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- PDB-1ir0: OXIDIZED [4Fe-4S] FERREDOXIN FROM BACILLUS THERMOPROTEOLYTICUS (F... -

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Basic information

Entry
Database: PDB / ID: 1ir0
TitleOXIDIZED [4Fe-4S] FERREDOXIN FROM BACILLUS THERMOPROTEOLYTICUS (FORM II)
ComponentsFerredoxin
KeywordsELECTRON TRANSPORT / FERREDOXIN / IRON-SULFER PROTEIN / ULTLAHIGH RESOLUTION ANALYSIS / GEOMETRY OF [4FE-4S] CLUSTER
Function / homology
Function and homology information


4 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-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
IRON/SULFUR CLUSTER / Ferredoxin
Similarity search - Component
Biological speciesBacillus thermoproteolyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1 Å
AuthorsFukuyama, K. / Okada, T. / Kakuta, Y. / Takahashi, Y.
Citation
Journal: J.Mol.Biol. / Year: 2002
Title: Atomic resolution structures of oxidized [4Fe-4S] ferredoxin from Bacillus thermoproteolyticus in two crystal forms: systematic distortion of [4Fe-4S] cluster in the protein.
Authors: Fukuyama, K. / Okada, T. / Kakuta, Y. / Takahashi, Y.
#1: Journal: J.Mol.Biol. / Year: 1989
Title: Structure of [4Fe-4S] ferredoxin from Bacillus thermoproteolyticus refined at 2.3 A resolution. Structural comparisons of bacterial ferredoxins.
Authors: Fukuyama, K. / Matsubara, H. / Tsukihara, T. / Katsube, Y.
#2: Journal: J.Mol.Biol. / Year: 1988
Title: Tertiary structure of Bacillus thermoproteolyticus [4Fe-4S] ferredoxin. Evolutionary implications for bacterial ferredoxins.
Authors: Fukuyama, K. / Nagahara, Y. / Tsukihara, T. / Katsube, Y. / Hase, T. / Matsubara, H.
History
DepositionAug 30, 2001Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 13, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,4135
Polymers8,7741
Non-polymers6404
Water2,324129
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.560, 30.380, 50.920
Angle α, β, γ (deg.)90.00, 124.02, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-224-

HOH

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Components

#1: Protein Ferredoxin


Mass: 8773.595 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus thermoproteolyticus (bacteria)
Plasmid: pET21a(+) / Production host: Escherichia coli (E. coli) / References: UniProt: P10245
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#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.: 129 / 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: 1.86 Å3/Da / Density % sol: 33.4 %
Crystal growTemperature: 277 K / Method: microdialysis / pH: 6.5
Details: ammonium sulfate, MES, pH 6.5, MICRODIALYSIS, temperature 277.0K
Crystal grow
*PLUS
PH range low: 7.2 / PH range high: 6.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
10.1 MMES11pH6.5-7.2 (or PIPES)
281.5 %saturatedammonium sulfate11

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.55 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: May 21, 2000
RadiationMonochromator: Rotated-inclined double-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.55 Å / Relative weight: 1
ReflectionResolution: 1→13.3 Å / Num. all: 35329 / Num. obs: 35329 / % possible obs: 97.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.4 % / Rmerge(I) obs: 0.046 / Net I/σ(I): 9.5
Reflection shellResolution: 1→1.05 Å / Redundancy: 4 % / Rmerge(I) obs: 0.064 / Mean I/σ(I) obs: 9.5 / % possible all: 95.4
Reflection
*PLUS
Num. measured all: 189925
Reflection shell
*PLUS
% possible obs: 95.4 %

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Processing

Software
NameVersionClassification
CNSrefinement
SHELXL-97refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2FXB

2fxb
PDB Unreleased entry


Resolution: 1→13.3 Å / Num. parameters: 6954 / Num. restraintsaints: 8164 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.139 1765 5 %RANDOM
Rwork0.112 ---
all0.112 35328 --
obs0.112 35328 97 %-
Refine analyzeNum. disordered residues: 3 / Occupancy sum hydrogen: 506 / Occupancy sum non hydrogen: 744
Refinement stepCycle: LAST / Resolution: 1→13.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms620 0 23 129 772
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.014
X-RAY DIFFRACTIONs_angle_d0.029
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0261
X-RAY DIFFRACTIONs_zero_chiral_vol0.089
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.097
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.055
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.006
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.037
X-RAY DIFFRACTIONs_approx_iso_adps0.054
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 5.3 % / Rfactor Rwork: 0.096
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_angle_d
X-RAY DIFFRACTIONs_angle_deg2

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