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- PDB-1dur: Replacement for 1FDX 2(4FE4S) ferredoxin from (NOW) Peptostreptoc... -

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Basic information

Entry
Database: PDB / ID: 1dur
TitleReplacement for 1FDX 2(4FE4S) ferredoxin from (NOW) Peptostreptococcus asaccharolyticus
Components2[4FE-4S] FERREDOXIN
KeywordsELECTRON TRANSPORT / TWO 4Fe-4S clusters
Function / homology
Function and homology information


4 iron, 4 sulfur cluster binding / metal ion binding
Similarity search - Function
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 speciesPeptoniphilus asaccharolyticus (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsAdman, E.T. / Sieker, L.C.
Citation
Journal: to be published
Title: The 2[4Fe-4S] Ferredoxins
Authors: Adman, E.T. / Sieker, L.C.
#1: Journal: J.Am.Chem.Soc. / Year: 1991
Title: The Environment of Fe4S4 Clusters in Ferredoxins and High-Potential Iron Proteins. New Information from X-ray Crystallography and Resonance Raman Spectroscopy
Authors: Backes, G. / Mino, Y. / Loehr, T.M. / Meyer, T.E. / Cusanovich, M. / Sweeney, W.V. / Adman, E.T. / Sanders-Loehr, J.
#2: Journal: J.Biol.Chem. / Year: 1976
Title: Structure of Peptococcus aerogenes Ferredoxin Refinement at 2 A Resolution
Authors: Adman, E.T. / Sieker, L.C. / Jensen, L.H.
#3: Journal: J.Biol.Chem. / Year: 1973
Title: The Structure of a Bacterial Ferredoxin
Authors: Adman, E.T. / Sieker, L.C. / Jensen, L.H.
History
DepositionJan 18, 2000Deposition site: RCSB / Processing site: RCSB
SupersessionMar 29, 2000ID: 1FDX
Revision 1.0Mar 29, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 13, 2014Group: Non-polymer description
Revision 1.4Oct 4, 2017Group: Refinement description / Category: software
Revision 1.5Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.6Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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: 2[4FE-4S] FERREDOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,2613
Polymers5,5571
Non-polymers7032
Water1,67593
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)30.52, 37.75, 39.37
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein 2[4FE-4S] FERREDOXIN


Mass: 5557.229 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: FORMERLY CALLED PEPTOCOCCUS AEROGENES / Source: (natural) Peptoniphilus asaccharolyticus (bacteria) / References: UniProt: P00193
#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.: 93 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.04 Å3/Da / Density % sol: 39.67 %
Crystal growTemperature: 277 K / Method: evaporation / pH: 7.5
Details: 3.3-3.5M ammonium sulfate, tris-chloride buffer, pH 7.5, EVAPORATION, temperature 277.0K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SEALED TUBE / Type: OTHER / Wavelength: 1.5418
DetectorType: PICKER / Detector: DIFFRACTOMETER / Date: Jan 1, 1972
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→10 Å / Num. all: 3220 / Num. obs: 3220 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.05

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Processing

Software
NameVersionClassification
X-PLOR3.843refinement
PICKERdata reduction
RefinementResolution: 2→10 Å / σ(F): 0 / σ(I): 1 / Stereochemistry target values: Engh and Huber
Details: Used Xplor positional and individual B refinement. Refinement with "modern" tools (PROLSQ, then XPLOR) revealed a new cysteine in position 22, subsequently verified by partial sequencing. ...Details: Used Xplor positional and individual B refinement. Refinement with "modern" tools (PROLSQ, then XPLOR) revealed a new cysteine in position 22, subsequently verified by partial sequencing. See Citation 1. The close contacts listed in remark 500 are waters that are regarded as alternative sites, not all occupied simultaneously.
RfactorNum. reflection
Rwork0.155 -
all0.155 3220
obs0.14 2963
Refinement stepCycle: LAST / Resolution: 2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms379 0 16 93 488

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