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- PDB-5xfs: Crystal structure of PE8-PPE15 in complex with EspG5 from M. tube... -

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Basic information

Entry
Database: PDB / ID: 5xfs
TitleCrystal structure of PE8-PPE15 in complex with EspG5 from M. tuberculosis
Components
  • ESX-5 secretion-associated protein EspG5
  • PE family protein PE8
  • PPE family protein PPE15
KeywordsPROTEIN TRANSPORT / Tuberculosis / Bacterial pathogenesis / Protein secretion / Protein complex / Protein structure
Function / homology
Function and homology information


peptidoglycan-based cell wall / plasma membrane / cytoplasm
Similarity search - Function
PPE family, C-terminal / PPE-SVP subfamily C-terminal region / PPE family / PPE family / PE-PGRS family, N-terminal / PE family / PPE superfamily / EspG family / EspG family
Similarity search - Domain/homology
PE family protein PE8 / ESX-5 secretion-associated protein EspG5 / PPE family protein PPE15
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsChen, X. / Au, S.W.N.
Funding support Hong Kong, 1items
OrganizationGrant numberCountry
Health and Medical Research Fund12110602 Hong Kong
CitationJournal: J. Biol. Chem. / Year: 2017
Title: Structural basis of the PE-PPE protein interaction in Mycobacterium tuberculosis.
Authors: Chen, X. / Cheng, H.F. / Zhou, J. / Chan, C.Y. / Lau, K.F. / Tsui, S.K. / Au, S.W.
History
DepositionApr 11, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 30, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Nov 22, 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

Downloads & links

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Assembly

Deposited unit
A: PE family protein PE8
B: PPE family protein PPE15
C: ESX-5 secretion-associated protein EspG5


Theoretical massNumber of molelcules
Total (without water)64,1143
Polymers64,1143
Non-polymers00
Water48627
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6680 Å2
ΔGint-62 kcal/mol
Surface area23340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.740, 69.960, 203.549
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein PE family protein PE8


Mass: 10271.424 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 1-99
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: PE8, Rv1040c / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: L7N667
#2: Protein PPE family protein PPE15 / Mycobacterial perilipin-1 / MPER1


Mass: 20312.930 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 1-194
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: PPE15, mper1, Rv1039c / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P9WI31
#3: Protein ESX-5 secretion-associated protein EspG5


Mass: 33529.695 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: espG5, Rv1794, LH57_09810 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O53943
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 27 / 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: 3.04 Å3/Da / Density % sol: 59.53 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 200 mM Sodium Chloride, 100 mM Tris pH 8.5, 25% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.69 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 26, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.69 Å / Relative weight: 1
ReflectionResolution: 2.9→29.6 Å / Num. obs: 17933 / % possible obs: 99.5 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.133 / Net I/σ(I): 6.7

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575)refinement
iMOSFLMdata processing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4W4L

4w4l


Resolution: 2.9→29.599 Å / SU ML: 0.42 / Cross valid method: NONE / σ(F): 1.36 / Phase error: 28 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2624 875 4.89 %
Rwork0.2133 --
obs0.2157 17900 99.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.9→29.599 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3853 0 0 27 3880
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093925
X-RAY DIFFRACTIONf_angle_d1.1065361
X-RAY DIFFRACTIONf_dihedral_angle_d25.6411373
X-RAY DIFFRACTIONf_chiral_restr0.218627
X-RAY DIFFRACTIONf_plane_restr0.006702
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9001-3.08160.35021630.29672786X-RAY DIFFRACTION100
3.0816-3.31930.37231160.26752817X-RAY DIFFRACTION100
3.3193-3.65270.30861510.2472826X-RAY DIFFRACTION100
3.6527-4.180.24811340.21222828X-RAY DIFFRACTION100
4.18-5.26160.27961450.17482853X-RAY DIFFRACTION99
5.2616-29.60030.18761660.18432915X-RAY DIFFRACTION97
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)
18.96316.1366-7.24587.4519-5.3953.03830.4235-0.34330.9670.54280.56781.481-0.0697-0.2878-0.93160.6290.06030.24650.67070.12430.9064-52.0612-9.14210.0704
25.7976.3166-5.35285.3813-5.54895.75610.0760.6670.13210.13910.51780.4056-0.0928-0.8489-0.46430.3880.02130.03850.6420.32690.6261-43.5981-9.2974-4.0037
36.8077-1.1014-2.37295.9448-1.86877.85350.08810.21370.43060.31760.4385-0.01320.4537-0.0757-0.44980.409-0.16580.22350.49680.27070.701-19.97187.765-24.8219
42.77612.2317-1.66013.9317-2.08963.38860.5347-0.74450.47910.8565-0.19470.3263-0.18590.383-0.41350.56760.02370.14290.52980.21930.6876-40.8723-6.85517.0766
58.15779.3066-8.44939.9097-8.30488.09650.382-0.12760.21350.4707-0.06870.3189-0.28960.0333-0.24770.33820.02260.00340.50120.27610.6251-29.9537-0.2004-5.2736
65.97694.8003-3.42915.8696-2.7642.81460.554-0.4385-0.09490.6708-0.4162-0.2043-0.92150.2522-0.21180.5329-0.05530.05970.37390.16090.5055-11.173114.5629-23.4333
72.2956-1.5674-0.07071.37261.24536.01670.0009-0.4504-1.42350.7493-0.7578-0.81150.81190.0430.78220.62850.006900.46380.26740.7193-37.2308-17.5206-1.9124
83.3522-0.71721.86067.52570.18059.68080.1873-0.3191-1.3014-0.33110.15750.1931.6388-0.1476-0.16140.62460.05530.12080.38920.17071.0935-1.2299-0.6039-33.1882
94.15920.2025-0.02677.6732-1.16273.1234-0.1004-0.0957-1.9814-0.05850.20480.24140.9807-0.345-0.05070.6654-0.07210.06950.49370.23241.027-0.3621-0.2939-28.3851
103.3391-0.03270.10116.9622-2.92585.9213-0.1049-0.1442-0.45570.13330.07110.02660.0211-0.27990.11190.3321-0.00310.14880.26930.02030.4383-1.446414.6193-36.4479
112.29510.0888-0.12046.7139-2.67373.73540.01990.1013-0.28-0.7163-0.6978-1.05260.38310.89820.59030.45650.01650.23890.53950.10140.803610.615617.3049-43.6429
123.3251-0.29622.045.4586-2.796.7306-0.2177-0.43291.37480.5578-0.11970.4669-1.0341-0.0720.04520.8276-0.07070.16440.36770.04220.8435-0.638943.0218-42.1985
132.3271-0.4291.10616.2273-2.06355.79870.1373-0.14570.20140.01430.0286-0.4838-0.48570.2720.03310.4266-0.11020.13540.37460.07730.59886.506629.9925-38.0939
143.814-1.39932.25885.35050.5521.67060.4352-0.54250.25360.3139-1.1296-1.36620.38032.17640.09420.378-0.1764-0.10870.70350.26750.98415.378222.6835-29.2781
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 7 through 37 )
2X-RAY DIFFRACTION2chain 'A' and (resid 38 through 84 )
3X-RAY DIFFRACTION3chain 'B' and (resid 1 through 13 )
4X-RAY DIFFRACTION4chain 'B' and (resid 14 through 58 )
5X-RAY DIFFRACTION5chain 'B' and (resid 59 through 122 )
6X-RAY DIFFRACTION6chain 'B' and (resid 123 through 161 )
7X-RAY DIFFRACTION7chain 'B' and (resid 162 through 173 )
8X-RAY DIFFRACTION8chain 'C' and (resid 7 through 24 )
9X-RAY DIFFRACTION9chain 'C' and (resid 25 through 79 )
10X-RAY DIFFRACTION10chain 'C' and (resid 80 through 133 )
11X-RAY DIFFRACTION11chain 'C' and (resid 134 through 171 )
12X-RAY DIFFRACTION12chain 'C' and (resid 172 through 202 )
13X-RAY DIFFRACTION13chain 'C' and (resid 203 through 274 )
14X-RAY DIFFRACTION14chain 'C' and (resid 275 through 299 )

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