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- PDB-5vtg: The structure of TamB963-1138 from Escherichia coli reveals a nov... -

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Basic information

Entry
Database: PDB / ID: 5vtg
TitleThe structure of TamB963-1138 from Escherichia coli reveals a novel hydrophobic Beta-taco fold
ComponentsTranslocation and assembly module subunit TamB
KeywordsCHAPERONE / Beta-sheet / Periplasm
Function / homologyTranslocation and assembly module TamB / TamB, inner membrane protein subunit of TAM complex / TAM protein secretion complex / protein localization to outer membrane / plasma membrane => GO:0005886 / protein secretion / Translocation and assembly module subunit TamB
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.859 Å
AuthorsGrinter, R. / Josts, I.
CitationJournal: Structure / Year: 2017
Title: The Structure of a Conserved Domain of TamB Reveals a Hydrophobic beta Taco Fold.
Authors: Josts, I. / Stubenrauch, C.J. / Vadlamani, G. / Mosbahi, K. / Walker, D. / Lithgow, T. / Grinter, R.
History
DepositionMay 17, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 22, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Dec 13, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Translocation and assembly module subunit TamB
B: Translocation and assembly module subunit TamB


Theoretical massNumber of molelcules
Total (without water)40,2372
Polymers40,2372
Non-polymers00
Water2,360131
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1740 Å2
ΔGint-7 kcal/mol
Surface area15820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.240, 57.240, 220.710
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Translocation and assembly module subunit TamB / Autotransporter assembly factor TamB


Mass: 20118.525 Da / Num. of mol.: 2 / Fragment: UNP residues 963-1138
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: tamB, ytfN, ytfO, b4221, JW4180 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P39321
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 131 / 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: 2.57 Å3/Da / Density % sol: 52.09 %
Description: Squat boxes with one square side and bowed edges
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.1 M HEPES, 15%(v/v) PEG 400, 0.2 M CaCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 18, 2013
RadiationMonochromator: SILICON CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.85→49.57 Å / Num. obs: 35019 / % possible obs: 94.5 % / Redundancy: 9.2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.041 / Net I/σ(I): 11.3
Reflection shellResolution: 1.85→1.89 Å / Redundancy: 6.8 % / Rmerge(I) obs: 2.887 / Mean I/σ(I) obs: 0.6 / Num. unique obs: 2208 / CC1/2: 0.586 / Rpim(I) all: 1.324 / % possible all: 99.2

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
Aimlessdata scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 1.859→49.571 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2507 1218 5.04 %
Rwork0.2078 --
obs0.21 24176 66.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.859→49.571 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2056 0 0 131 2187
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112135
X-RAY DIFFRACTIONf_angle_d1.3172909
X-RAY DIFFRACTIONf_dihedral_angle_d10.5251525
X-RAY DIFFRACTIONf_chiral_restr0.076329
X-RAY DIFFRACTIONf_plane_restr0.008394
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8586-1.9330.3925140.2138232X-RAY DIFFRACTION6
1.933-2.02090.1891320.1904721X-RAY DIFFRACTION19
2.0209-2.12750.2614710.21631429X-RAY DIFFRACTION37
2.1275-2.26080.2384860.25641945X-RAY DIFFRACTION68
2.2608-2.43530.2951840.24623347X-RAY DIFFRACTION99
2.4353-2.68040.30422350.23323812X-RAY DIFFRACTION100
2.6804-3.06820.28382150.21573835X-RAY DIFFRACTION100
3.0682-3.86540.25011620.18643728X-RAY DIFFRACTION94
3.8654-49.58890.21132190.19553909X-RAY DIFFRACTION95
Refinement TLS params.Method: refined / Origin x: 28.715 Å / Origin y: -24.2539 Å / Origin z: 249.4874 Å
111213212223313233
T0.0509 Å2-0.0255 Å2-0.0058 Å2-0.2889 Å20.0073 Å2--0.1554 Å2
L0.79 °2-0.1127 °2-1.0488 °2-0.5602 °2-0.1192 °2--2.8054 °2
S0.0074 Å °-0.0262 Å °-0.0164 Å °-0.0591 Å °-0.0126 Å °-0.0193 Å °-0.0249 Å °-0.0547 Å °-0.0054 Å °
Refinement TLS groupSelection details: all

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