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- PDB-4i8b: Crystal Structure of Thioredoxin from Schistosoma Japonicum -

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Basic information

Entry
Database: PDB / ID: 4i8b
TitleCrystal Structure of Thioredoxin from Schistosoma Japonicum
ComponentsThioredoxin
KeywordsOXIDOREDUCTASE / thioredoxin fold / protein-disulfide reductase
Function / homology
Function and homology information


protein-disulfide reductase activity / cytosol
Similarity search - Function
Thioredoxin / Thioredoxin / Thioredoxin, conserved site / Thioredoxin family active site. / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesSchistosoma japonicum (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsWu, Q. / Peng, Y. / Zhao, J. / Li, X. / Fan, X. / Zhou, X. / Chen, J. / Luo, Z. / Shi, D.
CitationJournal: Parasitology / Year: 2015
Title: Expression, characterization and crystal structure of thioredoxin from Schistosoma japonicum.
Authors: Li, Y. / Li, P. / Peng, Y. / Wu, Q. / Huang, F. / Liu, X. / Li, X. / Zhou, H. / Guo, D. / Shi, D. / Zhou, X.N. / Fan, X.
History
DepositionDec 3, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 4, 2013Provider: repository / Type: Initial release
Revision 1.1May 27, 2015Group: Database references
Revision 1.2Jun 3, 2015Group: Database references
Revision 1.3Jun 17, 2015Group: Database references
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

Downloads & links

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Assembly

Deposited unit
A: Thioredoxin
B: Thioredoxin


Theoretical massNumber of molelcules
Total (without water)23,4752
Polymers23,4752
Non-polymers00
Water2,198122
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)90.756, 149.364, 39.881
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-237-

HOH

21A-296-

HOH

31A-300-

HOH

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Components

#1: Protein Thioredoxin


Mass: 11737.380 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schistosoma japonicum (invertebrata) / Gene: Schistosoma japonicum / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9U8F3, protein-disulfide reductase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 122 / 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: 2.88 Å3/Da / Density % sol: 57.27 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 30% PEG 3350, 50 mM Bistris pH 6.5 and 10 mM BaCl2, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9707 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 16, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9707 Å / Relative weight: 1
ReflectionResolution: 1.996→37.34 Å / Num. all: 18886 / Num. obs: 18886 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1.8 / Redundancy: 7.9 % / Biso Wilson estimate: 21 Å2 / Rmerge(I) obs: 0.722 / Rsym value: 0.111 / Net I/σ(I): 411.8

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
BALBESphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→37.34 Å / SU ML: 0.48 / σ(F): 0 / σ(I): 0 / Phase error: 20.85 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2157 2759 10.02 %RANDOM
Rwork0.1861 ---
all0.1891 18898 --
obs0.1891 18886 99.7 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.745 Å2 / ksol: 0.355 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-3.5433 Å2-0 Å20 Å2
2---5.0429 Å2-0 Å2
3---1.4996 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a19 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 2→37.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1650 0 0 122 1772
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071691
X-RAY DIFFRACTIONf_angle_d0.9862286
X-RAY DIFFRACTIONf_dihedral_angle_d13.624626
X-RAY DIFFRACTIONf_chiral_restr0.07266
X-RAY DIFFRACTIONf_plane_restr0.005293
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.996-2.04560.27751240.23211159X-RAY DIFFRACTION98
2.0456-2.10090.24941320.20341199X-RAY DIFFRACTION100
2.1009-2.16270.23311300.19191198X-RAY DIFFRACTION100
2.1627-2.23250.25971360.19041209X-RAY DIFFRACTION100
2.2325-2.31230.23941340.19321185X-RAY DIFFRACTION100
2.3123-2.40490.23211400.19951187X-RAY DIFFRACTION100
2.4049-2.51430.2741360.21161227X-RAY DIFFRACTION100
2.5143-2.64680.23391330.18981207X-RAY DIFFRACTION100
2.6468-2.81260.20971370.19781209X-RAY DIFFRACTION100
2.8126-3.02970.25871360.21071215X-RAY DIFFRACTION100
3.0297-3.33440.21231330.18831216X-RAY DIFFRACTION100
3.3344-3.81650.18771380.16991237X-RAY DIFFRACTION100
3.8165-4.80680.19041420.16041241X-RAY DIFFRACTION100
4.8068-37.34750.1991420.18661304X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.42460.2325-0.53244.1614-1.333.34370.1225-0.0141-0.03490.2133-0.1644-0.0975-0.1750.08540.02710.13570.0111-0.00940.1793-0.01560.1164-12.8596-32.2745-2.1707
24.9667-2.21350.59415.27321.38264.97590.1144-0.2722-0.11290.8597-0.23821.07240.0471-0.27290.14440.55780.03780.1490.2666-0.06690.5433-32.7985-13.5706-1.9168
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B

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