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- PDB-4kxr: Structure of the Mycobacterium tuberculosis type VII secretion sy... -

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Basic information

Entry
Database: PDB / ID: 4kxr
TitleStructure of the Mycobacterium tuberculosis type VII secretion system chaperone EspG5 in complex with PE25-PPE41 dimer
Components
  • EspG5
  • PE25
  • PPE41
KeywordsPROTEIN TRANSPORT / ESX-5 / type VII secretion system / protein secretion / chaperone
Function / homology
Function and homology information


protein heterotrimerization / response to host immune response / peptidoglycan-based cell wall / protein heterodimerization activity / cell surface / extracellular region / plasma membrane / cytoplasm
Similarity search - Function
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
PE-PGRS family protein PE25 / PPE family protein PPE41 / ESX-5 secretion-associated protein EspG5 / PPE family protein PPE41
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsKorotkova, N. / Creekmore, C.C. / Korotkov, K.V.
CitationJournal: Mol.Microbiol. / Year: 2014
Title: Structure of the Mycobacterium tuberculosis type VII secretion system chaperone EspG5 in complex with PE25-PPE41 dimer.
Authors: Korotkova, N. / Freire, D. / Phan, T.H. / Ummels, R. / Creekmore, C.C. / Evans, T.J. / Wilmanns, M. / Bitter, W. / Parret, A.H. / Houben, E.N. / Korotkov, K.V.
History
DepositionMay 27, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 28, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 27, 2014Group: Database references
Revision 1.2Sep 3, 2014Group: Database references
Revision 1.3Oct 22, 2014Group: Database references
Revision 1.4Sep 20, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PE25
B: PPE41
C: EspG5


Theoretical massNumber of molelcules
Total (without water)65,2903
Polymers65,2903
Non-polymers00
Water1,964109
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7250 Å2
ΔGint-62 kcal/mol
Surface area24770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)139.100, 139.100, 171.010
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
11B-210-

HOH

21B-239-

HOH

31B-251-

HOH

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Components

#1: Protein PE25 / PE family protein


Mass: 10894.301 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: Rv2431c, RVBD_2431c / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) / References: UniProt: I6X486
#2: Protein PPE41 / PPE family protein


Mass: 21963.748 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: RV2430c, RVBD_2430c / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) / References: UniProt: I6YDD9, UniProt: Q79FE1*PLUS
#3: Protein EspG5


Mass: 32431.475 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: Rv1794, RVBD_1794 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) / References: UniProt: O53943
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 109 / 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: 3.66 Å3/Da / Density % sol: 66.37 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.6
Details: 0.1 M Tris-HCl, pH 8.6, 8% PEG8000, 0.2 M sodium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 22, 2013
RadiationMonochromator: Rosenbaum-Rock double-crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.6→49.241 Å / Num. obs: 30602 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 60.248 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 15.81
Reflection shell

Rmerge(I) obs: 0.015 / Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Mean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.6-2.671.824027220899.2
2.67-2.742.5240742162100
2.74-2.823.19235242107100
2.82-2.914.36227622046100
2.91-35.57221061983100
3-3.117.08213571921100
3.11-3.238.37206191860100
3.23-3.3611.219883179899.9
3.36-3.5114.48191031729100
3.51-3.6818.47181921655100
3.68-3.8822.16174441586100
3.88-4.1125.4916266149399.9
4.11-4.428.38154291417100
4.4-4.7532.86141781315100
4.75-5.232.04131211232100
5.2-5.8230.65118501123100
5.82-6.7232.36105091004100
6.72-8.2338.658736862100
8.23-11.63436700692100
11.6341.16342740997.1

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACT3.11data extraction
SERGUIdata collection
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2G38

2g38


Resolution: 2.6→49.241 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.908 / WRfactor Rfree: 0.2282 / WRfactor Rwork: 0.1815 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8534 / SU B: 16.601 / SU ML: 0.178 / SU R Cruickshank DPI: 0.3051 / SU Rfree: 0.247 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.305 / ESU R Free: 0.247 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2438 1553 5.1 %RANDOM
Rwork0.1939 ---
obs0.1963 30602 99.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 156.72 Å2 / Biso mean: 64.599 Å2 / Biso min: 30.78 Å2
Baniso -1Baniso -2Baniso -3
1-0.7 Å20.7 Å20 Å2
2--0.7 Å20 Å2
3----2.27 Å2
Refinement stepCycle: LAST / Resolution: 2.6→49.241 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4135 0 0 109 4244
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0194227
X-RAY DIFFRACTIONr_bond_other_d0.0010.024033
X-RAY DIFFRACTIONr_angle_refined_deg1.2661.955761
X-RAY DIFFRACTIONr_angle_other_deg0.76139231
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5285532
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.81423.838198
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.88215675
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.6181537
X-RAY DIFFRACTIONr_chiral_restr0.0680.2655
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0214838
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02957
X-RAY DIFFRACTIONr_mcbond_it1.7453.6192137
X-RAY DIFFRACTIONr_mcbond_other1.7453.6192136
X-RAY DIFFRACTIONr_mcangle_it2.8645.422663
LS refinement shellResolution: 2.6→2.668 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.324 127 -
Rwork0.281 2073 -
all-2200 -
obs--99.05 %
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)
121.1354-1.624-5.11612.10083.78377.11111.09010.9461.5731-0.26030.1309-0.6542-0.73480.2677-1.22110.5965-0.3161-0.08640.3480.25470.664386.341-9.541-16.588
218.26876.6366-7.65135.2236-3.8315.53830.25120.54830.93970.25140.06420.4138-0.3297-0.3577-0.31540.3225-0.03880.0020.0569-0.01380.18570.745-20.323-8.411
34.15382.7213-2.81084.2824-1.39044.63340.279-0.17780.03680.3168-0.20280.0914-0.4151-0.0441-0.07620.275-0.012-0.00570.1691-0.02350.149461.193-40.2655.427
46.4394.44352.876310.36645.82563.3283-0.1046-0.10080.22380.1501-0.01680.2203-0.0367-0.02950.12140.5605-0.0014-0.00010.17440.02250.070873.43-26.1671.338
54.90152.29714.65196.30461.46364.56030.39550.10380.75781.0711-0.9971-0.12790.16590.34950.60161.0091-0.60480.16830.5442-0.0920.700588.69-8.333-8.634
61.22090.8385-1.0195.4845-4.69785.2931-0.0485-0.0402-0.16070.0523-0.0464-0.08890.04930.09510.0950.20580.0083-0.010.1885-0.02820.165254.492-51.0817.777
77.36835.1665-4.33946.9297-3.79674.1672-0.25920.4826-0.07690.02040.1484-0.3885-0.0176-0.14440.11080.2449-0.0633-0.07430.19970.00140.186776.21-27.305-14.348
814.40138.953-3.36349.4702-2.25262.4501-0.30930.53060.1254-0.050.3141-0.6352-0.09850.336-0.00490.207-0.1005-0.07670.26240.02110.249885.158-28.348-9.594
92.69212.6134-1.68843.1608-1.85221.5334-0.17880.0107-0.1725-0.0950.0908-0.07050.1756-0.12160.0880.1831-0.03540.04760.1695-0.00260.151651.973-61.4937.872
1021.057512.398-6.063427.4126-5.18171.9553-0.03550.0669-0.02960.0949-0.1144-1.2663-0.21040.03680.14980.5571-0.1089-0.1090.1943-0.0140.212782.864-27.591-0.589
113.29361.66420.75012.2448-0.86891.4152-0.4636-0.23110.3316-0.09810.1565-0.1667-0.1325-0.08190.30710.23620.23890.04630.4454-0.12860.392262.263-70.41721.903
123.18630.08610.10622.89840.96051.550.111-0.3603-0.3070.1434-0.0178-0.8764-0.12660.0705-0.09320.21190.12990.01750.2690.13860.377762.078-76.82225.842
133.2890.4679-0.10774.24470.30871.40290.1298-0.5639-0.36030.238-0.131-0.15460.0870.13490.00120.18410.05020.09130.3130.12310.186552.493-78.44127.283
145.1690.98070.34973.02470.19571.8123-0.1557-0.4174-0.12150.1426-0.09090.352-0.05540.00490.24660.192-0.04280.10850.22850.11530.224427.983-84.70628.569
155.20750.43110.40672.7036-0.71511.3555-0.040.0263-0.6432-0.2489-0.0178-0.29150.16120.15860.05780.2212-0.06580.09580.16050.10610.283738.392-89.11822.816
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 16
2X-RAY DIFFRACTION2A17 - 34
3X-RAY DIFFRACTION3A35 - 58
4X-RAY DIFFRACTION4A59 - 72
5X-RAY DIFFRACTION5A73 - 91
6X-RAY DIFFRACTION6B1 - 27
7X-RAY DIFFRACTION7B28 - 55
8X-RAY DIFFRACTION8B56 - 87
9X-RAY DIFFRACTION9B88 - 166
10X-RAY DIFFRACTION10B167 - 174
11X-RAY DIFFRACTION11C8 - 51
12X-RAY DIFFRACTION12C52 - 96
13X-RAY DIFFRACTION13C97 - 156
14X-RAY DIFFRACTION14C157 - 198
15X-RAY DIFFRACTION15C199 - 298

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