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- PDB-2wci: Structure of E. coli monothiol glutaredoxin GRX4 homodimer -

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Basic information

Entry
Database: PDB / ID: 2wci
TitleStructure of E. coli monothiol glutaredoxin GRX4 homodimer
ComponentsGLUTAREDOXIN-4
KeywordsELECTRON TRANSPORT / REDOX-ACTIVE CENTER / IRON-SULFUR CLUSTER SCAFFOLDER / FE2S2 / HOMODIMER / TRANSPORT / GLUTATHIONE / THIOREDOXIN FOLD
Function / homology
Function and homology information


disulfide oxidoreductase activity / iron-sulfur cluster assembly complex / iron-sulfur cluster assembly / cell redox homeostasis / 2 iron, 2 sulfur cluster binding / intracellular iron ion homeostasis / protein homodimerization activity / metal ion binding / cytosol
Similarity search - Function
Monothiol glutaredoxin / Monothiol glutaredoxin-related / Glutaredoxin, PICOT-like / Glutaredoxin / Glutaredoxin / Glutaredoxin domain profile. / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FE2/S2 (INORGANIC) CLUSTER / GLUTATHIONE / Glutaredoxin 4
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å
AuthorsIwema, T. / Picchiocci, A. / Traore, D.A.K. / Ferrer, J.-L. / Chauvat, F. / Jacquamet, L.
CitationJournal: Biochemistry / Year: 2009
Title: Structural Basis for Delivery of the Intact [Fe2S2] Cluster by Monothiol Glutaredoxin.
Authors: Iwema, T. / Picciocchi, A. / Traore, D.A.K. / Ferrer, J.-L. / Chauvat, F. / Jacquamet, L.
History
DepositionMar 12, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 23, 2009Provider: repository / Type: Initial release
Revision 1.1Feb 29, 2012Group: Advisory / Atomic model ...Advisory / Atomic model / Database references / Derived calculations / Non-polymer description / Other / Structure summary
Revision 1.2May 8, 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 / 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 / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _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_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_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.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_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: GLUTAREDOXIN-4
B: GLUTAREDOXIN-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,9366
Polymers30,1222
Non-polymers8134
Water3,279182
1
A: GLUTAREDOXIN-4
B: GLUTAREDOXIN-4
hetero molecules

A: GLUTAREDOXIN-4
B: GLUTAREDOXIN-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,87112
Polymers60,2444
Non-polymers1,6278
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area6730 Å2
ΔGint-96.9 kcal/mol
Surface area23170 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2330 Å2
ΔGint-44.2 kcal/mol
Surface area12620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.300, 94.300, 62.660
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-2002-

HOH

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Components

#1: Protein GLUTAREDOXIN-4 / / GRX4 / MONOTHIOL GLUTAREDOXIN


Mass: 15061.066 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: GLUTATHIONE, FE2S2 CLUSTER / Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Plasmid: PET28 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0AC69
#2: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER / Iron–sulfur cluster


Mass: 175.820 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe2S2
#3: Chemical ChemComp-GSH / GLUTATHIONE / Glutathione


Mass: 307.323 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N3O6S
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 182 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE DIFFERENCES BETWEEN OUR SEQUENCE AND P0AC69 RELIES IN THE N-TERMINUS AND ARE DUE TO THE CLONING ...THE DIFFERENCES BETWEEN OUR SEQUENCE AND P0AC69 RELIES IN THE N-TERMINUS AND ARE DUE TO THE CLONING OF THE FULL LENGTH GRX4 CODING SEQUENCE IN PET28 THUS ADDING AN HIS- TAG, THE THROMBIN CLEAVAGE SITE AND AN ADDITIONAL HISTIDINE.

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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: 2.29 Å3/Da / Density % sol: 46.4 % / Description: NONE
Crystal growpH: 7.5 / Details: 25 % PEG 6000 0.1 M HEPES PH 7.5

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97931, 1.73944, 1.74128
DetectorType: ADSC CCD / Detector: CCD / Date: Feb 5, 2008
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979311
21.739441
31.741281
ReflectionResolution: 1.9→50 Å / Num. obs: 22331 / % possible obs: 97.6 % / Observed criterion σ(I): 0 / Redundancy: 14.1 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 22.8
Reflection shellResolution: 1.9→2.01 Å / Redundancy: 14.3 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 1.9 / % possible all: 94.4

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Processing

Software
NameVersionClassification
REFMAC5.4.0069refinement
XDSdata reduction
XSCALEdata scaling
SHELXphasing
RefinementMethod to determine structure: MAD
Starting model: NONE

Resolution: 1.9→47.14 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.92 / SU B: 5.946 / SU ML: 0.082 / Cross valid method: THROUGHOUT / ESU R: 0.257 / ESU R Free: 0.137 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.234 1141 5 %RANDOM
Rwork0.183 ---
obs0.186 21677 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.35 Å2
Baniso -1Baniso -2Baniso -3
1--0.1 Å20 Å20 Å2
2---0.1 Å20 Å2
3---0.2 Å2
Refinement stepCycle: LAST / Resolution: 1.9→47.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1766 0 45 182 1993
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0221833
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6322.0012484
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6265223
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.30325.69679
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.45715311
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.498157
X-RAY DIFFRACTIONr_chiral_restr0.1430.2271
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211393
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3161.51124
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.12921810
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.2983709
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.1544.5674
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.246 82 -
Rwork0.152 1572 -
obs--100 %

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