81.5

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
CNSrefinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1VJW

1vjw


Resolution: 2.25→35 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2888 337 -Random
Rwork0.2388 ---
obs0.2413 6508 96.8 %-
Refinement stepCycle: LAST / Resolution: 2.25→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms992 0 18 46 1056
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_mcbond_it0.02
X-RAY DIFFRACTIONc_scbond_it1.48
X-RAY DIFFRACTIONc_mcangle_it0.405
X-RAY DIFFRACTIONc_scangle_it2.951

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