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- PDB-1uvz: structure of human thioredoxin 2 -

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Basic information

Entry
Database: PDB / ID: 1uvz
Titlestructure of human thioredoxin 2
ComponentsTHIOREDOXIN
KeywordsOXIDOREDUCTASE / THIOREDOXIN / 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 / cell redox homeostasis / response to hormone ...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 / cell redox homeostasis / response to hormone / response to organic cyclic compound / response to oxidative stress / response to hypoxia / mitochondrial matrix / response to xenobiotic stimulus / neuronal cell body / dendrite / 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: 2.01 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
DepositionJan 27, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 16, 2005Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / 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

Downloads & links

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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
Water9,458525
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
MethodPQS
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
MethodPQS
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
MethodPQS
Unit cell
Length a, b, c (Å)49.038, 49.087, 78.977
Angle α, β, γ (deg.)87.96, 83.19, 79.08
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.18804, -0.98213, 0.00733), (-0.98215, 0.18806, 0.00345), (-0.00477, -0.00655, -0.99997)61.36439, 50.73463, 75.04037
2given(0.87441, -0.37925, -0.30262), (-0.38067, -0.92297, 0.05676), (-0.30083, 0.06557, -0.95142)24.50591, 64.28873, 67.63113
3given(0.1377, -0.9589, 0.2481), (0.99037, 0.12957, -0.04888), (0.01472, 0.25244, 0.9675)42.30188, -1.8223, -19.69132
4given(-0.99826, 0.05888, -0.00014), (0.0569, 0.96411, -0.25935), (-0.01514, -0.25891, -0.96578)55.53374, 9.29175, 94.42096
5given(0.19771, 0.98007, -0.01942), (-0.91825, 0.19211, 0.34627), (0.3431, -0.05063, 0.93793)-4.62847, 37.11396, 5.54049

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Components

#1: Protein
THIOREDOXIN / HUMAN THIOREDOXIN 2


Mass: 13288.154 Da / Num. of mol.: 6 / Fragment: RESIDUES 60-166
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Description: SYNTHETIC GENE / Organ: LIVER / Plasmid: PQE30 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): M15 (PREP4) / References: UniProt: Q99757
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 525 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsAMINO ACID NUMBERING STARTS AT THR1 WHICH IS THE FIRST AMINO ACID OF THE PROCESSED PROTEIN WITHOUT ...AMINO ACID NUMBERING STARTS AT THR1 WHICH IS THE FIRST AMINO ACID OF THE PROCESSED PROTEIN WITHOUT ITS MITOCHONDRIAL PRESEQUENCE. THUS, THR1 CORRESPONDS TO THR60 OF 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: 2.3 Å3/Da / Density % sol: 45.8 %
Crystal growpH: 4.6
Details: PEG 3350 22% (W/V), NA ACETATE 0.1M (PH: 4.6), AMMONIUM SULFATE 0.2M, DTT 1MM, pH 4.60

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.8441
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 2, 2002 / Details: BENT MIRROR
RadiationMonochromator: TRIANGULAR MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8441 Å / Relative weight: 1
ReflectionResolution: 2→23.5 Å / Num. obs: 47020 / % possible obs: 96.9 % / Redundancy: 2.11 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 9.72
Reflection shellResolution: 2→2.2 Å / Redundancy: 2 % / Rmerge(I) obs: 0.22 / Mean I/σ(I) obs: 4.22 / % possible all: 90.4

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
XDSdata reduction
XSCALEdata scaling
BEASTphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ERT

1ert


Resolution: 2.01→23.25 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.9 / SU B: 5.578 / SU ML: 0.153 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.206 / ESU R Free: 0.193 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE DISTANCES OBSERVED IN THE 3 MOLECULES BETWEEN THE CYSTEINYL SULFUR ATOMS (CYS 31 AND CYS 34) IS HALFWAY BETWEEN THE VALUE REQUIRED FOR ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE DISTANCES OBSERVED IN THE 3 MOLECULES BETWEEN THE CYSTEINYL SULFUR ATOMS (CYS 31 AND CYS 34) IS HALFWAY BETWEEN THE VALUE REQUIRED FOR THE FORMATION OF A DISULFIDE BOND (OXIDIZED FORM) AND THE VALUE REQUIRED IN THE ABSENCE OF SUCH A BOND (SUM OF VDW RADII IN THE REDUCED FORM). AN HYPOTHESIS COULD BE THAT ALTERNATE CONFORMATIONS (OXIDIZED AND REDUCED) COEXIST, BUT THE RESOLUTION ACHIEVED IS NOT HIGH ENOUGH TO OBSERVE ALTERNATE CONFORMATIONS. THE ELECTRON DENSITY IS THUS AN AVERAGE DENSITY BETWEEN BOTH CONFORMATIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.265 2395 5.1 %RANDOM
Rwork0.2 ---
obs0.203 44625 98.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 12.82 Å2
Baniso -1Baniso -2Baniso -3
1--1.21 Å20.86 Å20.09 Å2
2---0.15 Å2-1.11 Å2
3---1.09 Å2
Refinement stepCycle: LAST / Resolution: 2.01→23.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5074 0 0 525 5599
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0225167
X-RAY DIFFRACTIONr_bond_other_d0.0070.024694
X-RAY DIFFRACTIONr_angle_refined_deg2.0171.9546993
X-RAY DIFFRACTIONr_angle_other_deg1.345311010
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5575648
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.130.2806
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.025718
X-RAY DIFFRACTIONr_gen_planes_other0.010.02912
X-RAY DIFFRACTIONr_nbd_refined0.1880.21121
X-RAY DIFFRACTIONr_nbd_other0.20.25689
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0920.53053
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2470.4504
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1630.231
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2160.2103
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2390.448
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9911.53254
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.69925286
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.82831913
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.4454.51707
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: 2.01→2.06 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.367 165
Rwork0.354 2683
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)
11.2658-0.0773-0.4081.8476-0.16584.8480.0159-0.07370.076-0.14290.00270.08040.2151-0.2148-0.01860.0737-0.03780.0080.10650.05880.071341.63714.53753.048
21.9368-0.2483-0.29761.8219-0.70334.19180.023-0.11130.0768-0.10270.04080.0381-0.06190.2493-0.06380.1082-0.04120.02420.0750.04570.056339.52812.70121.612
30.86871.0456-0.04864.99961.1510.985-0.07410.10150.0696-0.12960.05260.1651-0.2163-0.12410.02140.2524-0.0205-0.02170.1020.07410.098739.02937.9335.766
41.1220.3838-1.87113.8941-1.77296.19060.1006-0.0773-0.0426-0.0681-0.06590.1496-0.1290.0335-0.03460.5199-0.0584-0.04630.14310.10980.163947.03438.57935.878
54.3811-0.323-2.35860.5176-0.74855.8068-0.0734-0.15390.1971-0.08380.0955-0.12060.0740.0008-0.02210.2003-0.04160.04420.46980.01360.160614.79711.88438.654
65.9289-0.0527-0.30570.89640.14210.98630.0491-0.31730.17560.0930.0691-0.0983-0.05810.3241-0.11830.0988-0.03070.01150.299-0.01120.078416.9620.1568.677
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-2 - 107
2X-RAY DIFFRACTION2B-2 - 107
3X-RAY DIFFRACTION3C1 - 107
4X-RAY DIFFRACTION4D-1 - 107
5X-RAY DIFFRACTION5E-2 - 107
6X-RAY DIFFRACTION6F0 - 107

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