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- PDB-2vlt: Crystal structure of barley thioredoxin h isoform 2 in the oxidiz... -

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Basic information

Entry
Database: PDB / ID: 2vlt
TitleCrystal structure of barley thioredoxin h isoform 2 in the oxidized state
ComponentsTHIOREDOXIN H ISOFORM 2.
KeywordsOXIDOREDUCTASE / PROTEIN DISULFIDE REDUCTASE / THIOREDOXIN-FOLD
Function / homology
Function and homology information


oxidoreductase activity, acting on a sulfur group of donors, disulfide as acceptor
Similarity search - Function
: / Thioredoxin / Thioredoxin, conserved site / Thioredoxin family active site. / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Phloem sap 13 kDa protein 1
Similarity search - Component
Biological speciesHORDEUM VULGARE VAR. DISTICHUM (barley)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsMaeda, K. / Hagglund, P. / Finnie, C. / Svensson, B. / Henriksen, A.
CitationJournal: Protein Sci. / Year: 2008
Title: Crystal Structures of Barley Thioredoxin H Isoforms Hvtrxh1 and Hvtrxh2 Reveal Features Involved in Protein Recognition and Possibly in Discriminating the Isoform Specificity.
Authors: Maeda, K. / Hagglund, P. / Finnie, C. / Svensson, B. / Henriksen, A.
History
DepositionJan 16, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 29, 2008Provider: repository / Type: Initial release
Revision 1.1Mar 28, 2012Group: Advisory / Other / Version format compliance
Revision 1.2Jul 12, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.3Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: THIOREDOXIN H ISOFORM 2.
B: THIOREDOXIN H ISOFORM 2.


Theoretical massNumber of molelcules
Total (without water)26,3592
Polymers26,3592
Non-polymers00
Water2,360131
1
A: THIOREDOXIN H ISOFORM 2.


Theoretical massNumber of molelcules
Total (without water)13,1791
Polymers13,1791
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: THIOREDOXIN H ISOFORM 2.


Theoretical massNumber of molelcules
Total (without water)13,1791
Polymers13,1791
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)47.256, 38.370, 56.554
Angle α, β, γ (deg.)90.00, 109.77, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein THIOREDOXIN H ISOFORM 2. / THIOREDOXIN


Mass: 13179.326 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HORDEUM VULGARE VAR. DISTICHUM (barley)
Variant: BARKE / Plasmid: PET11A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA
References: UniProt: Q7XZK2, thioredoxin-disulfide reductase (NADPH)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 131 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.85 Å3/Da / Density % sol: 33.06 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→23.6 Å / Num. obs: 12288 / % possible obs: 92.3 % / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 2.9
Reflection shellResolution: 2→2.11 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 2.3 / % possible all: 94.7

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Processing

SoftwareName: REFMAC / Version: 5.2.0019 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→53.22 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.87 / SU B: 5.636 / SU ML: 0.158 / Cross valid method: THROUGHOUT / ESU R: 0.262 / ESU R Free: 0.226 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.269 603 5 %RANDOM
Rwork0.186 ---
obs0.19 11533 92.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.62 Å2
Baniso -1Baniso -2Baniso -3
1--0.1 Å20 Å2-0.12 Å2
2---1.67 Å20 Å2
3---1.7 Å2
Refinement stepCycle: LAST / Resolution: 2→53.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1711 0 0 131 1842
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0221765
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8071.9582395
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.475223
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.825.71470
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.71915316
X-RAY DIFFRACTIONr_dihedral_angle_4_deg30.141154
X-RAY DIFFRACTIONr_chiral_restr0.1260.2279
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021298
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2010.2792
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3020.21184
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1810.2131
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2180.239
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1680.213
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1521.51160
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.57221812
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.653689
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.1344.5583
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: 2→2.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.246 35 -
Rwork0.208 866 -
obs--95.14 %

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