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- PDB-7fcf: Crystal structure of T6SS Hcp protein -

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Basic information

Entry
Database: PDB / ID: 7fcf
TitleCrystal structure of T6SS Hcp protein
Components(Fimbrial protein) x 2
KeywordsSTRUCTURAL PROTEIN / Hexamer
Function / homology: / Type VI secretion system effector Hcp / Hcp1-like superfamily / Type VI secretion system effector, Hcp / Fimbrial protein
Function and homology information
Biological speciesChromobacterium haemolyticum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsJobichen, C. / Sivaraman, J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Res.Microbiol. / Year: 2022
Title: Bacterial antagonism of Chromobacterium haemolyticum and characterization of its putative type VI secretion system.
Authors: Zwe, Y.H. / Yadav, M. / Ten, M.M.Z. / Srinivasan, M. / Jobichen, C. / Sivaraman, J. / Li, D.
History
DepositionJul 14, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 20, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 2, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fimbrial protein
B: Fimbrial protein
C: Fimbrial protein
D: Fimbrial protein
E: Fimbrial protein
F: Fimbrial protein


Theoretical massNumber of molelcules
Total (without water)105,7016
Polymers105,7016
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.205, 83.151, 156.083
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Fimbrial protein


Mass: 16771.779 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chromobacterium haemolyticum (bacteria)
Gene: B0T39_16745 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0A1W0CP47
#2: Protein
Fimbrial protein


Mass: 17785.938 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chromobacterium haemolyticum (bacteria)
Gene: B0T39_16745 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0A1W0CP47

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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: 2.41 Å3/Da / Density % sol: 48.99 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.2M Ammonium acetate, 0.1M HEPES pH 7.5, 25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9789 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 24, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 3.3→46.41 Å / Num. obs: 15808 / % possible obs: 97.17 % / Redundancy: 10.6 % / Biso Wilson estimate: 153.62 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 22.75
Reflection shellResolution: 3.3→3.42 Å / Rmerge(I) obs: 1.31 / Num. unique obs: 1191

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1Y12

1y12


Resolution: 3.3→46.41 Å / SU ML: 0.65 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 39.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3062 759 4.8 %
Rwork0.2712 --
obs0.2728 15808 97.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.3→46.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6448 0 0 0 6448
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0126580
X-RAY DIFFRACTIONf_angle_d1.5398859
X-RAY DIFFRACTIONf_dihedral_angle_d5.406858
X-RAY DIFFRACTIONf_chiral_restr0.099962
X-RAY DIFFRACTIONf_plane_restr0.0071133
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3-3.560.37611360.38442601X-RAY DIFFRACTION86
3.56-3.910.41421740.33883031X-RAY DIFFRACTION100
3.91-4.480.33211380.28383077X-RAY DIFFRACTION100
4.48-5.640.30621500.29073099X-RAY DIFFRACTION100
5.64-46.410.2781610.24213241X-RAY DIFFRACTION100

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