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- PDB-2vm2: Crystal structure of barley thioredoxin h isoform 1 crystallized ... -

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Basic information

Entry
Database: PDB / ID: 2vm2
TitleCrystal structure of barley thioredoxin h isoform 1 crystallized using PEG as precipitant
ComponentsTHIOREDOXIN H ISOFORM 1.
KeywordsOXIDOREDUCTASE / PROTEIN DISULFIDE REDUCTASE / THIOREDOXIN-FOLD
Function / homology
Function and homology information


plasmodesmata-mediated intercellular transport / oxidoreductase activity, acting on a sulfur group of donors, disulfide as acceptor / protein-disulfide reductase activity / enzyme inhibitor activity / response to cold / response to oxidative stress / cytoplasm
Similarity search - Function
: / Thioredoxin / Thioredoxin / Thioredoxin, conserved site / Thioredoxin family active site. / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily ...: / Thioredoxin / 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
Biological speciesHORDEUM VULGARE VAR. DISTICHUM (barley)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 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 21, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 29, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Mar 28, 2012Group: Other
Revision 1.3Jul 12, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Revision 1.5Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: THIOREDOXIN H ISOFORM 1.
B: THIOREDOXIN H ISOFORM 1.
C: THIOREDOXIN H ISOFORM 1.
D: THIOREDOXIN H ISOFORM 1.


Theoretical massNumber of molelcules
Total (without water)51,0794
Polymers51,0794
Non-polymers00
Water9,800544
1
A: THIOREDOXIN H ISOFORM 1.


Theoretical massNumber of molelcules
Total (without water)12,7701
Polymers12,7701
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: THIOREDOXIN H ISOFORM 1.


Theoretical massNumber of molelcules
Total (without water)12,7701
Polymers12,7701
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
C: THIOREDOXIN H ISOFORM 1.


Theoretical massNumber of molelcules
Total (without water)12,7701
Polymers12,7701
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4
D: THIOREDOXIN H ISOFORM 1.


Theoretical massNumber of molelcules
Total (without water)12,7701
Polymers12,7701
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)121.726, 33.663, 132.202
Angle α, β, γ (deg.)90.00, 112.48, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
THIOREDOXIN H ISOFORM 1. / THIOREDOXIN


Mass: 12769.681 Da / Num. of mol.: 4
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: Q7XZK3, thioredoxin-disulfide reductase (NADPH)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 544 / 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: 2.27 Å3/Da / Density % sol: 45.41 % / 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: 1.8→20.6 Å / Num. obs: 46412 / % possible obs: 99.3 % / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 6.5
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 2.1 / % possible all: 99.8

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Processing

SoftwareName: REFMAC / Version: 5.2.0005 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1EP7

1ep7


Resolution: 1.8→20.36 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.921 / SU B: 5.224 / SU ML: 0.088 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.134 / ESU R Free: 0.137 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.249 2352 5.1 %RANDOM
Rwork0.195 ---
obs0.198 44058 99.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.67 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20 Å20.01 Å2
2---0.04 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.8→20.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3329 0 0 544 3873
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0223466
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3421.9584695
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3155442
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.91925.072138
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.60515608
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.687158
X-RAY DIFFRACTIONr_chiral_restr0.10.2535
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022584
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2080.21630
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2990.22391
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1540.2386
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1850.288
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1580.239
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8211.52253
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.25523553
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.20931359
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.3624.51142
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: 1.8→1.85 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.403 176
Rwork0.305 3221
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.1555-0.53170.19761.69070.12911.4614-0.00330.03650.01660.04580.02560.06120.04280.0083-0.0223-0.1243-0.0078-0.0003-0.10240.0126-0.109117.0122-12.69414.7724
21.9514-0.9018-0.27911.89040.47110.85410.02970.0599-0.00950.0036-0.05470.00920.0174-0.02360.0249-0.08860.00850.0193-0.0930.0112-0.1318-10.627-2.870844.1268
31.3465-0.24421.23390.5884-0.15472.6799-0.02470.04740.023-0.041-0.02110.0171-0.1947-0.03350.0458-0.05980.01330.0081-0.0837-0.0008-0.115423.9099-8.718146.6494
41.87810.0048-0.46261.01910.01832.3097-0.00690.12780.1004-0.00340.0329-0.00360.04310.0876-0.026-0.1064-0.01720.01-0.0570.012-0.132113.324-2.8982-11.545
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 114
2X-RAY DIFFRACTION2B6 - 90
3X-RAY DIFFRACTION2B92 - 113
4X-RAY DIFFRACTION3C6 - 98
5X-RAY DIFFRACTION3C102 - 118
6X-RAY DIFFRACTION4D6 - 113

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