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- PDB-1qk8: TRYPAREDOXIN-I FROM CRITHIDIA FASCICULATA -

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Basic information

Entry
Database: PDB / ID: 1qk8
TitleTRYPAREDOXIN-I FROM CRITHIDIA FASCICULATA
ComponentsTRYPAREDOXIN-I
KeywordsTRYPAREDOXIN / CRITHIDIA FASCICULATA / THIOREDOXIN / TRYPANOSOME / ANOMALOUS DISPERSION / OXIDATIVE STRESS / OXIDOREDUCTASE
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 / MAD / Resolution: 1.4 Å
AuthorsAlphey, M.S. / Hunter, W.N.
CitationJournal: J.Biol.Chem. / Year: 1999
Title: The High Resolution Crystal Structure of Recombinant Crithidia Fasciculata Tryparedoxin-I
Authors: Alphey, M.S. / Leonard, G.A. / Gourley, D.G. / Tetaud, E. / Fairlamb, A.H. / Hunter, W.N.
History
DepositionJul 11, 1999Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 2, 2000Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Remark 650 HELIX DETERMINATION METHOD: DSSP
Remark 700 SHEET DETERMINATION METHOD: DSSP

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TRYPAREDOXIN-I


Theoretical massNumber of molelcules
Total (without water)16,4991
Polymers16,4991
Non-polymers00
Water4,270237
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)38.390, 50.700, 70.820
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 / TRYX-I


Mass: 16498.633 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CRITHIDIA FASCICULATA (eukaryote) / Cellular location: CYTOPLASM / Plasmid: PET15B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834 MET- / References: EMBL: AF055913, UniProt: O96438*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 237 / 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: 2.13 Å3/Da / Density % sol: 42 %
Crystal growpH: 7.5
Details: 6.75MG/ML PROTEIN, 7.5% PEG MME 2000, 0.025M TRIS/HCL PH8.2, 0.25% DMSO, pH 7.50
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 8.4 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
210 mMTris-HCl1drop
350-100 mMTris-HCl1reservoir
480 mM1reservoirNaCl
517-20 %PEG80001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.88, 0.97
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 15, 1998
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.881
20.971
ReflectionResolution: 1.4→19 Å / Num. obs: 49768 / % possible obs: 94.5 % / Redundancy: 2 % / Biso Wilson estimate: 11.413 Å2 / Rmerge(I) obs: 0.029 / Net I/σ(I): 145.1
Reflection shellResolution: 1.4→1.43 Å / Redundancy: 1 % / Rmerge(I) obs: 0.17 / Mean I/σ(I) obs: 103.1 / % possible all: 65.6
Reflection shell
*PLUS
% possible obs: 65.6 %

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Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 1.4→40 Å / SU B: 1.147 / SU ML: 0.0467 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.0724 / ESU R Free: 0.0742
Details: RESIDUES GLU A 12, LYS A 13, ASP A 18, GLU A 20, GLU A 22, GLU A 59, GLU A 73, GLU A 74, ASP A 75,GLN A 93, ASN A 105, ARG A 128, AND GLN A 139 WERE SEEN TO HAVE DUAL CONFORMATIONS WHICH ARE ...Details: RESIDUES GLU A 12, LYS A 13, ASP A 18, GLU A 20, GLU A 22, GLU A 59, GLU A 73, GLU A 74, ASP A 75,GLN A 93, ASN A 105, ARG A 128, AND GLN A 139 WERE SEEN TO HAVE DUAL CONFORMATIONS WHICH ARE DISCUSSED IN THE PAPER BY M.S.ALPHEY ET AL. THE C-TERMINAL RESIDUE WAS NOT SEEN IN THE DENSITY MAPS, THE FIRST TWO N-TERMINAL RESIDUES WERE NOT SEEN IN THE ELECTRON DENSITY MAPS
RfactorNum. reflection% reflectionSelection details
Rfree0.223 1379 5 %RANDOM
Rwork0.191 ---
obs-27853 97.78 %-
Displacement parametersBiso mean: 15.13 Å2
Refinement stepCycle: LAST / Resolution: 1.4→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1144 0 0 237 1381
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0140.02
X-RAY DIFFRACTIONp_angle_d0.030.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.120.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.2452
X-RAY DIFFRACTIONp_mcangle_it1.8213
X-RAY DIFFRACTIONp_scbond_it1.7662
X-RAY DIFFRACTIONp_scangle_it2.5043
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr0.1220.15
X-RAY DIFFRACTIONp_singtor_nbd0.1740.3
X-RAY DIFFRACTIONp_multtor_nbd0.2420.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1620.3
X-RAY DIFFRACTIONp_planar_tor17.97
X-RAY DIFFRACTIONp_staggered_tor13.415
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor26.620
X-RAY DIFFRACTIONp_special_tor015

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