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- PDB-1wou: Crystal Structure of human Trp14 -

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Basic information

Entry
Database: PDB / ID: 1wou
TitleCrystal Structure of human Trp14
Componentsthioredoxin -related protein, 14 kDa
KeywordsELECTRON TRANSPORT
Function / homology
Function and homology information


protein-disulfide reductase (NAD(P)H) activity / tumor necrosis factor-mediated signaling pathway / peroxidase activity / extracellular exosome / cytosol
Similarity search - Function
Thioredoxin domain-containing protein 17-like domain / Thioredoxin domain-containing protein 17-like, thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Thioredoxin domain-containing protein 17
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MAD / Resolution: 1.8 Å
AuthorsWoo, J.R. / Kim, S.J. / Jeong, W. / Cho, Y.H. / Lee, S.C. / Chung, Y.J. / Rhee, S.G. / Ryu, S.E.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: Structural basis of cellular redox regulation by human TRP14
Authors: Woo, J.R. / Kim, S.J. / Jeong, W. / Cho, Y.H. / Lee, S.C. / Chung, Y.J. / Rhee, S.G. / Ryu, S.E.
History
DepositionAug 25, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 14, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: thioredoxin -related protein, 14 kDa


Theoretical massNumber of molelcules
Total (without water)13,9581
Polymers13,9581
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)26.860, 48.390, 81.840
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein thioredoxin -related protein, 14 kDa / Trp14 / Trx-related protein / 14 kDa


Mass: 13957.786 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / References: UniProt: Q9BRA2

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 1.97 Å3/Da / Density % sol: 37 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: polyethylene glycol 8000, polyethylene glycol monomethylether 2000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
12911
21
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
Detector
TypeIDDetectorDateDetails
RIGAKU RAXIS IV1IMAGE PLATEFeb 21, 2001mirrors
ADSC QUANTUM 42CCDJun 28, 2001mirrors
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1mirrorsSINGLE WAVELENGTHMx-ray1
2mirrorsMADMx-ray1
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→40 Å / Num. all: 10425 / Num. obs: 10385 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.041

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
SHARPphasing
CNS0.9refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MAD / Resolution: 1.8→22.57 Å / Isotropic thermal model: isothermal / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.229 539 -random
Rwork0.219 ---
all0.229 10425 --
obs0.219 10385 99.6 %-
Refinement stepCycle: LAST / Resolution: 1.8→22.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms947 0 0 0 947

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