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- PDB-6vj5: Structure of PE25-PPE41(A124L) in complex with EspG5 chaperone fr... -

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Basic information

Entry
Database: PDB / ID: 6vj5
TitleStructure of PE25-PPE41(A124L) in complex with EspG5 chaperone from the type VII (ESX-5) secretion system
Components
  • ESX-5 secretion-associated protein EspG5
  • PE-PGRS family protein PE25
  • PPE family protein PPE41
KeywordsPROTEIN TRANSPORT / chaperone / protein secretion / mycobacteria
Function / homology
Function and homology information


protein heterotrimerization / response to host immune response / protein heterodimerization activity / cell surface / extracellular region / cytoplasm
Similarity search - Function
PPE family / PPE family / PE-PGRS family, N-terminal / PE family / EspG family / EspG family / PPE superfamily
Similarity search - Domain/homology
ESX-5 secretion-associated protein EspG5 / PE-PGRS family protein PE25 / PPE family protein PPE41
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
Mycobacterium marinum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.4 Å
AuthorsWilliamson, Z.A. / Korotkov, 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: To Be Published
Title: Molecular basis of diverse substrate recognition by EspG5 chaperone from mycobacterial ESX-5 Type VII Secretion System.
Authors: Williamson, Z.A. / Korotkova, N. / Korotkov, K.V.
History
DepositionJan 14, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 27, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 11, 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: PE-PGRS family protein PE25
B: PPE family protein PPE41
C: ESX-5 secretion-associated protein EspG5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,3555
Polymers65,2843
Non-polymers712
Water3,315184
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7800 Å2
ΔGint-88 kcal/mol
Surface area24610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)139.020, 139.020, 170.570
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-123-

HOH

21B-307-

HOH

31B-378-

HOH

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Components

#1: Protein PE-PGRS family protein PE25


Mass: 10894.301 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: PE25, Rv2431c, LH57_13295 / Plasmid: pET-28b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): Rosetta(DE3) / References: UniProt: I6X486
#2: Protein PPE family protein PPE41


Mass: 22005.828 Da / Num. of mol.: 1 / Mutation: A124L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: PPE41, Rv2430c, LH57_13290 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): Rosetta(DE3) / References: UniProt: Q79FE1
#3: Protein ESX-5 secretion-associated protein EspG5


Mass: 32384.338 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium marinum (strain ATCC BAA-535 / M) (bacteria)
Strain: ATCC BAA-535 / M / Gene: espG5, MMAR_2676 / Plasmid: pCDF-Duet1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): Rosetta(DE3) / References: UniProt: B2HSU5
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 184 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.64 Å3/Da / Density % sol: 66.25 % / Description: hexagonal prism
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop
Details: JCSG Core I Suite condition C9: 0.2M potassium thiocyanate, 20% (w/v) PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.9791 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 12, 2014
Details: Rosenbaum-Rock double-crystal monochromator: liquid nitrogen cooled; sagitally focusing 2nd crystal, Rosenbaum-Rock vertical focusing mirror
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.4→45.505 Å / Num. obs: 38512 / % possible obs: 99.7 % / Redundancy: 4.844 % / Biso Wilson estimate: 57.329 Å2 / CC1/2: 0.975 / Rmerge(I) obs: 0.154 / Rrim(I) all: 0.174 / Χ2: 0.927 / Net I/σ(I): 6.73
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.4-2.464.8980.9642.0113494277127550.7331.0899.4
2.46-2.534.9530.7982.3913602275327460.7770.89399.7
2.53-2.64.9580.6742.6813010263026240.8140.75399.8
2.6-2.684.9330.5523.1512874261326100.8430.61899.9
2.68-2.774.9630.423.7812373249624930.9030.4799.9
2.77-2.874.9240.3174.7611946242824260.940.35599.9
2.87-2.984.9280.2435.811601235523540.9540.271100
2.98-3.14.910.2016.6311180227822770.970.225100
3.1-3.244.910.1747.4110688217921770.9710.19599.9
3.24-3.394.8840.1498.3510183208620850.9760.167100
3.39-3.584.8450.1339.579573197819760.9750.14999.9
3.58-3.794.8310.12710.099208190619060.9760.142100
3.79-4.064.8090.12110.698521177217720.9730.137100
4.06-4.384.7850.12811.098010167616740.9690.14499.9
4.38-4.84.7330.12511.317293154415410.9610.14199.8
4.8-5.374.7140.12611.166651141714110.9650.14299.6
5.37-6.24.6090.12610.915715124412400.9620.14399.7
6.2-7.594.5730.12311.184962109110850.9690.1499.5
7.59-10.734.3020.13310.7236958628590.9490.15399.7
10.73-45.5053.940.13610.0319745325010.9730.15794.2

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Processing

Software
NameVersionClassification
XSCALEVERSION January 10, 2014 BUILT=20140307data scaling
PHENIX1.16_3549refinement
PDB_EXTRACT3.25data extraction
XDSVERSION January 10, 2014 BUILT=20140307data reduction
PHENIX1.8.4_1496phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 4KXR

4kxr


Resolution: 2.4→45.505 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.15 / Phase error: 24.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2538 3696 5.17 %
Rwork0.21 --
obs0.2121 38507 99.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 165.84 Å2 / Biso mean: 64.3017 Å2 / Biso min: 12.72 Å2
Refinement stepCycle: final / Resolution: 2.4→45.505 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4219 0 2 184 4405
Biso mean--79.54 51.78 -
Num. residues----545
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044317
X-RAY DIFFRACTIONf_angle_d0.595888
X-RAY DIFFRACTIONf_dihedral_angle_d14.4942611
X-RAY DIFFRACTIONf_chiral_restr0.041669
X-RAY DIFFRACTIONf_plane_restr0.003776
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.4-2.43150.35381440.2981255998
2.4315-2.46480.32491670.29562581100
2.4648-2.50010.2571570.2762627100
2.5001-2.53740.30921250.26932633100
2.5374-2.5770.27271500.27042643100
2.577-2.61930.30651350.25962629100
2.6193-2.66440.32231730.24982563100
2.6644-2.71290.27891590.25442640100
2.7129-2.7650.27041400.24492633100
2.765-2.82150.28211900.24522570100
2.8215-2.88280.32451410.23242625100
2.8828-2.94990.28541020.22752668100
2.9499-3.02360.23671320.22612647100
3.0236-3.10540.27831420.2246259399
3.1054-3.19670.30891390.2305263499
3.1967-3.29990.281280.2302262499
3.2999-3.41780.23761350.2225258699
3.4178-3.55460.24451490.208263199
3.5546-3.71630.24631540.1887257599
3.7163-3.91210.2371390.1894260799
3.9121-4.1570.24091210.1872260799
4.157-4.47770.25431380.172263499
4.4777-4.92790.24161360.1712258098
4.9279-5.63980.26581350.1997261699
5.6398-7.10120.20751450.2178258498
7.1012-45.5050.1941200.1928257197

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