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- PDB-1f5b: CRYSTAL STRUCTURE OF F2H FERREDOXIN 1 MUTANT FROM AZOTOBACTER VIN... -

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Basic information

Entry
Database: PDB / ID: 1f5b
TitleCRYSTAL STRUCTURE OF F2H FERREDOXIN 1 MUTANT FROM AZOTOBACTER VINELANDII AT 1.75 ANGSTROM RESOLUTION
ComponentsFERREDOXIN 1
KeywordsELECTRON TRANSPORT / beta-sheet / protein monomer / iron sulfur protein / 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 / : / 4Fe-4S binding domain / 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 ...Ferredoxin, C-terminal / Domain of unknown function (DUF3470) / 7Fe ferredoxin / : / 4Fe-4S binding domain / 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 / IRON/SULFUR CLUSTER / Ferredoxin-1
Similarity search - Component
Biological speciesAzotobacter vinelandii (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 1.62 Å
AuthorsChen, K. / Bonagura, C.A. / Tilley, G.J. / Jung, Y.S. / Armstrong, F.A. / Stout, C.D. / Burgess, B.K.
CitationJournal: Nat.Struct.Biol. / Year: 2002
Title: Crystal structures of ferredoxin variants exhibiting large changes in [Fe-S] reduction potential.
Authors: Chen, K. / Bonagura, C.A. / Tilley, G.J. / McEvoy, J.P. / Jung, Y.S. / Armstrong, F.A. / Stout, C.D. / Burgess, B.K.
History
DepositionJun 13, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 28, 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 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _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.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
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 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,6983
Polymers12,0511
Non-polymers6472
Water3,171176
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.381, 55.381, 92.780
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 1 / FDI


Mass: 12050.504 Da / Num. of mol.: 1 / Mutation: F2H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Azotobacter vinelandii (bacteria) / Plasmid: PKT230 / Production host: Escherichia coli (E. coli) / References: UniProt: P00214
#2: Chemical ChemComp-F3S / FE3-S4 CLUSTER


Mass: 295.795 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe3S4
#3: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 176 / 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: 2.95 Å3/Da / Density % sol: 58.3 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: Trizma base, ammonium sulfate, potassium phosphate, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 277.0K
Crystal grow
*PLUS
Temperature: 100 K
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
111 mg/mlprotein1drop
21.2 Mammonium sulfate1reservoir
30.4 MTris-HCl1reservoirpH7.4

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Data collection

DiffractionMean temperature: 115 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5408
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Nov 5, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5408 Å / Relative weight: 1
ReflectionResolution: 1.62→50 Å / Num. all: 19110 / Num. obs: 19082 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 11.83 % / Biso Wilson estimate: 21.6 Å2 / Rmerge(I) obs: 0.072 / Net I/σ(I): 9.6
Reflection shellResolution: 1.62→1.65 Å / Redundancy: 10 % / Rmerge(I) obs: 0.642 / Num. unique all: 921 / % possible all: 100
Reflection
*PLUS
Num. measured all: 225694
Reflection shell
*PLUS
% possible obs: 100 % / Mean I/σ(I) obs: 2.04

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 1.62→39.16 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 372801.63 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh and Huber / Details: used maximum likelihood (F)
RfactorNum. reflection% reflectionSelection details
Rfree0.244 899 4.8 %RANDOM
Rwork0.207 ---
obs0.207 18542 97.2 %-
all-19082 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 40.92 Å2 / ksol: 0.352 e/Å3
Displacement parametersBiso mean: 24.3 Å2
Baniso -1Baniso -2Baniso -3
1--0.55 Å20 Å20 Å2
2---0.55 Å20 Å2
3---1.1 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.18 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 1.62→39.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms845 0 15 176 1036
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_dihedral_angle_d23.4
X-RAY DIFFRACTIONc_improper_angle_d0.9
LS refinement shellResolution: 1.62→1.72 Å / Rfactor Rfree error: 0.031 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.364 136 4.8 %
Rwork0.343 2716 -
obs--91.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3PARAM19X.FSTOPH19.FS
X-RAY DIFFRACTION4SO4.PARSO4.TOP
Refinement
*PLUS
Lowest resolution: 39.2 Å / σ(F): 0 / % reflection Rfree: 4.8 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 24.3 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.79
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.9
LS refinement shell
*PLUS
Rfactor Rfree: 0.364 / % reflection Rfree: 4.8 % / Rfactor Rwork: 0.343

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