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- PDB-5vba: Structure of EspG1 chaperone from the type VII (ESX-1) secretion ... -

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Basic information

Entry
Database: PDB / ID: 5vba
TitleStructure of EspG1 chaperone from the type VII (ESX-1) secretion system determined with the assistance of N-terminal T4 lysozyme fusion
ComponentsLysozyme, ESX-1 secretion-associated protein EspG1 chimera
KeywordsCHAPERONE / HYDROLASE / ESX-1 / type VII secretion system / Rv3866 / snm5 / protein secretion
Function / homology
Function and homology information


viral release from host cell by cytolysis / peptidoglycan catabolic process / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / host cell cytoplasm / defense response to bacterium / cytoplasm
Similarity search - Function
EspG family / EspG family / Endolysin T4 type / T4-type lysozyme / : / Glycoside hydrolase, family 24 / Phage lysozyme / Lysozyme domain superfamily / Lysozyme-like domain superfamily
Similarity search - Domain/homology
Endolysin / Endolysin / ESX-1 secretion-associated protein EspG1
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
Mycobacterium kansasii ATCC 12478 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.27 Å
AuthorsKorotkov, K.V.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI119022 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P20GM103486 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P30GM110787 United States
CitationJournal: J. Mol. Biol. / Year: 2019
Title: Structural Variability of EspG Chaperones from Mycobacterial ESX-1, ESX-3, and ESX-5 Type VII Secretion Systems.
Authors: Tuukkanen, A.T. / Freire, D. / Chan, S. / Arbing, M.A. / Reed, R.W. / Evans, T.J. / Zenkeviciute, G. / Kim, J. / Kahng, S. / Sawaya, M.R. / Chaton, C.T. / Wilmanns, M. / Eisenberg, D. / ...Authors: Tuukkanen, A.T. / Freire, D. / Chan, S. / Arbing, M.A. / Reed, R.W. / Evans, T.J. / Zenkeviciute, G. / Kim, J. / Kahng, S. / Sawaya, M.R. / Chaton, C.T. / Wilmanns, M. / Eisenberg, D. / Parret, A.H.A. / Korotkov, K.V.
History
DepositionMar 29, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 5, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Nov 28, 2018Group: Data collection / 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Jan 30, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year
Revision 1.4Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lysozyme, ESX-1 secretion-associated protein EspG1 chimera
B: Lysozyme, ESX-1 secretion-associated protein EspG1 chimera
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,35412
Polymers95,9992
Non-polymers35510
Water1,00956
1
A: Lysozyme, ESX-1 secretion-associated protein EspG1 chimera
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,1776
Polymers48,0001
Non-polymers1775
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Lysozyme, ESX-1 secretion-associated protein EspG1 chimera
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,1776
Polymers48,0001
Non-polymers1775
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.140, 81.690, 160.020
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111(CHAIN A AND (RESID 16 THROUGH 46 OR RESID 56 THROUGH 160 OR RESID 165 THROUGH 1162))
211(CHAIN B AND (RESID 16 THROUGH 104 OR RESID 107...

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Components

#1: Protein Lysozyme, ESX-1 secretion-associated protein EspG1 chimera / EspG1


Mass: 47999.500 Da / Num. of mol.: 2
Fragment: T4 lysozyme (UNP residues 2-162) + EspG1 (UNP residues 16-271)
Mutation: lysozyme: C54T, C97A, K162A, EspG1: V16M, C114A, C170A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage T4 (virus), (gene. exp.) Mycobacterium kansasii ATCC 12478 (bacteria)
Gene: e, T4Tp126 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: D9IEF7, UniProt: X7YCN8, UniProt: P00720*PLUS, lysozyme
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 56 / 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: 2.33 Å3/Da / Density % sol: 47.23 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 0.1 M Bicine, pH 9.0, 1.0 M lithium chloride, 10% PEG6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Nov 5, 2015 / Details: SI(111)
RadiationMonochromator: Rosenbaum-Rock double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.27→59.536 Å / Num. obs: 39581 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 6.341 % / Biso Wilson estimate: 47.81 Å2 / Rmerge(I) obs: 0.097 / Net I/σ(I): 11.07
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.27-2.336.5411.111.7428740.5831.206100
2.33-2.396.5930.8862.328080.6980.962100
2.39-2.466.610.7442.7927570.7660.807100
2.46-2.546.6250.6023.4926630.8430.653100
2.54-2.626.6040.524.0125710.8830.564100
2.62-2.716.1510.4574.9825010.8910.599.7
2.71-2.826.5970.3126.2924330.9520.338100
2.82-2.936.5870.2447.7123370.9680.265100
2.93-3.066.560.1839.9322410.980.199100
3.06-3.216.4830.1412.1421480.9880.153100
3.21-3.386.4170.11714.4420390.990.127100
3.38-3.595.8340.09817.4219350.9890.10899.6
3.59-3.845.810.08219.3418070.9920.09199.3
3.84-4.145.7360.0721.6216910.9940.07798.9
4.14-4.546.0230.0624.3415960.9960.06599.6
4.54-5.086.1080.05425.2914180.9970.05999.6
5.08-5.866.1580.05224.3712940.9970.05799.8
5.86-7.186.1420.04825.0910930.9980.05399.8
7.18-10.155.9430.04227.058700.9980.04699.7
10.15-59.5365.2790.04826.265050.9960.05497.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.3 Å59.63 Å
Translation2.3 Å59.63 Å

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Processing

Software
NameVersionClassification
PHENIXDEV_2722refinement
XSCALENovember 3, 2014 BUILT=20141118data scaling
PHASER2.5.7phasing
PDB_EXTRACT3.22data extraction
XDSNovember 3, 2014data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 4GBR & 4L4W

4gbr

4l4w


Resolution: 2.27→59.54 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.92 / Phase error: 27.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.251 3530 4.74 %RANDOM SELECTION
Rwork0.214 ---
obs0.216 39576 99.2 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 67.68 Å2
Refinement stepCycle: LAST / Resolution: 2.27→59.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6288 0 10 56 6354
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046402
X-RAY DIFFRACTIONf_angle_d0.6578699
X-RAY DIFFRACTIONf_dihedral_angle_d13.1743835
X-RAY DIFFRACTIONf_chiral_restr0.0431015
X-RAY DIFFRACTIONf_plane_restr0.0051120
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDType
11A4645X-RAY DIFFRACTIONPOSITIONAL
12B4645X-RAY DIFFRACTIONPOSITIONAL
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.27-2.30110.33071320.32962879X-RAY DIFFRACTION100
2.3011-2.3340.39871530.30952823X-RAY DIFFRACTION100
2.334-2.36880.2961390.30752862X-RAY DIFFRACTION100
2.3688-2.40580.30231410.28932854X-RAY DIFFRACTION100
2.4058-2.44530.3541520.29222841X-RAY DIFFRACTION100
2.4453-2.48740.351330.29022834X-RAY DIFFRACTION100
2.4874-2.53270.33231560.27682915X-RAY DIFFRACTION100
2.5327-2.58140.28191410.27672849X-RAY DIFFRACTION100
2.5814-2.63410.3261270.25652835X-RAY DIFFRACTION100
2.6341-2.69130.35821140.29362819X-RAY DIFFRACTION97
2.6913-2.7540.31461500.25742857X-RAY DIFFRACTION100
2.754-2.82280.31841590.25182838X-RAY DIFFRACTION100
2.8228-2.89910.31061330.25742878X-RAY DIFFRACTION100
2.8991-2.98450.24391460.23572844X-RAY DIFFRACTION100
2.9845-3.08080.32521510.23752844X-RAY DIFFRACTION100
3.0808-3.19090.23321290.232860X-RAY DIFFRACTION100
3.1909-3.31860.2421370.232844X-RAY DIFFRACTION99
3.3186-3.46970.27221260.22562805X-RAY DIFFRACTION97
3.4697-3.65260.25431320.2072797X-RAY DIFFRACTION98
3.6526-3.88140.23191320.2072783X-RAY DIFFRACTION97
3.8814-4.1810.22431580.18892777X-RAY DIFFRACTION98
4.181-4.60160.20531630.1682833X-RAY DIFFRACTION99
4.6016-5.26710.21291310.1652827X-RAY DIFFRACTION99
5.2671-6.63460.2541290.19542846X-RAY DIFFRACTION99
6.6346-59.5560.19651660.17192785X-RAY DIFFRACTION98

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