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- PDB-4w4j: Crystal structure of EspG3 from the ESX-3 type VII secretion syst... -

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Basic information

Entry
Database: PDB / ID: 4w4j
TitleCrystal structure of EspG3 from the ESX-3 type VII secretion system of M. smegmatis
ComponentsEspG3
KeywordsPROTEIN TRANSPORT / signal recognition / virulence factor / protein secretion / adaptor
Function / homologyEspG family / EspG family / cytoplasm / ESX-3 secretion-associated protein EspG3
Function and homology information
Biological speciesMycobacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.803 Å
AuthorsEkiert, D.C. / Cox, J.S.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI081727 United States
Damon Runyon Cancer Research FoundationDRG-2140-12 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Structure of a PE-PPE-EspG complex from Mycobacterium tuberculosis reveals molecular specificity of ESX protein secretion.
Authors: Ekiert, D.C. / Cox, J.S.
History
DepositionAug 14, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 1, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 15, 2014Group: Database references
Revision 1.2Oct 29, 2014Group: Database references
Revision 1.3Sep 27, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Other / Refinement description / Source and taxonomy / Structure summary
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / software / struct_keywords
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.text
Revision 1.4Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Dec 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / refine_hist
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: EspG3
B: EspG3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,2695
Polymers67,9812
Non-polymers2883
Water0
1
A: EspG3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,2784
Polymers33,9901
Non-polymers2883
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: EspG3


Theoretical massNumber of molelcules
Total (without water)33,9901
Polymers33,9901
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)95.210, 95.210, 171.540
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 EspG3


Mass: 33990.277 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 / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 (BL21) / References: UniProt: A0QQ45
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4

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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: 3.33 Å3/Da / Density % sol: 63.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: 0.2 M lithium sulfate, 0.1 M phosphate-citrate pH 4.2, 10% (v/v) isopropanol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 0.980,0.957
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 12, 2012
RadiationMonochromator: Double flat crystal, Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.981
20.9571
ReflectionResolution: 2.8→50 Å / Num. obs: 22760 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 21.9 % / Biso Wilson estimate: 74.8 Å2 / Rsym value: 0.15 / Net I/σ(I): 19.8
Reflection shellResolution: 2.8→2.87 Å / Redundancy: 22.5 % / Rmerge(I) obs: 3.15 / Mean I/σ(I) obs: 1.2 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: dev_1727)refinement
Blu-Icedata collection
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MAD / Resolution: 2.803→47.605 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2354 2271 10 %RANDOM
Rwork0.1904 ---
obs0.195 22720 99.98 %-
Solvent computationShrinkage radii: 1 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 99.2 Å2
Refinement stepCycle: LAST / Resolution: 2.803→47.605 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3990 0 15 0 4005
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0114188
X-RAY DIFFRACTIONf_angle_d1.4015732
X-RAY DIFFRACTIONf_dihedral_angle_d13.4831486
X-RAY DIFFRACTIONf_chiral_restr0.059650
X-RAY DIFFRACTIONf_plane_restr0.008751
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.803-2.86390.44051390.36941241X-RAY DIFFRACTION100
2.8639-2.93060.34351380.31211245X-RAY DIFFRACTION100
2.9306-3.00380.31961370.25511256X-RAY DIFFRACTION100
3.0038-3.0850.28131410.2261272X-RAY DIFFRACTION100
3.085-3.17580.24581430.20361276X-RAY DIFFRACTION100
3.1758-3.27830.2751350.21771248X-RAY DIFFRACTION100
3.2783-3.39540.28381460.21851259X-RAY DIFFRACTION100
3.3954-3.53130.25381360.20061252X-RAY DIFFRACTION100
3.5313-3.6920.24051420.20481276X-RAY DIFFRACTION100
3.692-3.88650.26541400.18841265X-RAY DIFFRACTION100
3.8865-4.12990.21111410.18371303X-RAY DIFFRACTION100
4.1299-4.44860.21881450.16191251X-RAY DIFFRACTION100
4.4486-4.89580.19191440.14871297X-RAY DIFFRACTION100
4.8958-5.60330.21431400.17571304X-RAY DIFFRACTION100
5.6033-7.05590.26161510.21061302X-RAY DIFFRACTION100
7.0559-47.61180.20481530.17461402X-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)
11.9976-0.40340.47841.4656-0.10822.6936-0.12-0.0854-0.2879-0.3601-0.4814-0.39150.28051.1239-0.5820.34270.02570.02440.81860.1010.45142.218650.3536175.1453
20.6234-0.79610.23541.7284-0.58391.16090.1578-0.41210.2042-0.0053-0.05220.03570.0142-0.0734-0.00640.30240.0196-0.03970.7167-0.04410.392724.903351.0961182.1593
30.34920.232-0.92510.5843-1.29993.7830.0668-0.6688-1.0054-0.2508-0.41570.0181.18680.1789-0.27240.4702-0.1182-0.09830.7484-0.12440.847213.571226.5645187.5284
42.850.6904-0.79562.59731.27991.22310.0519-0.8639-0.14760.3589-0.02120.3223-0.0477-0.06890.39510.18610.0138-0.03580.83390.04620.411725.270142.7171193.6959
50.1872-0.1901-0.19980.31540.00650.242-0.2222-0.14030.28950.57950.65750.3028-0.1411-1.0228-0.00071.04360.14460.36721.174-0.05921.3267-12.270162.9639216.6604
60.6804-0.10360.7710.0166-0.12770.87970.543-1.2647-0.1460.07520.66580.154-0.4695-1.41350.10871.661-0.07870.65611.4098-0.18472.0368-18.497370.9263222.357
70.89430.2171-0.82021.4965-0.83481.83650.08630.14220.54630.13640.18520.2024-0.48070.4787-0.01480.5498-0.03260.1580.9571-0.11810.82030.253561.3249208.7353
81.98950.43170.40962.21771.84632.1278-0.0044-0.7179-0.35220.4938-0.33050.07540.31180.5101-1.09820.3707-0.2873-0.14121.62240.31430.493418.043638.6214219.6194
91.7804-0.13010.02910.8546-0.51361.56990.4988-0.4185-0.2922-0.1889-0.1569-0.15570.21930.42961.18220.2858-0.12470.06621.10650.04220.51636.594646.7675204.1712
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -1 through 100 )
2X-RAY DIFFRACTION2chain 'A' and (resid 101 through 145 )
3X-RAY DIFFRACTION3chain 'A' and (resid 146 through 191 )
4X-RAY DIFFRACTION4chain 'A' and (resid 192 through 264 )
5X-RAY DIFFRACTION5chain 'B' and (resid 2 through 36 )
6X-RAY DIFFRACTION6chain 'B' and (resid 37 through 54 )
7X-RAY DIFFRACTION7chain 'B' and (resid 55 through 145 )
8X-RAY DIFFRACTION8chain 'B' and (resid 146 through 191 )
9X-RAY DIFFRACTION9chain 'B' and (resid 192 through 264 )

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