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- PDB-1fg4: STRUCTURE OF TRYPAREDOXIN II -

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Basic information

Entry
Database: PDB / ID: 1fg4
TitleSTRUCTURE OF TRYPAREDOXIN II
ComponentsTRYPAREDOXIN II
KeywordsELECTRON TRANSPORT
Function / homology
Function and homology information


thioredoxin-disulfide reductase (NADPH) activity / negative regulation of Wnt signaling pathway / negative regulation of protein ubiquitination / nucleus
Similarity search - Function
TryX and NRX, thioredoxin domain / Thioredoxin-like / Thioredoxin-like fold / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesCrithidia fasciculata (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.9 Å
AuthorsHofmann, B. / Budde, H. / Bruns, K. / Guerrero, S.A. / Kalisz, H.M. / Menge, U. / Montemartini, M. / Nogoceke, E. / Steinert, P. / Wissing, J.B. ...Hofmann, B. / Budde, H. / Bruns, K. / Guerrero, S.A. / Kalisz, H.M. / Menge, U. / Montemartini, M. / Nogoceke, E. / Steinert, P. / Wissing, J.B. / Flohe, L. / Hecht, H.J.
Citation
Journal: Biol.Chem. / Year: 2001
Title: Structures of tryparedoxins revealing interaction with trypanothione.
Authors: Hofmann, B. / Budde, H. / Bruns, K. / Guerrero, S.A. / Kalisz, H.M. / Menge, U. / Montemartini, M. / Nogoceke, E. / Steinert, P. / Wissing, J.B. / Flohe, L. / Hecht, H.J.
#1: Journal: Biol.Chem. / Year: 1999
Title: Sequence, Heterologous Expression and Functional Characterization of a Novel Tryparedoxin from Crithidia fasciculata
Authors: Montemartini, M. / Kalisz, H.M. / Kiess, M. / Nogoceke, E. / Singh, M. / Steinert, P. / Flohe, L.
History
DepositionJul 28, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 25, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TRYPAREDOXIN II
B: TRYPAREDOXIN II


Theoretical massNumber of molelcules
Total (without water)33,5952
Polymers33,5952
Non-polymers00
Water3,207178
1
A: TRYPAREDOXIN II


Theoretical massNumber of molelcules
Total (without water)16,7971
Polymers16,7971
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: TRYPAREDOXIN II


Theoretical massNumber of molelcules
Total (without water)16,7971
Polymers16,7971
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)109.280, 109.280, 55.497
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212

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Components

#1: Protein TRYPAREDOXIN II


Mass: 16797.262 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Crithidia fasciculata (eukaryote) / Strain: HS6 / Plasmid: PET22B / Production host: Escherichia coli (E. coli) / References: UniProt: O77093
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 178 / 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: 2.47 Å3/Da / Density % sol: 50.12 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 8.2
Details: Sodium citrate, HEPES, pH 8.2, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Crystal grow
*PLUS
Temperature: 19 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
11.6 Msodium acetate1reservoir
20.1 MHEPES1reservoirpH8.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.07
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 1, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07 Å / Relative weight: 1
ReflectionResolution: 1.9→27.8 Å / Num. all: 26668 / Num. obs: 25175 / % possible obs: 94.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.4 % / Biso Wilson estimate: 21.5 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 4.7
Reflection shellResolution: 1.9→2 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.25 / Num. unique all: 3885 / % possible all: 97.8
Reflection
*PLUS
Rmerge(I) obs: 0.103
Reflection shell
*PLUS
% possible obs: 97.8 %

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
SOLVEphasing
SHARPphasing
REFMACrefinement
CCP4(SCALA)data scaling
RefinementResolution: 1.9→77 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.263 1253 5 %RANDOM
Rwork0.2038 ---
all0.20684 27070 --
obs0.2068 23921 93 %-
Displacement parametersBiso mean: 25.33 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3----1 Å2
Refinement stepCycle: LAST / Resolution: 1.9→77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2293 0 0 178 2471
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0320.022
X-RAY DIFFRACTIONp_mcbond_it3.0722
X-RAY DIFFRACTIONp_mcangle_it4.1763
X-RAY DIFFRACTIONp_scbond_it3.142
X-RAY DIFFRACTIONp_scangle_it4.4413
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.248 / Rfactor Rwork: 0.2038 / Highest resolution: 1.9 Å / Lowest resolution: 77 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.195
Solvent computation
*PLUS
Displacement parameters
*PLUS

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