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- PDB-4v3i: Crystal Structure of TssL from Vibrio cholerae. -

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Basic information

Entry
Database: PDB / ID: 4v3i
TitleCrystal Structure of TssL from Vibrio cholerae.
Components(VCA0115) x 2
KeywordsUNKNOWN FUNCTION / T6SS / VIBRIO CHOLERAE / TSSL / VCA0115
Function / homologyType IV / VI secretion system, DotU / Type IV / VI secretion system, DotU / Type IV / VI secretion system, DotU superfamily / Type VI secretion system protein DotU / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / membrane => GO:0016020 / Mainly Alpha / DotU domain-containing protein
Function and homology information
Biological speciesVIBRIO CHOLERAE (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.499 Å
AuthorsJeong, J.H. / Kim, Y.G.
CitationJournal: J. Microbiol. / Year: 2015
Title: Crystal structure of the bacterial type VI secretion system component TssL from Vibrio cholerae.
Authors: Chang, J.H. / Kim, Y.G.
History
DepositionOct 19, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 17, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 21, 2015Group: Database references
Revision 1.2May 10, 2017Group: Database references
Revision 1.3Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: VCA0115
B: VCA0115
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,4063
Polymers30,3132
Non-polymers921
Water1,20767
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area820 Å2
ΔGint-3.6 kcal/mol
Surface area8510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.361, 78.361, 49.456
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein VCA0115


Mass: 29711.797 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) VIBRIO CHOLERAE (bacteria) / Plasmid: PET30A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9KN50
#2: Protein/peptide VCA0115


Mass: 601.673 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) VIBRIO CHOLERAE (bacteria) / Plasmid: PET30A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9KN50
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / 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: 2.58 Å3/Da / Density % sol: 52.3 % / Description: NONE
Crystal growpH: 6.4
Details: 1.8 M SODIUM CHLORIDE, 0.1 M SODIUM POTASSIUM PHOSPHATE PH 6.4

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9795
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 4, 2013 / Details: MIRRORS
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMATER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 27803 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 11 % / Biso Wilson estimate: 14.82 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 59
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 8.5 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 6.63 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3U66

3u66


Resolution: 1.499→27.979 Å / SU ML: 0.12 / σ(F): 1.58 / Phase error: 19.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1939 2012 7.2 %
Rwork0.1793 --
obs0.1804 27800 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.499→27.979 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1281 0 6 67 1354
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091312
X-RAY DIFFRACTIONf_angle_d1.1911769
X-RAY DIFFRACTIONf_dihedral_angle_d14.623482
X-RAY DIFFRACTIONf_chiral_restr0.049194
X-RAY DIFFRACTIONf_plane_restr0.008224
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.499-1.53650.24711450.23271839X-RAY DIFFRACTION100
1.5365-1.5780.2161420.20551824X-RAY DIFFRACTION100
1.578-1.62450.23791350.19511844X-RAY DIFFRACTION100
1.6245-1.67690.22341420.17861844X-RAY DIFFRACTION100
1.6769-1.73680.18311460.1751819X-RAY DIFFRACTION100
1.7368-1.80630.17631440.17091855X-RAY DIFFRACTION100
1.8063-1.88850.21151430.17481829X-RAY DIFFRACTION100
1.8885-1.98810.21781470.17881809X-RAY DIFFRACTION100
1.9881-2.11260.20971420.16521857X-RAY DIFFRACTION100
2.1126-2.27560.1781450.16881842X-RAY DIFFRACTION100
2.2756-2.50450.19221440.17951857X-RAY DIFFRACTION100
2.5045-2.86660.19461410.18521860X-RAY DIFFRACTION100
2.8666-3.61040.17821480.17881857X-RAY DIFFRACTION100
3.6104-27.98410.18561480.17621852X-RAY DIFFRACTION97
Refinement TLS params.Method: refined / Origin x: 4.8855 Å / Origin y: 27.9566 Å / Origin z: -2.366 Å
111213212223313233
T0.0725 Å2-0.0092 Å20.0295 Å2-0.0809 Å20.0073 Å2--0.1153 Å2
L2.5907 °2-0.7914 °2-0.1423 °2-2.0716 °20.4406 °2--1.2541 °2
S-0.019 Å °-0.0243 Å °-0.1254 Å °0.0048 Å °0.0396 Å °-0.0263 Å °0.0662 Å °0.099 Å °-0.0149 Å °
Refinement TLS groupSelection details: ALL

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