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- PDB-1fxd: REFINED CRYSTAL STRUCTURE OF FERREDOXIN II FROM DESULFOVIBRIO GIG... -

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Basic information

Entry
Database: PDB / ID: 1fxd
TitleREFINED CRYSTAL STRUCTURE OF FERREDOXIN II FROM DESULFOVIBRIO GIGAS AT 1.7 ANGSTROMS
ComponentsFERREDOXIN II
KeywordsELECTRON TRANSFER(IRON-SULFUR)
Function / homology
Function and homology information


3 iron, 4 sulfur cluster binding / electron transfer activity / iron ion binding
Similarity search - Function
: / 3Fe-4S ferredoxin / 4Fe-4S single cluster domain of Ferredoxin I / Alpha-Beta Plaits - #20 / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / 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
FE3-S4 CLUSTER / Ferredoxin-2
Similarity search - Component
Biological speciesDesulfovibrio gigas (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 1.7 Å
AuthorsKissinger, C.R. / Sieker, L.C. / Adman, E.T. / Jensen, L.H.
Citation
Journal: J.Mol.Biol. / Year: 1991
Title: Refined crystal structure of ferredoxin II from Desulfovibrio gigas at 1.7 A.
Authors: Kissinger, C.R. / Sieker, L.C. / Adman, E.T. / Jensen, L.H.
#1: Journal: FEBS Lett. / Year: 1989
Title: The Crystal Structure of the Three-Iron Ferredoxin II from Desulfovibrio Gigas
Authors: Kissinger, C.R. / Adman, E.T. / Sieker, L.C. / Jensen, L.H. / Legall, J.
#2: Journal: J.Am.Chem.Soc. / Year: 1988
Title: Structure of the 3Fe-4S Cluster in Desulfovibrio Gigas Ferredoxin II
Authors: Kissinger, C.R. / Adman, E.T. / Sieker, L.C. / Jensen, L.H.
#3: Journal: J.Mol.Biol. / Year: 1984
Title: Crystallization and Preliminary X-Ray Diffraction Study of the 3-Fe Ferredoxin II from the Bacterium Desulfovibrio Gigas
Authors: Sieker, L.C. / Adman, E.T. / Jensen, L.H. / Legall, J.
History
DepositionApr 8, 1991Processing site: BNL
Revision 1.0Apr 15, 1993Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 2.0Mar 26, 2025Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _atom_site.occupancy / _database_2.pdbx_DOI ..._atom_site.occupancy / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_ref_seq_dif.details / _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 II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,6062
Polymers6,3101
Non-polymers2961
Water1,00956
1
A: FERREDOXIN II
hetero molecules

A: FERREDOXIN II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,2124
Polymers12,6202
Non-polymers5922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Unit cell
Length a, b, c (Å)40.870, 45.280, 26.470
Angle α, β, γ (deg.)90.00, 104.70, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-113-

HOH

21A-119-

HOH

31A-122-

HOH

41A-125-

HOH

51A-136-

HOH

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Components

#1: Protein FERREDOXIN II


Mass: 6310.010 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Desulfovibrio gigas (bacteria) / References: UniProt: P00209
#2: Chemical ChemComp-F3S / FE3-S4 CLUSTER


Mass: 295.795 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe3S4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 56 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.88 Å3/Da / Density % sol: 34.44 %
Crystal grow
*PLUS
Method: other / Details: Sieker, L.C., (1984) J. Mol. Biol., 179, 151.

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 1.7 Å / Lowest resolution: 2.3 Å / Num. obs: 6228 / Rmerge(I) obs: 0.09

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Processing

SoftwareName: PROFFT / Classification: refinement
RefinementRfactor obs: 0.157 / Highest resolution: 1.7 Å
Refinement stepCycle: LAST / Highest resolution: 1.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms432 0 7 56 495
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.02
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Refinement
*PLUS
Lowest resolution: 8 Å / Num. reflection obs: 4508
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0190.02
X-RAY DIFFRACTIONp_angle_d0.0410.03
X-RAY DIFFRACTIONp_planar_d0.0530.05
X-RAY DIFFRACTIONp_chiral_restr0.1620.15
X-RAY DIFFRACTIONp_mcbond_it1.752
X-RAY DIFFRACTIONp_scbond_it4.373
X-RAY DIFFRACTIONp_mcangle_it2.673
X-RAY DIFFRACTIONp_scangle_it6.364

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