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- PDB-1gh2: Crystal structure of the catalytic domain of a new human thioredo... -

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Basic information

Entry
Database: PDB / ID: 1gh2
TitleCrystal structure of the catalytic domain of a new human thioredoxin-like protein
ComponentsTHIOREDOXIN-LIKE PROTEIN
KeywordsELECTRON TRANSPORT / Redox-active center
Function / homology
Function and homology information


disulfide oxidoreductase activity / RHOBTB1 GTPase cycle / RND1 GTPase cycle / RND2 GTPase cycle / RND3 GTPase cycle / RHOV GTPase cycle / RHOU GTPase cycle / protein-disulfide reductase activity / RHOBTB2 GTPase cycle / proteasome complex ...disulfide oxidoreductase activity / RHOBTB1 GTPase cycle / RND1 GTPase cycle / RND2 GTPase cycle / RND3 GTPase cycle / RHOV GTPase cycle / RHOU GTPase cycle / protein-disulfide reductase activity / RHOBTB2 GTPase cycle / proteasome complex / nucleus / cytoplasm / cytosol
Similarity search - Function
PITH domain / PITH domain superfamily / PITH domain / PITH domain profile. / Thioredoxin / Thioredoxin, conserved site / Thioredoxin family active site. / Thioredoxin domain / Galactose-binding-like domain superfamily / Glutaredoxin ...PITH domain / PITH domain superfamily / PITH domain / PITH domain profile. / Thioredoxin / Thioredoxin, conserved site / Thioredoxin family active site. / Thioredoxin domain / Galactose-binding-like domain superfamily / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Thioredoxin-like protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.22 Å
AuthorsJin, J. / Chen, X. / Guo, Q. / Yuan, J. / Qiang, B. / Rao, Z.
CitationJournal: Eur.J.Biochem. / Year: 2002
Title: Crystal structure of the catalytic domain of a human thioredoxin-like protein.
Authors: Jin, J. / Chen, X. / Zhou, Y. / Bartlam, M. / Guo, Q. / Liu, Y. / Sun, Y. / Gao, Y. / Ye, S. / Li, G. / Rao, Z. / Qiang, B. / Yuan, J.
History
DepositionNov 1, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 1, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: THIOREDOXIN-LIKE PROTEIN


Theoretical massNumber of molelcules
Total (without water)11,6281
Polymers11,6281
Non-polymers00
Water79344
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)87.5, 48.5, 29.8
Angle α, β, γ (deg.)90, 99.59, 90
Int Tables number5
Space group name H-MC121

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Components

#1: Protein THIOREDOXIN-LIKE PROTEIN


Mass: 11628.187 Da / Num. of mol.: 1 / Fragment: RESIDUES 2 - 108, CATALYTIC N-TERMINAL DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Tissue: FETAL BRAIN / Plasmid: PGEX-4T-3 / Production host: Escherichia coli (E. coli) / References: UniProt: O43396
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / Source method: isolated from a natural source / Formula: H2O

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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: 2.68 Å3/Da / Density % sol: 54.12 %
Crystal growTemperature: 291 K / Method: evaporation / pH: 5
Details: ammonium sulfate, pH 5.0, EVAPORATION, temperature 291.0K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
Common name: ammonium sulfate

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Data collection

DiffractionMean temperature: 115 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Aug 28, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.22→100 Å / Num. all: 6184 / Num. obs: 6170 / % possible obs: 97.8 % / Observed criterion σ(I): -3 / Redundancy: 7.2 % / Biso Wilson estimate: 20.7 Å2 / Rmerge(I) obs: 0.089 / Net I/σ(I): 8.4
Reflection shellResolution: 2.22→2.3 Å / Redundancy: 6 % / Rmerge(I) obs: 0.316 / Num. unique all: 624 / % possible all: 98.7
Reflection
*PLUS
Num. obs: 6710 / % possible obs: 99.8 %
Reflection shell
*PLUS
% possible obs: 98.7 % / Num. unique obs: 624

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS0.9refinement
RefinementResolution: 2.22→15 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: CNS
RfactorNum. reflection% reflection
Rfree0.253 337 -
Rwork0.221 --
all-6026 -
obs-5689 92.3 %
Refinement stepCycle: LAST / Resolution: 2.22→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms816 0 0 44 860
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.019
X-RAY DIFFRACTIONc_angle_d1.975
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refinement
*PLUS
Rfactor Rwork: 0.222
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.02
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg1.97

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