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- PDB-4uqy: Coevolution of the ATPase ClpV, the TssB-TssC Sheath and the Acce... -

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Basic information

Entry
Database: PDB / ID: 4uqy
TitleCoevolution of the ATPase ClpV, the TssB-TssC Sheath and the Accessory HsiE Protein Distinguishes Two Type VI Secretion Classes
Components
  • HSIB1
  • HSIE1
KeywordsPROTEIN TRANSPORT / SECRETION / SHEATH / DISASSEMBLY / REGULATION / BACTERIAL
Function / homology
Function and homology information


Type VI secretion system accessory component TagJ / ImpE protein / Type VI secretion system sheath protein TssB1 / Type VI secretion system, VipA, VC_A0107 or Hcp2 / Tetratricopeptide repeat / Tetratricopeptide repeat domain / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Mainly Alpha
Similarity search - Domain/homology
Type VI secretion system accessory component TagJ / Type VI secretion system sheath protein TssB1
Similarity search - Component
Biological speciesPSEUDOMONAS AERUGINOSA PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsForster, A. / Planamente, S. / Manoli, E. / Lossi, N.S. / Freemont, P.S. / Filloux, A.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Coevolution of the ATPase Clpv, the Sheath Proteins Tssb and Tssc and the Accessory Protein Tagj/Hsie1 Distinguishes Type Vi Secretion Classes.
Authors: Forster, A. / Planamente, S. / Manoli, E. / Lossi, N.S. / Freemont, P.S. / Filloux, A.
History
DepositionJun 25, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 22, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 3, 2014Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HSIE1
B: HSIB1


Theoretical massNumber of molelcules
Total (without water)30,9052
Polymers30,9052
Non-polymers00
Water3,549197
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1500 Å2
ΔGint-4.9 kcal/mol
Surface area12340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.220, 63.970, 94.540
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein HSIE1


Mass: 28665.506 Da / Num. of mol.: 1 / Fragment: RESIDUES 21-281
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS AERUGINOSA PAO1 (bacteria) / Production host: ESCHERICHIA COLI B (bacteria) / Strain (production host): B834 / References: UniProt: Q9I746
#2: Protein/peptide HSIB1


Mass: 2239.558 Da / Num. of mol.: 1 / Fragment: N TERMINUS, RESIDUES 1-20 / Source method: obtained synthetically / Source: (synth.) PSEUDOMONAS AERUGINOSA PAO1 (bacteria) / References: UniProt: Q9I749
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 197 / 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: 2.14 Å3/Da / Density % sol: 42.59 % / Description: NONE
Crystal growpH: 6.5
Details: 50 MM MES (PH 6.5) 100 MM AMMONIUM ACETATE 10% GLYCEROL 28% PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.98
DetectorType: ADSC ADSC CCD / Detector: CCD / Date: Feb 3, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.6→53 Å / Num. obs: 36309 / % possible obs: 99.8 % / Observed criterion σ(I): 1.5 / Redundancy: 3.2 % / Biso Wilson estimate: 18.08 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 10.7
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 2.2 / % possible all: 98.5

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ZBP

1zbp


Resolution: 1.6→30.298 Å / SU ML: 0.15 / σ(F): 1.35 / Phase error: 20.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2051 1806 5 %
Rwork0.1766 --
obs0.178 35818 96.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.74 Å2
Refinement stepCycle: LAST / Resolution: 1.6→30.298 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2079 0 0 197 2276
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062182
X-RAY DIFFRACTIONf_angle_d1.0322983
X-RAY DIFFRACTIONf_dihedral_angle_d12.396810
X-RAY DIFFRACTIONf_chiral_restr0.041338
X-RAY DIFFRACTIONf_plane_restr0.005401
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.64330.29471450.28182536X-RAY DIFFRACTION97
1.6433-1.69160.27431330.23832599X-RAY DIFFRACTION97
1.6916-1.74620.22621450.2082580X-RAY DIFFRACTION97
1.7462-1.80860.23381420.20312597X-RAY DIFFRACTION97
1.8086-1.8810.24991400.18962571X-RAY DIFFRACTION97
1.881-1.96660.22161300.17572657X-RAY DIFFRACTION98
1.9666-2.07030.19981370.17132629X-RAY DIFFRACTION99
2.0703-2.20.21011530.16722654X-RAY DIFFRACTION99
2.2-2.36980.23311570.16992674X-RAY DIFFRACTION99
2.3698-2.60810.1931210.17512685X-RAY DIFFRACTION99
2.6081-2.98530.21281430.18122692X-RAY DIFFRACTION99
2.9853-3.760.17811340.16142718X-RAY DIFFRACTION98
3.76-30.30340.17531260.16522420X-RAY DIFFRACTION84
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)
11.61630.01940.1911.84830.54962.11780.0329-0.4758-0.25910.58850.0633-0.14680.54840.0506-0.07160.47850.03110.00250.29120.05460.18317.9273-10.2540.6225
25.91970.18324.23912.46920.86528.0179-0.0662-0.31330.12340.11840.0996-0.046-0.426-0.0277-0.00750.25260.00670.05470.1814-0.00820.156719.03430.4143-12.4426
33.3470.57330.93511.02030.49395.2238-0.07520.1130.2028-0.11840.09670.066-0.1847-0.4747-0.0280.2420.0268-0.00840.13650.04050.165910.2489-0.4219-34.9037
41.03180.40260.10421.96310.00222.5045-0.00820.0098-0.09330.01650.0415-0.14270.08840.1184-0.02390.15710.02250.02490.0917-0.00460.163821.9963-10.4824-25.3179
51.58313.167-3.55516.4835-6.98768.0564-0.33330.3228-0.0241-0.64720.56180.12810.6808-0.6138-0.14020.2729-0.0304-0.00620.1575-0.01970.19714.3239-19.6604-32.0782
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 30 THROUGH 88 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 89 THROUGH 112 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 113 THROUGH 156 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 157 THROUGH 286 )
5X-RAY DIFFRACTION5CHAIN 'B' AND (RESID 8 THROUGH 20 )

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