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- PDB-2vm1: Crystal structure of barley thioredoxin h isoform 1 crystallized ... -

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Basic information

Entry
Database: PDB / ID: 2vm1
TitleCrystal structure of barley thioredoxin h isoform 1 crystallized using ammonium sulfate 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: 1.7 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 1.2Jul 12, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.3Nov 6, 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

Downloads & links

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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.
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,4638
Polymers51,0794
Non-polymers3844
Water8,359464
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.
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,8662
Polymers12,7701
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
C: THIOREDOXIN H ISOFORM 1.
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,8662
Polymers12,7701
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4
D: THIOREDOXIN H ISOFORM 1.
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,9623
Polymers12,7701
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)120.881, 33.533, 131.048
Angle α, β, γ (deg.)90.00, 112.31, 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: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 464 / 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: 2.2 Å3/Da / Density % sol: 43.61 % / 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: 1.7→20.5 Å / Num. obs: 53797 / % possible obs: 99 % / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 9
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 1.6 / % possible all: 96

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Processing

SoftwareName: REFMAC / Version: 5.2.0005 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→121.27 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.938 / SU B: 3.883 / SU ML: 0.066 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.106 / ESU R Free: 0.105 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.216 2732 5.1 %RANDOM
Rwork0.181 ---
obs0.182 51064 98.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.46 Å2
Baniso -1Baniso -2Baniso -3
1--0.21 Å20 Å2-0.22 Å2
2--0.35 Å20 Å2
3----0.31 Å2
Refinement stepCycle: LAST / Resolution: 1.7→121.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3372 0 20 464 3856
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0223604
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1811.9614892
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.055470
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.50125.278144
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.71715633
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.39158
X-RAY DIFFRACTIONr_chiral_restr0.0850.2547
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022704
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2030.21712
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3020.22515
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1210.2362
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1770.2103
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1260.230
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7551.52332
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.18623696
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.07231408
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.3554.51195
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: 1.7→1.74 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.363 193
Rwork0.3 3615
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)
11.2194-0.28220.3111.02710.18250.98690.0120.02430.02080.0426-0.01320.01890.04440.02210.0012-0.0560.0035-0.0181-0.01430.0025-0.050416.767-12.57314.798
21.644-0.6376-0.23171.33360.66941.31060.03490.0021-0.03150.0108-0.0084-0.06020.0035-0.0116-0.0265-0.05180.0080.0138-0.02440.0065-0.0625-10.349-2.62143.802
31.1005-0.27950.77140.4193-0.32121.5863-0.019-0.06710.0126-0.0059-0.0210.0177-0.0737-0.08960.04-0.05610.0057-0.0180.0133-0.0166-0.059623.972-8.39346.158
41.010.197-0.10680.70540.07051.3632-0.0150.05120.0524-0.01420.02830.016-0.00590.1281-0.0132-0.0496-0.01460.0020.01430.0003-0.068913.423-2.65-11.488
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 114
2X-RAY DIFFRACTION2B5 - 114
3X-RAY DIFFRACTION3C6 - 118
4X-RAY DIFFRACTION4D6 - 114

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