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- PDB-7xux: Crystal structure of a FIC domain containnig protein -

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Basic information

Entry
Database: PDB / ID: 7xux
TitleCrystal structure of a FIC domain containnig protein
ComponentsFido domain-containing protein
KeywordsTOXIN / FIC domain protein
Function / homology
Function and homology information


Fido domain-containing protein / Fido-like domain / Fic-like fold / Fido-like domain superfamily / Fic/DOC family / Fido domain / Fido domain profile. / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Fido domain-containing protein
Similarity search - Component
Biological speciesYersinia pseudotuberculosis serotype I
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.78 Å
AuthorsZhen, X. / Ouyang, S.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32170045 China
CitationJournal: Nat Commun / Year: 2022
Title: A secreted effector with a dual role as a toxin and as a transcriptional factor.
Authors: Wang, D. / Zhu, L. / Zhen, X. / Yang, D. / Li, C. / Chen, Y. / Wang, H. / Qu, Y. / Liu, X. / Yin, Y. / Gu, H. / Xu, L. / Wan, C. / Wang, Y. / Ouyang, S. / Shen, X.
History
DepositionMay 20, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 21, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 11, 2023Group: 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
Revision 1.2May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fido domain-containing protein
B: Fido domain-containing protein


Theoretical massNumber of molelcules
Total (without water)85,4492
Polymers85,4492
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1530 Å2
ΔGint-9 kcal/mol
Surface area32920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.464, 282.767, 73.571
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number21
Space group name H-MC222

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Components

#1: Protein Fido domain-containing protein


Mass: 42724.719 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pseudotuberculosis serotype I (strain IP32953) (bacteria)
Strain: IP32953 / Gene: YPTB3117 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q666X7

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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: 3.51 Å3/Da / Density % sol: 65 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1 M MES pH 6.5, 25% Glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.979813 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 30, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979813 Å / Relative weight: 1
ReflectionResolution: 2.78→141.38 Å / Num. obs: 406690 / % possible obs: 100 % / Redundancy: 13.2 % / Biso Wilson estimate: 75.08 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.206 / Net I/σ(I): 0.8
Reflection shellResolution: 2.78→2.85 Å / Rmerge(I) obs: 4.06 / Num. unique obs: 30176

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.20.1_4487refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
AutoSolphasing
RefinementMethod to determine structure: MAD / Resolution: 2.78→33.86 Å / SU ML: 0.45 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 29.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2574 3770 6.5 %
Rwork0.2291 --
obs0.231 30864 99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.78→33.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5721 0 0 0 5721
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025855
X-RAY DIFFRACTIONf_angle_d0.5067922
X-RAY DIFFRACTIONf_dihedral_angle_d4.261782
X-RAY DIFFRACTIONf_chiral_restr0.034893
X-RAY DIFFRACTIONf_plane_restr0.0051013
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.78-2.820.40851380.39671948X-RAY DIFFRACTION97
2.82-2.850.35311410.38212023X-RAY DIFFRACTION98
2.85-2.890.37211410.37661944X-RAY DIFFRACTION98
2.89-2.930.43931350.35532008X-RAY DIFFRACTION98
2.93-2.980.36981440.35742019X-RAY DIFFRACTION98
2.98-3.020.33391380.35871973X-RAY DIFFRACTION99
3.02-3.070.37751410.35342005X-RAY DIFFRACTION98
3.07-3.130.38061340.31542001X-RAY DIFFRACTION99
3.13-3.180.30631370.31922033X-RAY DIFFRACTION99
3.18-3.240.33551350.28161977X-RAY DIFFRACTION99
3.24-3.310.32561420.3012039X-RAY DIFFRACTION100
3.31-3.380.33541370.2872014X-RAY DIFFRACTION99
3.38-3.460.31451450.28742026X-RAY DIFFRACTION99
3.46-3.550.34481310.2561991X-RAY DIFFRACTION100
3.55-3.640.27621420.25452007X-RAY DIFFRACTION100
3.64-3.750.29111410.23412026X-RAY DIFFRACTION100
3.75-3.870.22051370.22472054X-RAY DIFFRACTION100
3.87-4.010.23531420.20411997X-RAY DIFFRACTION100
4.01-4.170.2481430.20382011X-RAY DIFFRACTION100
4.17-4.360.29451430.19482046X-RAY DIFFRACTION100
4.36-4.590.19051410.18992041X-RAY DIFFRACTION100
4.59-4.870.20621440.182001X-RAY DIFFRACTION100
4.87-5.250.22751420.19622049X-RAY DIFFRACTION100
5.25-5.770.25191410.22991996X-RAY DIFFRACTION100
5.77-6.60.29471390.22752036X-RAY DIFFRACTION100
6.61-8.30.19961420.19552027X-RAY DIFFRACTION100
8.3-33.860.15841340.15141903X-RAY DIFFRACTION93
Refinement TLS params.Method: refined / Origin x: -35.945 Å / Origin y: -40.5135 Å / Origin z: -13.4023 Å
111213212223313233
T0.4909 Å20.0222 Å2-0.0386 Å2-0.4572 Å20.0662 Å2--0.5028 Å2
L0.7094 °2-0.0899 °2-0.1048 °2-0.3795 °20.288 °2--0.5842 °2
S0.0355 Å °-0.0162 Å °0.0599 Å °0.0238 Å °0.0044 Å °-0.0979 Å °-0.0425 Å °0.0624 Å °-0.0323 Å °
Refinement TLS groupSelection details: all

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