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- PDB-4w4l: Crystal structure of EspG5 in complex with PE25 and PPE41 from th... -

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Basic information

Entry
Database: PDB / ID: 4w4l
TitleCrystal structure of EspG5 in complex with PE25 and PPE41 from the ESX-5 type VII secretion system of M. tuberculosis
Components
  • EspG5
  • PE family protein PE25
  • PPE family protein PPE41
KeywordsPROTEIN TRANSPORT / ternary complex / signal recognition / virulence factor / protein secretion
Function / homology
Function and homology information


PPE superfamily / PPE family / PPE family / PE-PGRS family, N-terminal / PE family / HP0062-like domain / EspG family / EspG family / PPE superfamily / Ferritin ...PPE superfamily / PPE family / PPE family / PE-PGRS family, N-terminal / PE family / HP0062-like domain / EspG family / EspG family / PPE superfamily / Ferritin / Helix Hairpins / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Uncharacterized protein / PPE family protein / PE family protein / PPE family protein / PE family protein / Uncharacterized protein
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsEkiert, D.C. / Cox, J.S.
Funding support United States, United Kingdom, 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 Kingdom
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_assembly_gen / pdbx_struct_assembly_prop / 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_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _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 1.5Sep 27, 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 / 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: PE family protein PE25
B: PPE family protein PPE41
C: EspG5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,3114
Polymers65,2493
Non-polymers621
Water1,36976
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7680 Å2
ΔGint-60 kcal/mol
Surface area25350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.640, 138.640, 169.680
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-204-

HOH

21B-311-

HOH

31B-319-

HOH

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Components

#1: Protein PE family protein PE25


Mass: 11902.331 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: Erdman / Gene: PE25, ERDMAN_2675, Q643_02517 / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 (BL21) / References: UniProt: H8ETC7, UniProt: A0A0H3LBR3*PLUS
#2: Protein PPE family protein PPE41


Mass: 19966.570 Da / Num. of mol.: 1 / Fragment: UNP residues 1-174
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: Erdman / Gene: PPE41, ERDMAN_2674, Q643_02516 / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 (BL21) / References: UniProt: H8ETC6, UniProt: A0A0H3LBN6*PLUS
#3: Protein EspG5


Mass: 33380.328 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: Erdman / Gene: ERDMAN_1984, Q643_01851 / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 (BL21) / References: UniProt: H8F3E2, UniProt: A0A0H3LAM1*PLUS
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 76 / 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: 3.61 Å3/Da / Density % sol: 65.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1 M HEPES pH 6.5, 5% (w/v) PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.116 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 26, 2012
RadiationMonochromator: Double flat crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.116 Å / Relative weight: 1
ReflectionResolution: 2.45→50 Å / Num. obs: 35773 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 87.3 % / Biso Wilson estimate: 43.7 Å2 / Rsym value: 0.32 / Net I/σ(I): 26.1
Reflection shellResolution: 2.45→2.51 Å / Redundancy: 89.3 % / Rmerge(I) obs: 8.7 / Mean I/σ(I) obs: 1.2 / % possible all: 98.9

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: dev_1727)refinement
Blu-Icedata collection
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4W4J,4W4K

4w4j

4w4k


Resolution: 2.45→49.005 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2297 1460 4.09 %RANDOM
Rwork0.2018 ---
obs0.203 35727 99.36 %-
Solvent computationShrinkage radii: 1.1 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 82.9 Å2
Refinement stepCycle: LAST / Resolution: 2.45→49.005 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4283 0 4 76 4363
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044478
X-RAY DIFFRACTIONf_angle_d0.7636111
X-RAY DIFFRACTIONf_dihedral_angle_d13.7161648
X-RAY DIFFRACTIONf_chiral_restr0.028688
X-RAY DIFFRACTIONf_plane_restr0.004812
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.45-2.53760.3491400.31993314X-RAY DIFFRACTION98
2.5376-2.63920.3441430.3073344X-RAY DIFFRACTION99
2.6392-2.75930.31391430.28343352X-RAY DIFFRACTION99
2.7593-2.90470.28451440.24743381X-RAY DIFFRACTION99
2.9047-3.08670.25381450.22273392X-RAY DIFFRACTION99
3.0867-3.3250.28511440.23593377X-RAY DIFFRACTION99
3.325-3.65950.26541460.20993432X-RAY DIFFRACTION100
3.6595-4.18870.22881470.18863451X-RAY DIFFRACTION100
4.1887-5.27640.19211490.16853505X-RAY DIFFRACTION100
5.2764-49.0150.18681590.1763719X-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)
10.66640.7532-0.25320.8257-0.31571.21410.09920.72480.55160.19050.27080.3871-0.7699-0.48670.11470.9053-0.11930.01060.41040.00990.73784.6846102.4098-9.7578
21.78890.1810.59121.62880.43780.29770.5041-0.39760.3151.17-0.3620.0079-0.91810.2421-0.04340.7331-0.2599-0.04160.3426-0.1010.39153.251793.41030.7031
30.52530.0949-0.80770.406-0.68831.6884-0.0202-0.04490.0961-0.02660.01540.0406-0.23740.0646-0.00010.5834-0.1411-0.04890.52320.02140.4926-1.542683.6102-5.039
40.54640.2414-0.95011.0224-0.88091.488-0.3459-0.0932-0.5418-0.138-0.0044-0.43640.166-0.06810.00010.4815-0.0886-0.00990.45510.01590.4919-7.813568.85483.066
50.86060.80620.04750.7608-0.14980.5411-0.09990.04-0.23640.03810.1078-0.41530.16290.09450.00030.80180.20110.11091.12470.09140.9551-2.62548.841122.3049
63.15341.2216-0.34771.4424-0.17721.7811-0.2075-0.3913-0.739-0.0009-0.0247-0.20620.46590.0796-0.00030.8753-0.04450.26440.76120.18940.9172-28.25635.22823.8108
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 7 through 36 )
2X-RAY DIFFRACTION2chain 'A' and (resid 37 through 90 )
3X-RAY DIFFRACTION3chain 'B' and (resid 1 through 58 )
4X-RAY DIFFRACTION4chain 'B' and (resid 59 through 174 )
5X-RAY DIFFRACTION5chain 'C' and (resid 6 through 79 )
6X-RAY DIFFRACTION6chain 'C' and (resid 80 through 302 )

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