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- PDB-1ff2: CRYSTAL STRUCTURE OF THE C42D MUTANT OF AZOTOBACTER VINELANDII 7F... -

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Basic information

Entry
Database: PDB / ID: 1ff2
TitleCRYSTAL STRUCTURE OF THE C42D MUTANT OF AZOTOBACTER VINELANDII 7FE FERREDOXIN (FDI)
ComponentsFERREDOXIN I
KeywordsELECTRON TRANSPORT / 7Fe ferredoxin
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 / Resolution: 2.3 Å
AuthorsStout, C.D. / Burgess, B.K.
CitationJournal: J.Biol.Chem. / Year: 2000
Title: Structure of C42D Azotobacter vinelandii FdI. A Cys-X-X-Asp-X-X-Cys motif ligates an air-stable [4Fe-4S]2+/+ cluster
Authors: Jung, Y.S. / Bonagura, C.A. / Tilley, G.J. / Gao-Sheridan, H.S. / Armstrong, F.A. / Stout, C.D. / Burgess, B.K.
History
DepositionJul 24, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 21, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Nov 3, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Feb 7, 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 I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,7193
Polymers12,0711
Non-polymers6472
Water86548
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.30, 55.30, 90.59
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Cell settingtetragonal
Space group name H-MP41212

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Components

#1: Protein FERREDOXIN I / FDI / FERREDOXIN [3FE-4S][4FE-4S]


Mass: 12071.476 Da / Num. of mol.: 1 / Mutation: C42D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Azotobacter vinelandii (bacteria) / Production host: Escherichia coli (E. coli) / 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 48 / 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: 2.87 Å3/Da / Density % sol: 57.09 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 7.8
Details: Ammonium sulfate, Tris-HCL, pH 7.8, VAPOR DIFFUSION, temperature 277.0K
Crystal grow
*PLUS
Temperature: 2 ℃ / pH: 7.4 / Details: Shen, B., (1994) J.Biol.Chem., 269, 8564.
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: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: May 1, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→28 Å / Num. all: 48416 / Num. obs: 48416 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.3 % / Biso Wilson estimate: 25 Å2 / Rmerge(I) obs: 0.171 / Net I/σ(I): 11.8
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.78 / Num. unique all: 306 / % possible all: 99.7
Reflection
*PLUS
Lowest resolution: 40 Å / Num. obs: 6640 / Num. measured all: 48416
Reflection shell
*PLUS
% possible obs: 99.7 % / Mean I/σ(I) obs: 3.1

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Processing

Software
NameVersionClassification
DENZOdata reduction
X-PLORmodel building
X-PLOR3.851refinement
SCALEPACKdata scaling
X-PLORphasing
RefinementResolution: 2.3→23.8 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: X-Plor 3.8
RfactorNum. reflection% reflectionSelection details
Rfree0.269 316 5 %Random
Rwork0.217 ---
all0.217 6640 --
obs0.217 6320 95.8 %-
Refinement stepCycle: LAST / Resolution: 2.3→23.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms843 0 15 48 906
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.017
X-RAY DIFFRACTIONx_angle_deg2.64
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 23.8 Å / σ(F): 0 / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS

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