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- PDB-1axq: FERRICYANIDE OXIDIZED FDI -

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Basic information

Entry
Database: PDB / ID: 1axq
TitleFERRICYANIDE OXIDIZED FDI
ComponentsFERREDOXIN
KeywordsELECTRON TRANSPORT
Function / homology
Function and homology information


3 iron, 4 sulfur cluster binding / 4 iron, 4 sulfur cluster binding / electron transfer activity / DNA binding / metal ion binding
Similarity search - Function
Ferredoxin, C-terminal / : / Domain of unknown function (DUF3470) / 7Fe ferredoxin / : / Alpha-Beta Plaits - #20 / 4Fe-4S binding domain / 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. ...Ferredoxin, C-terminal / : / Domain of unknown function (DUF3470) / 7Fe ferredoxin / : / Alpha-Beta Plaits - #20 / 4Fe-4S binding domain / 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 / IRON/SULFUR CLUSTER / Ferredoxin-1
Similarity search - Component
Biological speciesAzotobacter vinelandii (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsStout, C.D.
CitationJournal: J.Biol.Inorg.Chem. / Year: 1998
Title: Crystal structures of ferricyanide-oxidized [Fe-S] clusters in Azotobacter vinelandii ferredoxin I.
Authors: Sridhar, V. / Prasad, G.S. / Burgess, B.K. / Stout, C.D.
History
DepositionOct 17, 1997Processing site: BNL
Revision 1.0Jan 28, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 2, 2023Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: FERREDOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,7073
Polymers12,0601
Non-polymers6472
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.600, 55.600, 95.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein FERREDOXIN


Mass: 12059.530 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: THIS 7FE FERREDOXIN FROM A. VINELANDII TREATED WITH 9\:1 MOLE RATIO OF FERRICYANIDE IN THE CRYSTALS. THE [FE-S] CLUSTERS HAVE BEEN PARTIALLY OXIDIZED.
Source: (gene. exp.) Azotobacter vinelandii (bacteria) / Strain: JG100
Description: WILD TYPE FERREDOXIN OVER-EXPRESSED FROM A PLASMID IN A. VINELANDII
Gene: FDXA / Plasmid: PKT320 / Gene (production host): FDXA / Production host: Azotobacter vinelandii (bacteria) / Strain (production host): JG100 / References: UniProt: P00214
#2: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4
#3: Chemical ChemComp-F3S / FE3-S4 CLUSTER


Mass: 295.795 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe3S4

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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: 2.8 Å3/Da / Density % sol: 59.9 %
Crystal growpH: 7.8 / Details: 4.8 M AMMONIUM SULFATE, 0.45 M TRIS-HCL PH 7.8
Crystal grow
*PLUS
Temperature: 2 ℃ / pH: 7.4 / Method: vapor diffusion / Details: Stout, C.D., (1979) J. Biol. Chem., 254, 3598.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
17-10 mg/mlprotein1drop
20.5 Mpotassium phosphate1drop
31.2 Mammonium sulfate1drop
43.5 Mammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 291 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Jan 10, 1996
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. obs: 8124 / % possible obs: 88.4 % / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Rsym value: 0.101 / Net I/σ(I): 11.2
Reflection shellResolution: 2.1→2.25 Å / Redundancy: 3.9 % / Mean I/σ(I) obs: 1.5 / % possible all: 88.4
Reflection
*PLUS
Rmerge(I) obs: 0.101

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Processing

Software
NameVersionClassification
X-PLOR3.8model building
X-PLOR3.8refinement
XENGENdata reduction
XENGENdata scaling
X-PLOR3.8phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 5FD1

5fd1


Resolution: 2.1→8 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / σ(F): 0
Details: MODIFIED PARAMETER AND TOPOLOGY FILES TO REFINE OXIDIZED, DISTORTED [FE-S] CLUSTERS OXIDIZED [FE-S] CLUSTERS WERE REFINED WITH MODIFIED TOPOLOGY AND PARAMETER FILES TO ALLOW FIT OF FE AND S ...Details: MODIFIED PARAMETER AND TOPOLOGY FILES TO REFINE OXIDIZED, DISTORTED [FE-S] CLUSTERS OXIDIZED [FE-S] CLUSTERS WERE REFINED WITH MODIFIED TOPOLOGY AND PARAMETER FILES TO ALLOW FIT OF FE AND S TO DENSITY RESULTING FOR FERRICYANIDE OXIDATION OF THE CRYSTALS. THE RESULTING GEOMETRY IS DISTORTED COMPARED TO IDEAL [FE-S] CLUSTERS.
RfactorNum. reflection% reflection
Rwork0.255 --
obs0.255 7446 88.4 %
Displacement parametersBiso mean: 19.3 Å2
Refinement stepCycle: LAST / Resolution: 2.1→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms841 0 15 0 856
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.019
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg3.19
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.83
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Version: 3.8 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.83
X-RAY DIFFRACTIONx_plane_restr1.83

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