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- PDB-3d21: Crystal structure of a poplar wild-type thioredoxin h, PtTrxh4 -

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Basic information

Entry
Database: PDB / ID: 3d21
TitleCrystal structure of a poplar wild-type thioredoxin h, PtTrxh4
ComponentsThioredoxin H-type
KeywordsOXIDOREDUCTASE / thioredoxin h / Electron transport / Transport / Cytoplasm / Redox-active center
Function / homology
Function and homology information


: / 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 speciesPopulus trichocarpa x Populus deltoides (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsKoh, C.S. / Didierjean, C. / Corbier, C. / Rouhier, N. / Jacquot, J.P. / Gelhaye, E.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: An Atypical Catalytic Mechanism Involving Three Cysteines of Thioredoxin.
Authors: Koh, C.S. / Navrot, N. / Didierjean, C. / Rouhier, N. / Hirasawa, M. / Knaff, D.B. / Wingsle, G. / Samian, R. / Jacquot, J.P. / Corbier, C. / Gelhaye, E.
History
DepositionMay 7, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Apr 3, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site
Revision 1.4Nov 6, 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-type
B: Thioredoxin H-type


Theoretical massNumber of molelcules
Total (without water)31,3342
Polymers31,3342
Non-polymers00
Water1,11762
1
A: Thioredoxin H-type


Theoretical massNumber of molelcules
Total (without water)15,6671
Polymers15,6671
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Thioredoxin H-type


Theoretical massNumber of molelcules
Total (without water)15,6671
Polymers15,6671
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)47.355, 47.355, 195.996
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Thioredoxin H-type / Trxh4


Mass: 15666.770 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Populus trichocarpa x Populus deltoides (plant)
Plasmid: pSBET / Production host: Escherichia coli (E. coli) / References: UniProt: P85801
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.02 Å3/Da / Density % sol: 39.25 %
Crystal growTemperature: 293 K / Method: microbatch under oil / pH: 7.5
Details: 0.1 M Na HEPES (pH 7.5), 30 % (w/v) PEG 4000, 0.2 M CaCl2) with 1 mM DTT added to the initial protein solution, microbatch under oil, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.8123 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Mar 16, 2005 / Details: mirrors
RadiationMonochromator: Si [111], horizontally focussing / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8123 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. all: 13453 / Num. obs: 13453 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.053 / Net I/σ(I): 22.9
Reflection shellResolution: 2.15→2.23 Å / Rmerge(I) obs: 0.392 / Mean I/σ(I) obs: 2.6 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0019refinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: SeMet Model solved using SAD method

Resolution: 2.15→41 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.927 / SU B: 7.664 / SU ML: 0.2 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.27 / ESU R Free: 0.238 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.285 660 4.9 %RANDOM
Rwork0.21 ---
all0.213 13385 --
obs0.213 13385 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 56.534 Å2
Baniso -1Baniso -2Baniso -3
1--1.32 Å2-0.66 Å20 Å2
2---1.32 Å20 Å2
3---1.98 Å2
Refine analyzeLuzzati coordinate error obs: 0.39 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.38 Å
Refinement stepCycle: LAST / Resolution: 2.15→41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1780 0 0 62 1842
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0310.0221826
X-RAY DIFFRACTIONr_angle_refined_deg2.531.962476
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.65220
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.75924.63482
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.48315322
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.56158
X-RAY DIFFRACTIONr_chiral_restr0.230.2274
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.021368
X-RAY DIFFRACTIONr_nbd_refined0.2560.2756
X-RAY DIFFRACTIONr_nbtor_refined0.3270.21176
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1980.2103
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.230.229
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4210.28
X-RAY DIFFRACTIONr_mcbond_it1.8141.51160
X-RAY DIFFRACTIONr_mcangle_it2.85421796
X-RAY DIFFRACTIONr_scbond_it3.7663805
X-RAY DIFFRACTIONr_scangle_it5.0994.5680
LS refinement shellResolution: 2.15→2.208 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.325 43 -
Rwork0.253 902 -
all-945 -
obs-902 100 %

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