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- PDB-1ewx: Crystal structure of native tryparedoxin I from Crithidia fasciculata -

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Basic information

Entry
Database: PDB / ID: 1ewx
TitleCrystal structure of native tryparedoxin I from Crithidia fasciculata
ComponentsTRYPAREDOXIN I
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: 1.7 Å
AuthorsHofmann, B. / Guerrero, S.A. / Kalisz, H.M. / Menge, U. / Nogoceke, E. / Montemartini, M. / Singh, M. / 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: Acta Crystallogr.,Sect.D / Year: 1998
Title: Crystallization and preliminary X-ray analysis of tryparedoxin I from Crithidia fasciculata
Authors: Kalisz, H.M. / Nogoceke, E. / Gommel, D.U. / Hofmann, B. / Flohe, L. / Hecht, H.-J.
History
DepositionApr 28, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 10, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TRYPAREDOXIN I


Theoretical massNumber of molelcules
Total (without water)16,3931
Polymers16,3931
Non-polymers00
Water4,197233
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.940, 51.390, 71.460
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 TRYPAREDOXIN I


Mass: 16393.475 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Crithidia fasciculata (eukaryote) / Strain: HS6 / References: UniProt: O96438
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 233 / 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: 2.12 Å3/Da / Density % sol: 42.08 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 8.7
Details: PEG 4000, Tris/HCl, Sodium acetate, pH 8.7, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Crystal grow
*PLUS
Temperature: 294 K
Details: Kalisz, H.M., (1998) Acta Crystallogr., Sect.D, 55, 696.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
113.5 mg/mlenzyme1drop
233 %(w/w)PEG40001reservoir
30.1 MTris-HCl1reservoirpH8.7
450 mMsodium acetate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.1
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 6, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.7→23.2 Å / Num. all: 15563 / Num. obs: 15563 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Biso Wilson estimate: 13.74 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 5.9
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.089 / Num. unique all: 2288 / % possible all: 100
Reflection shell
*PLUS
% possible obs: 100 %

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
REFMACrefinement
CCP4(SCALA)data scaling
RefinementResolution: 1.7→41.9 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.214 776 -RANDOM
Rwork0.168 ---
all0.172 15563 --
obs0.168 14787 97.1 %-
Refinement stepCycle: LAST / Resolution: 1.7→41.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1153 0 0 233 1386
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.021
X-RAY DIFFRACTIONp_angle_d0.036
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.213 / Rfactor Rwork: 0.169
Solvent computation
*PLUS
Displacement parameters
*PLUS

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