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- PDB-1fxa: CRYSTALLIZATION AND STRUCTURE DETERMINATION TO 2.5-ANGSTROMS RESO... -

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Basic information

Entry
Database: PDB / ID: 1fxa
TitleCRYSTALLIZATION AND STRUCTURE DETERMINATION TO 2.5-ANGSTROMS RESOLUTION OF THE OXIDIZED [2FE-2S] FERREDOXIN ISOLATED FROM ANABAENA 7120
Components[2FE-2S] FERREDOXIN
KeywordsELECTRON TRANSPORT
Function / homology2Fe-2S ferredoxin-type iron-sulfur binding domain / 2Fe-2S ferredoxin, iron-sulphur binding site / Ferredoxin [2Fe-2S], plant / Beta-grasp domain superfamily / 2Fe-2S ferredoxin-like superfamily / 2Fe-2S iron-sulfur cluster binding domain / 2Fe-2S ferredoxin-type iron-sulfur binding region signature. / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / 2 iron, 2 sulfur cluster binding / electron transfer activity ...2Fe-2S ferredoxin-type iron-sulfur binding domain / 2Fe-2S ferredoxin, iron-sulphur binding site / Ferredoxin [2Fe-2S], plant / Beta-grasp domain superfamily / 2Fe-2S ferredoxin-like superfamily / 2Fe-2S iron-sulfur cluster binding domain / 2Fe-2S ferredoxin-type iron-sulfur binding region signature. / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / 2 iron, 2 sulfur cluster binding / electron transfer activity / metal ion binding / Ferredoxin-1
Function and homology information
Specimen sourceNostoc sp. (Cyanobacteria)
MethodX-RAY DIFFRACTION / 2.5 Å resolution
AuthorsRypniewski, W.R. / Breiter, D.R. / Benning, M.M. / Wesenberg, G. / Oh, B.-H. / Markley, J.L. / Rayment, I. / Holden, H.M.
CitationJournal: Biochemistry / Year: 1991
Title: Crystallization and structure determination to 2.5-A 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.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jan 9, 1991 / Release: Jul 15, 1992
RevisionDateData content typeGroupProviderType
1.0Jul 15, 1992Structure modelrepositoryInitial release
1.1Mar 24, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelSource and taxonomy / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: [2FE-2S] FERREDOXIN
B: [2FE-2S] FERREDOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,7634
Polyers21,4112
Non-polymers3522
Water4,216234
1
A: [2FE-2S] FERREDOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,8812
Polyers10,7061
Non-polymers1761
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: [2FE-2S] FERREDOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,8812
Polyers10,7061
Non-polymers1761
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
γ
α
β
Length a, b, c (Å)37.420, 38.120, 147.120
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP 21 21 21

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Components

#1: Protein/peptide [2FE-2S] FERREDOXIN


Mass: 10705.624 Da / Num. of mol.: 2 / Source: (gene. exp.) Nostoc sp. (Cyanobacteria) / Genus: Nostoc / Strain: PCC 7120 / References: UniProt: P0A3C7
#2: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 2 / Formula: Fe2S2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 234 / Formula: H2O / Water

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.45 / Density percent sol: 49.79 %
Crystal grow
*PLUS
Temp: 4 ℃ / pH: 5.5 / Method: vapor diffusion, hanging drop
components of the solutions
*PLUS
IDConcCommon nameCrystal IDSol ID
12.6 Mammonium sulfate1drop
250 mMpotassium succinate1drop
31 %MPD1drop

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
D resolution high: 2.5 Å / D resolution low: 3 Å / Number obs: 7672 / Number measured all: 27168 / Rmerge I obs: 0.045

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Processing

SoftwareName: TNT / Classification: refinement
Least-squares processR factor obs: 0.187 / Highest resolution: 2.5 Å / Lowest resolution: 3 Å
Refine hist #LASTHighest resolution: 2.5 Å / Lowest resolution: 3 Å
Number of atoms included #LASTProtein: 1500 / Nucleic acid: 0 / Ligand: 8 / Solvent: 234 / Total: 1742
Refine LS restraints
Refine IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.014
X-RAY DIFFRACTIONt_angle_deg2.6
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd
Least-squares process
*PLUS
Number reflection obs: 7672
Refine LS restraints
*PLUS
Refine IDTypeDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg24.775
X-RAY DIFFRACTIONt_planar_d0.011
X-RAY DIFFRACTIONt_plane_restr0.012

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