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- PDB-2hze: Crystal structures of a poxviral glutaredoxin in the oxidized and... -

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Basic information

Entry
Database: PDB / ID: 2hze
TitleCrystal structures of a poxviral glutaredoxin in the oxidized and reduced states show redox-correlated structural changes
Components(Glutaredoxin-1GLRX) x 2
KeywordsELECTRON TRANSPORT / OXIDOREDUCTASE / thioredoxin fold / arsenic / dimethylarsenite.
Function / homology
Function and homology information


: / Glutaredoxin subgroup / Glutaredoxin, eukaryotic/virial / Glutaredoxin active site / Glutaredoxin active site. / Glutaredoxin / Glutaredoxin / Glutaredoxin domain profile. / Glutaredoxin / Glutaredoxin ...: / Glutaredoxin subgroup / Glutaredoxin, eukaryotic/virial / Glutaredoxin active site / Glutaredoxin active site. / Glutaredoxin / Glutaredoxin / Glutaredoxin domain profile. / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesEctromelia virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsBacik, J.P. / Hazes, B.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Crystal Structures of a Poxviral Glutaredoxin in the Oxidized and Reduced States Show Redox-correlated Structural Changes.
Authors: Bacik, J.P. / Hazes, B.
History
DepositionAug 8, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 21, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glutaredoxin-1
B: Glutaredoxin-1


Theoretical massNumber of molelcules
Total (without water)26,4242
Polymers26,4242
Non-polymers00
Water2,324129
1
A: Glutaredoxin-1


Theoretical massNumber of molelcules
Total (without water)13,1601
Polymers13,1601
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glutaredoxin-1


Theoretical massNumber of molelcules
Total (without water)13,2641
Polymers13,2641
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.627, 66.668, 108.096
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-164-

HOH

21B-111-

HOH

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Components

#1: Protein Glutaredoxin-1 / GLRX


Mass: 13160.028 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ectromelia virus / Genus: Orthopoxvirus / Strain: Moscow / Gene: EVM053 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21AI
References: UniProt: Q8JLF5, glutathione dehydrogenase (ascorbate)
#2: Protein Glutaredoxin-1 / GLRX


Mass: 13264.012 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ectromelia virus / Genus: Orthopoxvirus / Strain: Moscow / Gene: EVM053 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21AI / References: UniProt: Q8JLF5
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 129 / 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: 2.13 Å3/Da / Density % sol: 42.38 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 3.6
Details: 0.1 M NaCacodylate pH 5.2, 12.5% MPD, 10 mM Tris pH 8.0, 50 mM NaCl. Cryo solution containing 0.1 M NaCacodylate pH 5.2, 40% MPD and 50 mM GSH added 5 minutes before flash-freezing., pH 3.6, ...Details: 0.1 M NaCacodylate pH 5.2, 12.5% MPD, 10 mM Tris pH 8.0, 50 mM NaCl. Cryo solution containing 0.1 M NaCacodylate pH 5.2, 40% MPD and 50 mM GSH added 5 minutes before flash-freezing., pH 3.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Sep 23, 2005
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.8→54.07 Å / Num. all: 21297 / Num. obs: 21297 / % possible obs: 99.6 % / Observed criterion σ(F): 3.97 / Observed criterion σ(I): 1.76
Reflection shellResolution: 1.8→1.87 Å / % possible all: 97.3

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Processing

Software
NameVersionClassification
REFMAC5.2.0001refinement
ADSCQUANTUMdata collection
MOSFLMdata reduction
CCP4(SCALA)data scaling
XFITdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1KTE

1kte


Resolution: 1.8→19.54 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.95 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.132 / ESU R Free: 0.117 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20804 1065 5 %RANDOM
Rwork0.18568 ---
all0.18679 21297 --
obs0.18679 21297 99.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 28.305 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.8→19.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1757 0 0 129 1886
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0221799
X-RAY DIFFRACTIONr_bond_other_d00.021635
X-RAY DIFFRACTIONr_angle_refined_deg1.9061.952423
X-RAY DIFFRACTIONr_angle_other_deg3.6133796
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9715219
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.98624.33390
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.22115318
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.2221511
X-RAY DIFFRACTIONr_chiral_restr0.5730.2267
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022003
X-RAY DIFFRACTIONr_gen_planes_other0.010.02388
X-RAY DIFFRACTIONr_nbd_refined0.2130.2351
X-RAY DIFFRACTIONr_nbd_other0.2380.21375
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.1070.2910
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1750.283
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1420.216
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3370.247
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2660.215
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.0661.51088
X-RAY DIFFRACTIONr_mcbond_other01.5453
X-RAY DIFFRACTIONr_mcangle_it3.31121757
X-RAY DIFFRACTIONr_scbond_it5.963711
X-RAY DIFFRACTIONr_scangle_it8.6114.5666
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.846 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.298 84
Rwork0.274 1397

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