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- PDB-7xq3: Crystal structure of the tetramer of thioredoxin domain containin... -

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Basic information

Entry
Database: PDB / ID: 7xq3
TitleCrystal structure of the tetramer of thioredoxin domain containing-protein of Oncomelania hupensis(OhTRP14)
ComponentsThioredoxin domain-containing protein 17
KeywordsELECTRON TRANSPORT / Oncomelania hupensis / TRP14 / Redox regulation / Immunological properties
Function / homologyThioredoxin domain-containing protein 17-like domain / Thioredoxin domain-containing protein 17-like / Thioredoxin domain-containing protein 17-like, thioredoxin domain / protein-disulfide reductase [NAD(P)H] activity / Thioredoxin-like superfamily / cytosol / Thioredoxin domain-containing protein 17
Function and homology information
Biological speciesOncomelania hupensis (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.77 Å
AuthorsWang, S.Q. / Huang, S.Q.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Fish Shellfish Immunol. / Year: 2022
Title: Structural insights into the redox regulation of Oncomelania hupensis TRP14 and its potential role in the snail host response to parasite invasion.
Authors: Huang, S. / Wang, S. / Su, Z. / Cao, Y. / Hong, W. / Lin, T.
History
DepositionMay 6, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 12, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Thioredoxin domain-containing protein 17
B: Thioredoxin domain-containing protein 17
C: Thioredoxin domain-containing protein 17
D: Thioredoxin domain-containing protein 17


Theoretical massNumber of molelcules
Total (without water)55,4994
Polymers55,4994
Non-polymers00
Water9,998555
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.665, 46.017, 94.115
Angle α, β, γ (deg.)90.000, 108.320, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Thioredoxin domain-containing protein 17


Mass: 13874.693 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oncomelania hupensis (invertebrata) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2P1CXZ6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 555 / 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: 2.24 Å3/Da / Density % sol: 44.99 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4 / Details: 30% PEG 3350, 0.2M Sodium malonate pH 4.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9793 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jan 6, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.77→50 Å / Num. obs: 47643 / % possible obs: 100 % / Redundancy: 6.6 % / Biso Wilson estimate: 20.31 Å2 / Rmerge(I) obs: 0.109 / Rsym value: 0.109 / Net I/σ(I): 15.528
Reflection shellResolution: 1.77→1.8 Å / Rmerge(I) obs: 0.273 / Num. unique obs: 47643 / CC1/2: 0.967 / Rsym value: 0.273

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1WOU

1wou


Resolution: 1.77→35.74 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.923 / SU B: 3.355 / SU ML: 0.108 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.201 / ESU R Free: 0.181 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.3051 4689 9.9 %RANDOM
Rwork0.2583 ---
obs0.2629 42863 99.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 70.33 Å2 / Biso mean: 22.43 Å2 / Biso min: 8.09 Å2
Baniso -1Baniso -2Baniso -3
1-0.35 Å2-0 Å20.1 Å2
2---0.29 Å2-0 Å2
3----0.1 Å2
Refinement stepCycle: final / Resolution: 1.77→35.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3822 0 0 555 4377
Biso mean---31.26 -
Num. residues----485
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0133972
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173584
X-RAY DIFFRACTIONr_angle_refined_deg1.8011.6425384
X-RAY DIFFRACTIONr_angle_other_deg1.4481.5818393
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0155496
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.50824.366213
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.71715683
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.5341516
X-RAY DIFFRACTIONr_chiral_restr0.0930.2497
X-RAY DIFFRACTIONr_gen_planes_refined0.010.024493
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02799
LS refinement shellResolution: 1.77→1.815 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.296 291 -
Rwork0.283 3133 -
obs--97.91 %

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