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- PDB-1w89: Structure of the reduced form of human thioredoxin 2 -

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Basic information

Entry
Database: PDB / ID: 1w89
TitleStructure of the reduced form of human thioredoxin 2
ComponentsTHIOREDOXIN
KeywordsELECTRON TRANSPORT / ANTIOXIDANT ENZYME / MITOCHONDRION
Function / homology
Function and homology information


peptide-methionine (R)-S-oxide reductase activity / Degradation of cysteine and homocysteine / peptide-methionine (S)-S-oxide reductase activity / Detoxification of Reactive Oxygen Species / cellular response to nutrient levels / protein-disulfide reductase activity / response to axon injury / response to glucose / response to hormone / cell redox homeostasis ...peptide-methionine (R)-S-oxide reductase activity / Degradation of cysteine and homocysteine / peptide-methionine (S)-S-oxide reductase activity / Detoxification of Reactive Oxygen Species / cellular response to nutrient levels / protein-disulfide reductase activity / response to axon injury / response to glucose / response to hormone / cell redox homeostasis / response to organic cyclic compound / response to oxidative stress / response to hypoxia / mitochondrial matrix / response to xenobiotic stimulus / dendrite / neuronal cell body / protein-containing complex binding / nucleolus / mitochondrion
Similarity search - Function
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
Thioredoxin, mitochondrial
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSmeets, A. / Evrard, C. / Declercq, J.P.
Citation
Journal: Protein Sci. / Year: 2005
Title: Crystal Structures of Oxidized and Reduced Forms of Human Mitochondrial Thioredoxin 2.
Authors: Smeets, A. / Evrard, C. / Landtmeters, M. / Marchand, C. / Knoops, B. / Declercq, J.P.
#1: Journal: J.Biol.Chem. / Year: 2002
Title: Human Mitochondrial Thioredoxin
Authors: Damdimopoulos, A.E. / Miranda-Vizuete, A. / Pelto-Huikkos, M. / Gustafsson, J.A. / Spyrou, G.
History
DepositionSep 17, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 5, 2005Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Refinement description / Version format compliance
Revision 1.2Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Dec 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: THIOREDOXIN
B: THIOREDOXIN
C: THIOREDOXIN
D: THIOREDOXIN
E: THIOREDOXIN
F: THIOREDOXIN


Theoretical massNumber of molelcules
Total (without water)79,7296
Polymers79,7296
Non-polymers00
Water8,971498
1
A: THIOREDOXIN
B: THIOREDOXIN


Theoretical massNumber of molelcules
Total (without water)26,5762
Polymers26,5762
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area930 Å2
ΔGint-9.5 kcal/mol
Surface area13640 Å2
MethodPISA
2
C: THIOREDOXIN
D: THIOREDOXIN


Theoretical massNumber of molelcules
Total (without water)26,5762
Polymers26,5762
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area810 Å2
ΔGint-15.9 kcal/mol
Surface area13070 Å2
MethodPISA
3
E: THIOREDOXIN
F: THIOREDOXIN


Theoretical massNumber of molelcules
Total (without water)26,5762
Polymers26,5762
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1360 Å2
ΔGint-12.4 kcal/mol
Surface area13300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.580, 49.610, 80.020
Angle α, β, γ (deg.)87.77, 82.30, 79.31
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
THIOREDOXIN / / MITOCHONDRIAL PRECURSOR / MT-TRX / THIOREDOXIN 2 / HUMAN THIOREDOXIN 2


Mass: 13288.154 Da / Num. of mol.: 6 / Fragment: ACTIVE SITE, RESIDUES 60-166
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Organ: LIVER / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): M15 (PREP4) / References: UniProt: Q99757
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 498 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHR1 CORRESPONDS TO THR60 IN Q99757

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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: 2.6 Å3/Da / Density % sol: 52.6 %
Crystal growpH: 4.6
Details: PEG 3350 22% (W/V), NA ACETATE 0.1M (PH 4.6), AMMONIUM SULFATE 0.2M, DTT 1MM. SOACKING IN A TRISHYDROXIMETHYLPHOSPHINE SOLUTION 10MM

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 0.9686
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 1, 2004 / Details: BENT MIRROR
RadiationMonochromator: DOUBLE CRYSTAL FOCUSSING MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 2→19.4 Å / Num. obs: 50114 / % possible obs: 97.1 % / Observed criterion σ(I): 0 / Redundancy: 2.68 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 11.42
Reflection shellResolution: 2→2.1 Å / Redundancy: 2.53 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 4.29 / % possible all: 97.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1UVZ

1uvz


Resolution: 2→19.23 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.88 / SU B: 11.824 / SU ML: 0.171 / TLS residual ADP flag: UNVERIFIED / Cross valid method: THROUGHOUT / ESU R: 0.215 / ESU R Free: 0.203 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.284 2442 5 %RANDOM
Rwork0.217 ---
obs0.22 46290 97.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.23 Å2
Baniso -1Baniso -2Baniso -3
1--0.16 Å20.15 Å20.16 Å2
2--0.11 Å2-0.11 Å2
3----0.04 Å2
Refinement stepCycle: LAST / Resolution: 2→19.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5074 0 0 498 5572
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0225167
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.3241.966999
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.1095648
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.74426.234231
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.74915920
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1611512
X-RAY DIFFRACTIONr_chiral_restr0.1550.2806
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.023864
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.0590.12413
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2830.53323
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2170.5568
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0370.186
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2570.544
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.08623406
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.03435292
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it6.4454.52020
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it8.33861707
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
Rfree0.357 170
Rwork0.269 3452
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)
12.13750.2481-0.36021.5696-0.134.6174-0.0184-0.08960.0504-0.09980.00220.0480.1599-0.08220.0162-0.1980.00490.0106-0.177-0.0081-0.207342.93614.43753.597
21.99810.012-0.37951.6151-0.96094.73170.0051-0.0708-0.0713-0.12040.01120.02580.0280.2257-0.0163-0.1581-0.0030.0152-0.1986-0.0144-0.209740.69612.69721.987
31.18510.8424-0.35885.68881.01070.84890.04810.25340.2714-0.13550.00370.0367-0.2944-0.173-0.05170.00970.0130.0229-0.10730.0419-0.050839.64538.4956.031
40.6365-0.1591.26953.3838-0.28939.61740.0710.20770.2254-0.0615-0.1961-0.0182-0.41050.37680.12510.0811-0.0608-0.0523-0.05620.05170.043448.7938.48335.907
53.08850.0033-1.14690.3312-0.32694.2652-0.0302-0.05820.03850.0147-0.0197-0.02490.04560.06610.0499-0.0877-0.00620.01940.0491-0.025-0.107115.34511.83739.228
64.6227-0.0628-0.0590.6425-0.0030.98310.0684-0.18560.11650.10870.0111-0.0641-0.09760.0177-0.0795-0.12860.02130.0308-0.0191-0.0232-0.181517.5920.30969.372
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A98 - 107
2X-RAY DIFFRACTION2B98 - 107
3X-RAY DIFFRACTION3C101 - 107
4X-RAY DIFFRACTION4D99 - 107
5X-RAY DIFFRACTION5E98 - 107
6X-RAY DIFFRACTION6F100 - 107

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