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- PDB-4rcl: Structure of EspG3 chaperone from the type VII (ESX-3) secretion ... -

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Basic information

Entry
Database: PDB / ID: 4rcl
TitleStructure of EspG3 chaperone from the type VII (ESX-3) secretion system, space group P43212
ComponentsESPG3
KeywordsCHAPERONE / ESX-3 / type VII secretion system / RV0289 / protein secretion
Function / homologyEspG family / EspG family / cytoplasm / ESX-3 secretion-associated protein EspG3
Function and homology information
Biological speciesMycobacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsKorotkov, K.V.
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
DepositionSep 16, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 16, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 5, 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 1.2Mar 6, 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 1.3Sep 20, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ESPG3
B: ESPG3


Theoretical massNumber of molelcules
Total (without water)63,7342
Polymers63,7342
Non-polymers00
Water25214
1
A: ESPG3


Theoretical massNumber of molelcules
Total (without water)31,8671
Polymers31,8671
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ESPG3


Theoretical massNumber of molelcules
Total (without water)31,8671
Polymers31,8671
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)92.679, 92.679, 158.850
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein ESPG3


Mass: 31866.906 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium smegmatis (bacteria) / Strain: ATCC 700084 / mc(2)155 / Gene: MSMEG_0622, MSMEI_0606 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) / References: UniProt: A0QQ45
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 14 / 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: 2.68 Å3/Da / Density % sol: 54.04 %
Crystal growTemperature: 295 K / pH: 6
Details: 0.1M SODIUM CACODYLATE, PH 6.0, 15% PEG200, 5% PEG3350, vapor diffusion, hanging drop, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 15, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→46.34 Å / Num. obs: 36408 / % possible obs: 99.8 % / Redundancy: 11.1 % / Biso Wilson estimate: 67.77 Å2 / Rsym value: 0.087 / Net I/σ(I): 19.8
Reflection shellResolution: 2.7→2.84 Å / Redundancy: 11.3 % / Mean I/σ(I) obs: 2.3 / Rsym value: 138.9 / % possible all: 99.3

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHENIX1.9_1692refinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4L4W

4l4w


Resolution: 2.7→46.34 Å / SU ML: 0.44 / σ(F): 1.16 / Phase error: 29.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.278 1852 5.09 %
Rwork0.23 --
obs0.233 36397 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 100.56 Å2
Refinement stepCycle: LAST / Resolution: 2.7→46.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3709 0 0 14 3723
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033798
X-RAY DIFFRACTIONf_angle_d0.7225195
X-RAY DIFFRACTIONf_dihedral_angle_d10.5321340
X-RAY DIFFRACTIONf_chiral_restr0.03601
X-RAY DIFFRACTIONf_plane_restr0.004679
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.76930.4011440.34772621X-RAY DIFFRACTION98
2.7693-2.85080.3841230.32352690X-RAY DIFFRACTION100
2.8508-2.94280.36351390.32742646X-RAY DIFFRACTION100
2.9428-3.04790.33441510.29062662X-RAY DIFFRACTION100
3.0479-3.170.38131430.29912656X-RAY DIFFRACTION100
3.17-3.31420.3171730.26742618X-RAY DIFFRACTION100
3.3142-3.48890.2631570.25172668X-RAY DIFFRACTION100
3.4889-3.70740.25131600.24852660X-RAY DIFFRACTION100
3.7074-3.99350.31521490.23022628X-RAY DIFFRACTION100
3.9935-4.39510.24521480.21282671X-RAY DIFFRACTION100
4.3951-5.03040.20081090.17232673X-RAY DIFFRACTION100
5.0304-6.33520.28281550.21212654X-RAY DIFFRACTION100
6.3352-46.34630.23781010.20532698X-RAY DIFFRACTION100
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)
14.76680.62921.63644.58040.21132.4392-0.2666-0.11420.53890.4740.1501-0.5696-0.56080.58030.20010.8273-0.3355-0.06010.9183-0.13230.85457.47329.407-15.092
23.3443.2586-0.75226.1599-1.18542.88660.1506-0.08340.09820.0028-0.0247-0.3004-0.44620.7298-0.11390.4785-0.10170.0480.4054-0.05230.3968-3.07313.143-19.58
37.99622.07034.05033.6137-1.07138.4616-0.0544-0.7998-0.21550.7802-0.03130.1186-0.5049-0.3137-0.08350.7630.1621-0.04010.63940.04190.6264-16.905-2.053-0.7
42.6095-0.9209-0.3893.5681-0.27223.04120.0087-0.23720.1763-0.1125-0.0366-0.0895-0.22910.20160.01980.4559-0.00080.03010.2383-0.02170.3969-14.2425.64-16.825
52.8176-0.5890.45043.5339-0.07970.8972-0.0789-0.7676-0.77480.9843-0.0783-0.19980.83770.12790.08421.99820.22810.13260.5560.22720.7616-23.30521.3743.604
62.35241.6152-1.91044.8487-2.70154.6295-0.0986-0.3406-0.17091.65490.04240.0038-0.17220.14030.09661.13070.12790.0060.4480.00120.5406-25.32936.333-1.95
75.98240.9203-2.13482.90071.82942.50450.70550.1020.65890.7410.005-1.04820.76582.2066-0.91320.86180.0691-0.25811.452-0.31291.1214-6.63348.391-9.599
83.36-0.4759-0.1294.7224-0.6022.1423-0.2-0.1855-0.23931.05560.0082-0.02030.41020.07360.07730.84580.0229-0.00180.2833-0.00510.5202-23.41636.329-11.937
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 2:64 )
2X-RAY DIFFRACTION2(CHAIN A AND RESID 65:151 )
3X-RAY DIFFRACTION3(CHAIN A AND RESID 152:180 )
4X-RAY DIFFRACTION4(CHAIN A AND RESID 181:265 )
5X-RAY DIFFRACTION5(CHAIN B AND RESID 2:100 )
6X-RAY DIFFRACTION6(CHAIN B AND RESID 101:156 )
7X-RAY DIFFRACTION7(CHAIN B AND RESID 157:191 )
8X-RAY DIFFRACTION8(CHAIN B AND RESID 192:265 )

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