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- PDB-1blu: STRUCTURE OF THE 2[4FE-4S] FERREDOXIN FROM CHROMATIUM VINOSUM -

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Basic information

Entry
Database: PDB / ID: 1blu
TitleSTRUCTURE OF THE 2[4FE-4S] FERREDOXIN FROM CHROMATIUM VINOSUM
ComponentsFERREDOXIN
KeywordsELECTRON TRANSPORT / FERREDOXIN
Function / homology
Function and homology information


4 iron, 4 sulfur cluster binding / metal ion binding
Similarity search - Function
: / 4Fe-4S dicluster domain / 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
IRON/SULFUR CLUSTER / Ferredoxin
Similarity search - Component
Biological speciesAllochromatium vinosum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / molecular replacement / Resolution: 2.1 Å
AuthorsDauter, Z. / Wilson, K.S. / Sieker, L.C. / Moulis, J.M.
CitationJournal: Protein Sci. / Year: 1996
Title: Crystal structure of the 2[4Fe-4S] ferredoxin from Chromatium vinosum: evolutionary and mechanistic inferences for [3/4Fe-4S] ferredoxins.
Authors: Moulis, J.M. / Sieker, L.C. / Wilson, K.S. / Dauter, Z.
History
DepositionApr 16, 1996Processing site: BNL
Revision 1.0Nov 8, 1996Provider: 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: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: database_2 / diffrn_source ...database_2 / diffrn_source / 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 / _diffrn_source.pdbx_synchrotron_site / _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_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

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Assembly

Deposited unit
A: FERREDOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,7673
Polymers9,0641
Non-polymers7032
Water1,53185
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.000, 52.000, 77.200
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: 9064.004 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Allochromatium vinosum (bacteria) / References: UniProt: P00208
#2: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 85 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.32 Å3/Da / Density % sol: 63 %
Crystal growpH: 6.5
Details: CRYSTALS WERE GROWN AT ROOM TEMPERATURE IN 0.1M TRIS-MALEATE BUFFER, PH 6.5 CONTAINING 2.9 M AMMONIUM SULPHATE AND 0.1 M NACL
Temp details: room temp
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 8 ℃ / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
170 %satammonium sulfate1reservoir
2100 mM1reservoirNaCl
3100 mMTris-maleate1reservoir

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.92
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 1, 1993
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. obs: 7178 / % possible obs: 97 % / Observed criterion σ(I): 0 / Redundancy: 5 % / Rmerge(I) obs: 0.081

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Processing

Software
NameClassification
AMoREphasing
PROLSQrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: molecular replacement
Starting model: 1FDX

1fdx
PDB Unreleased entry


Resolution: 2.1→20 Å / σ(F): 0 /
Num. reflection% reflection
obs7178 97 %
Refine analyzeLuzzati sigma a obs: 0.25 Å
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms612 0 16 85 713
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0210.02
X-RAY DIFFRACTIONp_angle_d0.0430.03
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.050.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it3.43
X-RAY DIFFRACTIONp_mcangle_it5.25
X-RAY DIFFRACTIONp_scbond_it5.94
X-RAY DIFFRACTIONp_scangle_it9.56
X-RAY DIFFRACTIONp_plane_restr0.0160.02
X-RAY DIFFRACTIONp_chiral_restr0.2110.15
X-RAY DIFFRACTIONp_singtor_nbd0.210.3
X-RAY DIFFRACTIONp_multtor_nbd0.2720.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.2120.3
X-RAY DIFFRACTIONp_planar_tor35
X-RAY DIFFRACTIONp_staggered_tor19.615
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor1220
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.192 / Rfactor Rwork: 0.192
Solvent computation
*PLUS
Displacement parameters
*PLUS

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