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- PDB-1m2d: Crystal structure at 1.05 Angstroms resolution of the Cys59Ser va... -

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Basic information

Entry
Database: PDB / ID: 1m2d
TitleCrystal structure at 1.05 Angstroms resolution of the Cys59Ser variant of the thioredoxin-like [2Fe-2S] ferredoxin from Aquifex aeolicus
Components[2Fe-2S] ferredoxin
KeywordsELECTRON TRANSPORT / ferredoxin / thioredoxin-like fold / [2Fe-2S] cluster / Cys59Ser variant
Function / homology
Function and homology information


2 iron, 2 sulfur cluster binding / metal ion binding
Similarity search - Function
Thioredoxin-like [2Fe-2S] ferredoxin / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FE2/S2 (INORGANIC) CLUSTER / Ferredoxin, 2Fe-2S
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.05 Å
AuthorsYeh, A.P. / Ambroggio, X.I. / Andrade, S.L.A. / Einsle, O. / Chatelet, C. / Meyer, J. / Rees, D.C.
Citation
Journal: J.Biol.Chem. / Year: 2002
Title: High-resolution crystal structures of the wild type and Cys-55-->Ser and Cys-59-->Ser variants of the thioredoxin-like [2Fe-2S] ferredoxin from Aquifex aeolicus
Authors: Yeh, A.P. / Ambroggio, X.I. / Andrade, S.L.A. / Einsle, O. / Chatelet, C. / Meyer, J. / Rees, D.C.
#1: Journal: J.Mol.Biol. / Year: 2000
Title: Structure of a thioredoxin-like [2Fe-2S] ferredoxin from Aquifex aeolicus
Authors: Yeh, A.P. / Chatelet, C. / Soltis, S.M. / Kuhn, P. / Meyer, J. / Rees, D.C.
History
DepositionJun 22, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 18, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 14, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: [2Fe-2S] ferredoxin
B: [2Fe-2S] ferredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,7324
Polymers24,3802
Non-polymers3522
Water3,567198
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1530 Å2
ΔGint-43 kcal/mol
Surface area10110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.300, 59.800, 46.800
Angle α, β, γ (deg.)90.00, 109.30, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-207-

HOH

21A-221-

HOH

31B-202-

HOH

41B-231-

HOH

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Components

#1: Protein [2Fe-2S] ferredoxin


Mass: 12190.091 Da / Num. of mol.: 2 / Mutation: C59S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Gene: Fdx4 / Plasmid: pT7-7 / Production host: Escherichia coli (E. coli) / Strain (production host): K38 / References: UniProt: O66511
#2: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe2S2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 198 / 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: 1.82 Å3/Da / Density % sol: 32.46 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 1,6 hexanediol, cobalt chloride, sodium acetate, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal grow
*PLUS
pH: 8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
167 mg/mlprotein1drop
220 mMTris-HCl1droppH8.0
30.2 M1dropNaCl
41.0 M1,6-hexanediol1reservoir
50.01 M1reservoirCoCl2
60.1 Msodium acetate1reservoirpH4.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.958 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 18, 2001
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.958 Å / Relative weight: 1
ReflectionResolution: 1.05→31.2 Å / Num. all: 77950 / Num. obs: 77950 / % possible obs: 95.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 2 / Redundancy: 4.6 % / Rmerge(I) obs: 0.035 / Rsym value: 0.035 / Net I/σ(I): 38.2
Reflection shellResolution: 1.05→1.07 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.216 / Mean I/σ(I) obs: 6.4 / Num. unique all: 3725 / Rsym value: 0.216 / % possible all: 92
Reflection
*PLUS
Num. measured all: 358550 / Rmerge(I) obs: 0.035
Reflection shell
*PLUS
% possible obs: 92 % / Rmerge(I) obs: 0.216

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Processing

Software
NameClassification
CNSrefinement
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 1M2B, Cys55Ser Aquifex aeolicus [2Fe-2S] ferredoxin structure

1m2b


Resolution: 1.05→31.2 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.162 2336 3 %random
Rwork0.137 ---
obs0.138 77914 95.6 %-
all-77914 --
Refine analyzeLuzzati coordinate error obs: 0.19 Å
Refinement stepCycle: LAST / Resolution: 1.05→31.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1574 0 8 198 1780
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.017
X-RAY DIFFRACTIONc_angle_deg2.666
Software
*PLUS
Name: SHELXL / Version: 97 / Classification: refinement
Refinement
*PLUS
% reflection Rfree: 3 % / Rfactor obs: 0.138 / Rfactor Rfree: 0.162 / Rfactor Rwork: 0.138
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d
X-RAY DIFFRACTIONs_angle_deg
X-RAY DIFFRACTIONs_dihedral_angle_d
X-RAY DIFFRACTIONs_dihedral_angle_deg26.38
X-RAY DIFFRACTIONs_improper_angle_d
X-RAY DIFFRACTIONs_improper_angle_deg1.83

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