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

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Basic information

Entry
Database: PDB / ID: 4uqx
TitleCoevolution of the ATPase ClpV, the TssB-TssC Sheath and the Accessory HsiE Protein Distinguishes Two Type VI Secretion Classes
ComponentsHSIE1
KeywordsPROTEIN TRANSPORT / SECRETION / SHEATH / DISASSEMBLY / REGULATION / BACTERIAL
Function / homology
Function and homology information


Type VI secretion system accessory component TagJ / ImpE protein / 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
ACETATE ION / Type VI secretion system accessory component TagJ
Similarity search - Component
Biological speciesPSEUDOMONAS AERUGINOSA PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 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 2.0Oct 23, 2019Group: Atomic model / Data collection / Other / Category: atom_site / pdbx_database_status
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_database_status.status_code_sf
Revision 2.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _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: HSIE1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9624
Polymers28,6671
Non-polymers2953
Water5,837324
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.760, 45.870, 59.470
Angle α, β, γ (deg.)90.00, 109.98, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein HSIE1


Mass: 28666.510 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: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 324 / 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: 2.4 Å3/Da / Density % sol: 48.7 % / Description: NONE
Crystal growpH: 4.6
Details: 30% 2-METHYL 2,4-PENTANEDIOL 0.1 M SODIUM ACETATE (PH 4.6) 20 MM CACL2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 31, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.2→55.9 Å / Num. obs: 88118 / % possible obs: 98.1 % / Observed criterion σ(I): 1.5 / Redundancy: 2.7 % / Biso Wilson estimate: 11.51 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 8.2
Reflection shellResolution: 1.2→1.22 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 1.9 / % possible all: 98.2

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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: 1.2→34.78 Å / SU ML: 0.12 / σ(F): 1.34 / Phase error: 17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1577 1760 2 %
Rwork0.1511 --
obs0.1512 88068 97.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 16.74 Å2
Refinement stepCycle: LAST / Resolution: 1.2→34.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2006 0 20 324 2350
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082322
X-RAY DIFFRACTIONf_angle_d1.283208
X-RAY DIFFRACTIONf_dihedral_angle_d12.601868
X-RAY DIFFRACTIONf_chiral_restr0.069362
X-RAY DIFFRACTIONf_plane_restr0.007436
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2-1.23240.30121340.2726623X-RAY DIFFRACTION98
1.2324-1.26870.25271290.24086539X-RAY DIFFRACTION97
1.2687-1.30970.22691230.21676622X-RAY DIFFRACTION98
1.3097-1.35650.22021310.19426623X-RAY DIFFRACTION98
1.3565-1.41080.20711330.18646559X-RAY DIFFRACTION98
1.4108-1.4750.19811480.17516612X-RAY DIFFRACTION97
1.475-1.55280.16641570.14876601X-RAY DIFFRACTION98
1.5528-1.650.14421110.13766645X-RAY DIFFRACTION98
1.65-1.77740.13731470.13456651X-RAY DIFFRACTION98
1.7774-1.95630.13791530.13356643X-RAY DIFFRACTION98
1.9563-2.23930.13631260.12726704X-RAY DIFFRACTION99
2.2393-2.82110.13811180.13476731X-RAY DIFFRACTION98
2.8211-34.79440.14721500.14746755X-RAY DIFFRACTION97
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)
17.6025-3.11221.09835.96760.81994.4982-0.17-0.1579-0.80340.0090.09130.06370.36160.21520.04320.16780.03870.03640.21060.06640.186332.5537-23.015127.0237
21.5761-2.4103-0.92074.48193.28455.0179-0.0038-0.1730.13040.04470.19-0.33830.20190.4973-0.16820.12330.0185-0.00430.19660.01440.110640.2009-20.564118.9667
31.8746-2.5753-1.36454.99911.17342.8371-0.1121-0.0833-0.05050.10710.05130.04350.13640.06060.05050.06480.0082-0.00820.12130.00240.050932.2752-18.359214.5629
41.411-3.2281-1.93147.54924.11713.28150.08450.02820.0503-0.2266-0.0947-0.0163-0.14190.05560.01860.08370.0116-0.00780.1113-0.00090.075334.2808-16.54366.6496
51.4003-2.0483-0.54774.76060.81710.33770.00530.0492-0.0162-0.0521-0.03-0.0522-0.01250.0358-0.00910.0911-0.000300.112200.091224.6187-10.73355.1919
61.4271-0.8392-0.25681.88380.02110.5232-0.03320.06930.0992-0.08740.01340.0564-0.10830.0067-0.0030.0988-0.0098-0.0070.08090.01410.06410.44294.77244.95
75.1373.52582.37557.04152.752.9828-0.0813-0.31460.4330.1677-0.19550.3275-0.2028-0.26920.22470.15640.022-0.02290.1188-0.01530.14846.717911.932413.5857
86.3806-0.57510.19864.6362-4.76788.4255-0.0035-0.2898-0.4251-0.04620.22850.48640.5305-0.1825-0.25580.1294-0.00870.03880.1703-0.05180.179-4.3993-10.113713.6457
90.9087-0.1320.10991.07490.10370.54650.00190.0257-0.0542-0.0265-0.01140.06280.0102-0.03560.00230.0598-0.0075-0.00090.07070.00080.052810.5474-11.8649.0454
102.30250.28430.35451.49280.38041.432-0.0468-0.1110.01330.07190.03760.0081-0.0506-0.03470.01540.09480.01460.01350.08350.00550.040712.3534-8.085220.0696
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 26 THROUGH 39 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 40 THROUGH 57 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 58 THROUGH 73 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 74 THROUGH 88 )
5X-RAY DIFFRACTION5CHAIN 'A' AND (RESID 89 THROUGH 112 )
6X-RAY DIFFRACTION6CHAIN 'A' AND (RESID 113 THROUGH 139 )
7X-RAY DIFFRACTION7CHAIN 'A' AND (RESID 140 THROUGH 156 )
8X-RAY DIFFRACTION8CHAIN 'A' AND (RESID 157 THROUGH 169 )
9X-RAY DIFFRACTION9CHAIN 'A' AND (RESID 170 THROUGH 233 )
10X-RAY DIFFRACTION10CHAIN 'A' AND (RESID 234 THROUGH 287 )

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