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- PDB-1rgv: Crystal Structure of the Ferredoxin from Thauera aromatica -

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Basic information

Entry
Database: PDB / ID: 1rgv
TitleCrystal Structure of the Ferredoxin from Thauera aromatica
Componentsferredoxin
KeywordsELECTRON TRANSPORT
Function / homology
Function and homology information


4 iron, 4 sulfur cluster binding / metal ion binding
Similarity search - Function
: / 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
IRON/SULFUR CLUSTER / Ferredoxin
Similarity search - Component
Biological speciesThauera aromatica (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsUnciuleac, M. / Boll, M. / Warkentin, E. / Ermler, U.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2004
Title: Crystallization of 4-hydroxybenzoyl-CoA reductase and the structure of its electron donor ferredoxin.
Authors: Unciuleac, M. / Boll, M. / Warkentin, E. / Ermler, U.
History
DepositionNov 13, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 10, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Aug 23, 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_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_seq_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.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_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)9,6673
Polymers8,9641
Non-polymers7032
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.000, 79.000, 49.300
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein ferredoxin


Mass: 8963.895 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thauera aromatica (bacteria) / Strain: K172 / References: UniProt: O88151
#2: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4

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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: 5.3 Å3/Da / Density % sol: 76.8 %
Crystal growTemperature: 281 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: sodium citrate, ammonium phosphate, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 281K
Crystal grow
*PLUS
Temperature: 303 K / pH: 7.8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 %(w/v)PEG40001reservoir
215 %(w/v)MPD1reservoir
30.1 MHEPES1reservoirpH7.5
415-20 mg/mlprotein1drop
55 mMtriethanolamine1drop
62 mM1dropMgCl2
72 mMdithiothreitol1droppH7.8

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 18, 2001
RadiationMonochromator: Multilayer / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. all: 3953 / Num. obs: 3953 / % possible obs: 95.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3 % / Biso Wilson estimate: 1.3 Å2 / Rsym value: 0.094 / Net I/σ(I): 12.4
Reflection shellResolution: 2.9→3 Å / Redundancy: 1.7 % / Mean I/σ(I) obs: 2.7 / Num. unique all: 282 / Rsym value: 0.38 / % possible all: 70
Reflection
*PLUS
Num. obs: 3753 / Redundancy: 2.9 % / Rmerge(I) obs: 0.081
Reflection shell
*PLUS
Lowest resolution: 3 Å / % possible obs: 70 % / Rmerge(I) obs: 0.37

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Ferredoxin from Allochromatium vinosum (PDB 1BLU)

1blu


Resolution: 2.9→25.86 Å / Rfactor Rfree error: 0.016 / Data cutoff high absF: 1092461.4 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.219 198 5.3 %RANDOM
Rwork0.197 ---
all0.197 3753 --
obs0.197 3753 91.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 28.1492 Å2 / ksol: 0.366861 e/Å3
Displacement parametersBiso mean: 48.7 Å2
Baniso -1Baniso -2Baniso -3
1-3.31 Å29.98 Å20 Å2
2--3.31 Å20 Å2
3----6.63 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a0.19 Å0.49 Å
Refinement stepCycle: LAST / Resolution: 2.9→25.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms621 0 16 0 637
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d23.3
X-RAY DIFFRACTIONc_improper_angle_d0.83
X-RAY DIFFRACTIONc_mcbond_it0.91.5
X-RAY DIFFRACTIONc_mcangle_it1.612
X-RAY DIFFRACTIONc_scbond_it1.452
X-RAY DIFFRACTIONc_scangle_it2.162.5
LS refinement shellResolution: 2.9→3.08 Å / Rfactor Rfree error: 0.044 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.226 26 5.7 %
Rwork0.329 433 -
obs--68.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2PARAM.FESTOPH.FES
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
Refinement
*PLUS
Highest resolution: 2.9 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.22
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.83
LS refinement shell
*PLUS
Rfactor Rfree: 0.25 / Rfactor Rwork: 0.33

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