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- PDB-4w4k: Crystal structure of a PE25-PPE41 heterodimer from a type VII sec... -

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Basic information

Entry
Database: PDB / ID: 4w4k
TitleCrystal structure of a PE25-PPE41 heterodimer from a type VII secretion system of M. tuberculosis
Components
  • PE family protein PE25
  • PPE family protein PPE41
KeywordsPROTEIN TRANSPORT / antigen / virulence factor / protein secretion / adaptor
Function / homology
Function and homology information


PPE superfamily / PPE family / PPE family / PE-PGRS family, N-terminal / PE family / HP0062-like domain / PPE superfamily / Ferritin / Helix Hairpins / Up-down Bundle ...PPE superfamily / PPE family / PPE family / PE-PGRS family, N-terminal / PE family / HP0062-like domain / PPE superfamily / Ferritin / Helix Hairpins / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PPE family protein / PE family protein / PPE family protein / PE family protein
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 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_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: PE family protein PE25
D: PPE family protein PPE41


Theoretical massNumber of molelcules
Total (without water)63,6864
Polymers63,6864
Non-polymers00
Water1,65792
1
A: PE family protein PE25
B: PPE family protein PPE41


Theoretical massNumber of molelcules
Total (without water)31,8432
Polymers31,8432
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4180 Å2
ΔGint-49 kcal/mol
Surface area13720 Å2
MethodPISA
2
C: PE family protein PE25
D: PPE family protein PPE41


Theoretical massNumber of molelcules
Total (without water)31,8432
Polymers31,8432
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4020 Å2
ΔGint-46 kcal/mol
Surface area13480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.980, 49.480, 284.350
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number17
Space group name H-MP2221

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Components

#1: Protein PE family protein PE25


Mass: 11876.294 Da / Num. of mol.: 2
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.: 2 / 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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 92 / 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: 2.26 Å3/Da / Density % sol: 45.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 0.1 M sodium acetate pH 4.5, 5% (w/v) PEG 1000, 50% (v/v) ethylene glycol

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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: Sep 19, 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: 1.95→50 Å / Num. obs: 43451 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 6.9 % / Biso Wilson estimate: 35.8 Å2 / Rsym value: 0.09 / Net I/σ(I): 12.1
Reflection shellResolution: 1.95→2 Å / Redundancy: 7.1 % / Rmerge(I) obs: 1.94 / Mean I/σ(I) obs: 1.1 / % possible all: 99.9

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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: 2G38

2g38


Resolution: 1.95→47.392 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.263 1714 3.96 %RANDOM
Rwork0.2223 ---
obs0.2239 43322 99.59 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 63.2 Å2
Refinement stepCycle: LAST / Resolution: 1.95→47.392 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3994 0 0 92 4086
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034169
X-RAY DIFFRACTIONf_angle_d0.6765699
X-RAY DIFFRACTIONf_dihedral_angle_d12.2241530
X-RAY DIFFRACTIONf_chiral_restr0.025634
X-RAY DIFFRACTIONf_plane_restr0.004753
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-2.00740.48331390.39253350X-RAY DIFFRACTION100
2.0074-2.07220.40811410.35413444X-RAY DIFFRACTION100
2.0722-2.14630.31441390.313398X-RAY DIFFRACTION100
2.1463-2.23220.3261410.27383394X-RAY DIFFRACTION100
2.2322-2.33380.32841400.25683428X-RAY DIFFRACTION100
2.3338-2.45690.28781430.24813467X-RAY DIFFRACTION100
2.4569-2.61080.27141410.23673430X-RAY DIFFRACTION100
2.6108-2.81230.33111430.23533476X-RAY DIFFRACTION100
2.8123-3.09530.23451430.22043485X-RAY DIFFRACTION100
3.0953-3.54310.30661440.23033506X-RAY DIFFRACTION100
3.5431-4.46340.2131470.18313550X-RAY DIFFRACTION100
4.4634-47.40560.22191530.19793680X-RAY DIFFRACTION98
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)
12.72230.0161-2.35860.38750.94624.5157-0.0168-0.3512-0.2450.73960.01550.40640.6683-0.4094-1.67951.00070.19490.1930.89630.06180.3692-23.8042-6.4869-24.64
20.2730.15070.49120.90830.76761.17140.1398-0.49960.28320.38950.1286-0.1545-0.45930.39490.17360.69630.06840.07210.7396-0.07130.2742-17.61550.681-32.9018
32.6173-0.10590.44011.62091.06070.79720.23230.0166-0.26260.4203-0.2198-0.0899-0.53880.47420.05110.4963-0.01080.10450.6710.01810.2398-7.3643-5.5384-66.0993
42.9178-0.9102-3.22781.12311.41045.0581-0.11070.0132-0.23330.5032-0.30260.53970.2171-0.8731-0.37810.79560.05230.17490.9667-0.08110.4123-31.8609-3.931-29.1088
51.4005-0.1375-1.57070.61530.4891.98920.04510.2350.0080.1502-0.26880.2878-0.6064-1.19610.25080.6330.1960.05660.8020.00260.3149-27.64450.9905-40.5022
60.7579-0.39-1.54091.13071.51457.76140.15670.30590.014-0.1149-0.05680.0466-0.63-0.45090.02840.43960.01960.07930.66180.03220.3073-8.5852-5.6236-78.2938
71.68020.69680.53020.3183-0.0883.4720.5574-0.10040.4339-0.3384-0.30740.0321-1.6876-0.40620.53160.87190.1730.13950.5882-0.01730.3154-22.90427.8632-33.8971
82.9741-1.5398-1.12451.82443.10526.6693-0.27860.6665-0.7561-0.3431-0.24010.39610.6434-1.4805-1.71491.1718-0.08640.13990.7339-0.06480.4246-9.1306-23.8942-46.6597
90.41560.0698-0.14540.3541-0.09680.3705-0.13340.2906-0.0257-0.5515-0.1131-0.2270.14820.0772-7.65480.84770.09770.20840.4250.0754-0.0862-2.3439-17.3308-34.0964
101.70540.2302-0.34472.52612.05342.5805-0.04680.0131-0.1649-0.1655-0.1072-0.21750.1096-0.1002-1.12410.97110.06050.08130.46140.0610.321-7.4802-23.0562-25.3837
114.6466-0.34965.5993.45510.68397.13820.9204-0.6298-0.25951.2147-0.3213-0.43930.3416-0.7471-0.12021.4891-1.0772-0.07812.4408-0.09922.07251.8984-42.1974-61.0499
122.13680.4757-0.21950.1227-0.05240.0264-0.20630.1462-0.3568-0.2631-0.3132-0.34740.18240.1763-8.72980.91970.27150.16180.40940.1170.3646-1.2279-28.8823-30.3964
130.67150.41080.67190.583-0.10761.69020.0061-0.44890.1480.23120.0423-0.24650.10560.7721-0.28250.68830.0366-0.03510.7618-0.04920.3382-4.9096-14.36881.236
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 8 through 38 )
2X-RAY DIFFRACTION2chain 'A' and (resid 39 through 89 )
3X-RAY DIFFRACTION3chain 'B' and (resid 2 through 21 )
4X-RAY DIFFRACTION4chain 'B' and (resid 22 through 58 )
5X-RAY DIFFRACTION5chain 'B' and (resid 59 through 102 )
6X-RAY DIFFRACTION6chain 'B' and (resid 103 through 163 )
7X-RAY DIFFRACTION7chain 'B' and (resid 164 through 174 )
8X-RAY DIFFRACTION8chain 'C' and (resid 7 through 38 )
9X-RAY DIFFRACTION9chain 'C' and (resid 39 through 83 )
10X-RAY DIFFRACTION10chain 'D' and (resid 2 through 53 )
11X-RAY DIFFRACTION11chain 'D' and (resid 54 through 58 )
12X-RAY DIFFRACTION12chain 'D' and (resid 59 through 102 )
13X-RAY DIFFRACTION13chain 'D' and (resid 103 through 174 )

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