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- PDB-5zf2: Crystal structure of Trxlp from Edwardsiella tarda EIB202 -

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Basic information

Entry
Database: PDB / ID: 5zf2
TitleCrystal structure of Trxlp from Edwardsiella tarda EIB202
ComponentsThioredoxin (H-type,TRX-H)
KeywordsOXIDOREDUCTASE / Thioredoxin-like protein / T4SS effector / ASK1-MAPK signaling cascades.
Function / homologyThioredoxin / Thioredoxin domain profile. / Thioredoxin domain / Thioredoxin-like superfamily / Thioredoxin (H-type,TRX-H)
Function and homology information
Biological speciesEdwardsiella tarda (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.98 Å
AuthorsYang, C. / Quan, S.
CitationJournal: Plos Pathog. / Year: 2019
Title: The Edwardsiella piscicida thioredoxin-like protein inhibits ASK1-MAPKs signaling cascades to promote pathogenesis during infection.
Authors: Yang, D. / Liu, X. / Xu, W. / Gu, Z. / Yang, C. / Zhang, L. / Tan, J. / Zheng, X. / Wang, Z. / Quan, S. / Zhang, Y. / Liu, Q.
History
DepositionMar 2, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 6, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 18, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: Thioredoxin (H-type,TRX-H)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,7182
Polymers11,6221
Non-polymers961
Water1,78399
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area120 Å2
ΔGint-8 kcal/mol
Surface area5780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.273, 34.273, 264.702
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-309-

HOH

21A-348-

HOH

31A-393-

HOH

41A-397-

HOH

51A-399-

HOH

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Components

#1: Protein Thioredoxin (H-type,TRX-H) / Trxlp


Mass: 11622.009 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: CCTCC M208068
Source: (gene. exp.) Edwardsiella tarda (strain EIB202) (bacteria)
Strain: EIB202 / Gene: ETAE_2186 / Production host: Escherichia coli (E. coli) / Variant (production host): Rosetta / References: UniProt: D0Z9P5
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 99 / Source method: isolated from a natural source / Formula: H2O

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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: 1.93 Å3/Da / Density % sol: 36.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 30% PEG 8000, 100mM sodium acetate, pH6.5, 200mM lithium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97852 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 21, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97852 Å / Relative weight: 1
ReflectionResolution: 1.97→50 Å / Num. obs: 7481 / % possible obs: 99.9 % / Redundancy: 30.4 % / Rmerge(I) obs: 0.076 / Rpim(I) all: 0.014 / Rrim(I) all: 0.078 / Χ2: 1.203 / Net I/σ(I): 8.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.97-229.30.23510.9930.0370.2031.02699.7
2-2.0432.70.1813500.9970.0320.1841.032100
2.04-2.0833.10.1683360.9970.0290.171.154100
2.08-2.1230.60.173890.9970.0310.1731.147100
2.12-2.17320.1513480.9950.0260.1531.206100
2.17-2.2232.50.1363400.9980.0240.1381.208100
2.22-2.2729.20.1343730.9970.0250.1361.22199.5
2.27-2.3430.10.1223450.9980.0220.1241.195100
2.34-2.432.40.1153560.9990.020.1171.201100
2.4-2.4830.50.1113790.9980.020.1121.278100
2.48-2.57320.1053540.9980.0180.1061.205100
2.57-2.6729.80.1013680.9980.0190.1031.266100
2.67-2.829.20.093590.9990.0160.0911.235100
2.8-2.9429.70.0863800.9990.0160.0871.166100
2.94-3.1331.10.0793840.9980.0140.0811.29100
3.13-3.3730.70.0713720.9990.0130.0721.241100
3.37-3.7128.80.0653890.9990.0120.0661.33399.7
3.71-4.2431.10.064080.9990.0110.0611.374100
4.24-5.35300.0564010.9990.010.0571.22499.8
5.35-5025.30.0484990.9990.010.0491.03399.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-3000data scaling
PHASERphasing
PHENIX(1.10.1_2155: ???)refinement
PDB_EXTRACT3.24data extraction
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2YZU

2yzu


Resolution: 1.98→22.059 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 19.67
RfactorNum. reflection% reflection
Rfree0.2154 727 10.01 %
Rwork0.177 --
obs0.181 7263 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 75.79 Å2 / Biso mean: 25.3487 Å2 / Biso min: 8.9 Å2
Refinement stepCycle: final / Resolution: 1.98→22.059 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms818 0 5 99 922
Biso mean--27.3 33.68 -
Num. residues----103
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009838
X-RAY DIFFRACTIONf_angle_d0.9231138
X-RAY DIFFRACTIONf_chiral_restr0.06126
X-RAY DIFFRACTIONf_plane_restr0.006151
X-RAY DIFFRACTIONf_dihedral_angle_d13.982512
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.9801-2.13280.23991390.166812541393
2.1328-2.34720.23591370.172612331370
2.3472-2.68640.23571430.183612881431
2.6864-3.38260.22281460.192513151461
3.3826-22.05990.19341620.169614461608
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)
12.6923-1.15351.78882.0184-0.40651.99140.09670.2984-0.0779-0.3113-0.0406-0.19690.593-0.0794-0.05390.2079-0.04090.0150.15320.02090.132718.826113.8313114.8245
25.7871-0.7605-0.22422.41650.39751.91160.28930.15210.7306-0.09890.01540.14460.1546-0.5985-0.29390.1301-0.03650.0010.24910.10520.199211.263921.8108120.8647
30.7972-0.139-0.33411.5540.97563.23780.21160.48790.2674-0.4076-0.08680.6113-0.0352-1.043-0.22690.31780.1054-0.01710.32530.08140.237611.364731.3874120.2902
43.17612.07972.60653.891-0.38263.87720.5352-0.32760.09380.5045-0.5061-0.5822-0.83380.5438-0.09690.2073-0.0250.10320.11950.03820.214526.028728.8301114.9577
51.28850.1623-0.54481.0364-0.51070.707-0.0479-0.0306-0.04490.21170.29260.26950.2034-0.5228-0.19480.1757-0.06370.01560.26580.07250.229610.33715.7254123.8555
61.24-0.62170.31694.07090.15471.43640.06240.04220.04250.1329-0.005-0.316-0.18020.0362-0.10170.1323-0.01490.0070.11850.04410.116320.826625.0307127.083
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 15 )A0 - 15
2X-RAY DIFFRACTION2chain 'A' and (resid 16 through 28 )A16 - 28
3X-RAY DIFFRACTION3chain 'A' and (resid 29 through 43 )A29 - 43
4X-RAY DIFFRACTION4chain 'A' and (resid 44 through 50 )A44 - 50
5X-RAY DIFFRACTION5chain 'A' and (resid 51 through 73 )A51 - 73
6X-RAY DIFFRACTION6chain 'A' and (resid 74 through 102 )A74 - 102

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