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- PDB-2fdn: 2[4FE-4S] FERREDOXIN FROM CLOSTRIDIUM ACIDI-URICI -

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Basic information

Entry
Database: PDB / ID: 2fdn
Title2[4FE-4S] FERREDOXIN FROM CLOSTRIDIUM ACIDI-URICI
ComponentsFERREDOXIN
KeywordsELECTRON TRANSPORT / IRON-SULFUR / 4FE-4S
Function / homology
Function and homology information


4 iron, 4 sulfur cluster binding / electron transfer activity / metal ion binding
Similarity search - Function
7Fe ferredoxin / Alpha-Beta Plaits - #20 / 4Fe-4S dicluster 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 / 4Fe-4S ferredoxin FdxA
Similarity search - Component
Biological speciesClostridium acidurici (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / TAKEN FROM PDB ENTRY 1FDN / Resolution: 0.94 Å
AuthorsDauter, Z. / Wilson, K.S. / Sieker, L.C. / Meyer, J. / Moulis, J.M.
Citation
Journal: Biochemistry / Year: 1997
Title: Atomic resolution (0.94 A) structure of Clostridium acidurici ferredoxin. Detailed geometry of [4Fe-4S] clusters in a protein.
Authors: Dauter, Z. / Wilson, K.S. / Sieker, L.C. / Meyer, J. / Moulis, J.M.
#1: Journal: J.Mol.Biol. / Year: 1994
Title: Refined Crystal Structure of the 2[4Fe-4S] Ferredoxin from Clostridium Acidurici at 1.84 A Resolution
Authors: Duee, E.D. / Fanchon, E. / Vicat, J. / Sieker, L.C. / Meyer, J. / Moulis, J.M.
History
DepositionOct 1, 1997Processing site: BNL
Revision 1.0Apr 8, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_database_status / 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_database_status.process_site / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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)6,2433
Polymers5,5401
Non-polymers7032
Water1,69394
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)33.950, 33.950, 74.820
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-149-

HOH

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Components

#1: Protein FERREDOXIN /


Mass: 5540.179 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Clostridium acidurici (bacteria) / References: UniProt: P00198
#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.: 94 / 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: 1.85 Å3/Da / Density % sol: 35 %
Crystal growpH: 7
Details: 55-60% AMMONIUM SULFATE, 100 MM TRISMALEATE PH 6.6-7.0 MIXED 1:1 WITH 10 MG/ML PROTEIN SOLUTION.
PH range: 6.6-7.0
Crystal grow
*PLUS
Temperature: 281 K / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
255-60 %satammonium sulfate1drop
3100 mMTrisMaleate1drop
455-60 %satammonium sulfate1reservoir
5100 mMTrisMaleate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.883
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 1, 1995 / Details: MIRRORS
RadiationMonochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.883 Å / Relative weight: 1
ReflectionResolution: 0.94→20 Å / Num. obs: 28084 / % possible obs: 98.7 % / Redundancy: 4 % / Rmerge(I) obs: 0.073 / Rsym value: 0.073 / Net I/σ(I): 15
Reflection shellResolution: 0.94→0.95 Å / Redundancy: 4 % / Rmerge(I) obs: 0.483 / Mean I/σ(I) obs: 2 / Rsym value: 0.483 / % possible all: 93.7
Reflection
*PLUS
Num. measured all: 47452
Reflection shell
*PLUS
% possible obs: 93.7 %

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Processing

Software
NameClassification
SHELXmodel building
SHELXrefinement
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing
RefinementMethod to determine structure: TAKEN FROM PDB ENTRY 1FDN / Resolution: 0.94→20 Å / Num. parameters: 5145 / Num. restraintsaints: 5081 / Stereochemistry target values: ENGH AND HUBER / Details: NO RESTRAINTS ON [4FE-4S] CLUSTERS
RfactorNum. reflection% reflection
obs0.1003 -98.7 %
all-47452 -
Solvent computationSolvent model: SHELX SWAT
Refine analyzeNum. disordered residues: 6 / Occupancy sum hydrogen: 272 / Occupancy sum non hydrogen: 472
Refinement stepCycle: LAST / Resolution: 0.94→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms381 0 16 96 493
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.027
X-RAY DIFFRACTIONs_angle_d0.038
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes0.017
X-RAY DIFFRACTIONs_zero_chiral_vol
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.36
X-RAY DIFFRACTIONs_anti_bump_dis_restr
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.006
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.033
X-RAY DIFFRACTIONs_approx_iso_adps0.075
Software
*PLUS
Name: SHELXL-96 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_planar_d0.052
X-RAY DIFFRACTIONs_mcbond_it0.78
X-RAY DIFFRACTIONs_scbond_it1.97
X-RAY DIFFRACTIONs_mcangle_it1.03
X-RAY DIFFRACTIONs_scangle_it2.32

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