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- PDB-1fxi: STRUCTURE OF THE [2FE-2S] FERREDOXIN I FROM THE BLUE-GREEN ALGA A... -

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Entry
Database: PDB / ID: 1fxi
TitleSTRUCTURE OF THE [2FE-2S] FERREDOXIN I FROM THE BLUE-GREEN ALGA APHANOTHECE SACRUM AT 2.2 ANGSTROMS RESOLUTION
ComponentsFERREDOXIN I
KeywordsELECTRON TRANSFER (IRON-SULFUR PROTEIN)
Function / homology
Function and homology information


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. / 2Fe-2S iron-sulfur cluster binding domain / Beta-grasp 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. / 2Fe-2S iron-sulfur cluster binding domain / Beta-grasp 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 speciesAphanothece sacrum (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.2 Å
AuthorsTsukihara, T.
Citation
Journal: J.Mol.Biol. / Year: 1990
Title: Structure of the [2Fe-2S] ferredoxin I from the blue-green alga Aphanothece sacrum at 2.2 A resolution.
Authors: Tsukihara, T. / Fukuyama, K. / Mizushima, M. / Harioka, T. / Kusunoki, M. / Katsube, Y. / Hase, T. / Matsubara, H.
#1: Journal: J.Biochem.(Tokyo) / Year: 1983
Title: Main Chain Fold of a [2Fe-2S] Ferredoxin I from Aphanothece Sacrum at 2.5 Angstroms Resolution
Authors: Tsutsui, T. / Tsukihara, T. / Fukuyama, K. / Katsube, Y. / Hase, T. / Matsubara, H. / Nishikawa, Y. / Tanaka, N.
#2: Journal: J.Biochem.(Tokyo) / Year: 1978
Title: Crystallization and a 5 Angstroms X-Ray Diffraction Study of Aphanothece Sacrum Ferredoxin
Authors: Kunita, A. / Koshibe, M. / Nishikawa, Y. / Fukuyama, K. / Tsukihara, T. / Katsube, Y. / Matsuura, Y. / Tanaka, N. / Kakudo, M. / Hase, T. / Matsubara, H.
History
DepositionAug 28, 1990Processing site: BNL
Revision 1.0Oct 15, 1991Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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 / _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

Downloads & links

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Assembly

Deposited unit
A: FERREDOXIN I
B: FERREDOXIN I
C: FERREDOXIN I
D: FERREDOXIN I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,9608
Polymers41,2574
Non-polymers7034
Water2,846158
1
A: FERREDOXIN I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,4902
Polymers10,3141
Non-polymers1761
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: FERREDOXIN I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,4902
Polymers10,3141
Non-polymers1761
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: FERREDOXIN I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,4902
Polymers10,3141
Non-polymers1761
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: FERREDOXIN I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,4902
Polymers10,3141
Non-polymers1761
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)92.200, 92.200, 47.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: Protein
FERREDOXIN I /


Mass: 10314.291 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aphanothece sacrum (bacteria) / References: UniProt: P00250
#2: Chemical
ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER / Iron–sulfur cluster


Mass: 175.820 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe2S2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 158 / Source method: isolated from a natural source / Formula: H2O

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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 Å3/Da / Density % sol: 49.81 %
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: microdialysis / Details: Kunita, A., (1978) J.Biochem.(Tokyo), 84, 989.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
11-3 %protein solution11
275 %satammonium sulfate12
30.7 M12NaCl
40.1 MTris-HCl12

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Num. obs: 21790 / Num. measured all: 42249

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 2.2→6 Å / σ(F): 2 /
RfactorNum. reflection
obs0.23 13487
Refinement stepCycle: LAST / Resolution: 2.2→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2884 0 16 158 3058
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0190.02
X-RAY DIFFRACTIONp_angle_d0.0740.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0820.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it3.262
X-RAY DIFFRACTIONp_mcangle_it4.013
X-RAY DIFFRACTIONp_scbond_it4.053
X-RAY DIFFRACTIONp_scangle_it4.564
X-RAY DIFFRACTIONp_plane_restr0.0210.02
X-RAY DIFFRACTIONp_chiral_restr0.1890.15
X-RAY DIFFRACTIONp_singtor_nbd0.2960.5
X-RAY DIFFRACTIONp_multtor_nbd0.420.5
X-RAY DIFFRACTIONp_xhyhbond_nbd0.4210.5
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor3.63
X-RAY DIFFRACTIONp_staggered_tor2915
X-RAY DIFFRACTIONp_orthonormal_tor41.220
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor

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