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- PDB-7vep: Crystal structure and biophysical characterization of TPR domain ... -

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Basic information

Entry
Database: PDB / ID: 7vep
TitleCrystal structure and biophysical characterization of TPR domain of EccA5 from ESX-5 pathway of Mycobacterium tuberculosis H37RVR
ComponentsESX-5 secretion system protein EccA5
KeywordsHYDROLASE / EccA5 / AAA+ATPase / TPR domain
Function / homology
Function and homology information


ATP hydrolysis activity / ATP binding / plasma membrane / cytoplasm
Similarity search - Function
Type VII secretion system AAA-ATPase, EccA / CbxX/CfxQ / CbbX, AAA lid domain / AAA lid domain / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / Tetratricopeptide-like helical domain superfamily / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ESX-5 secretion system protein EccA5
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.15 Å
AuthorsRamachandran, R. / Sharma, V.K. / Vishwakarma, J.
Funding support India, 1items
OrganizationGrant numberCountry
Council of Scientific & Industrial Research (CSIR) India
CitationJournal: To Be Published
Title: Crystal structure and biophysical characterization of TPR domain of EccA5 from ESX-5 pathway of Mycobacterium tuberculosis H37RVR
Authors: Ramachandran, R. / Sharma, V.K. / Vishwakarma, J.
History
DepositionSep 9, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 14, 2022Provider: repository / Type: Initial release
Revision 1.1May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ESX-5 secretion system protein EccA5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,4036
Polymers30,9311
Non-polymers4725
Water2,702150
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, Small Angle X-ray Scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area640 Å2
ΔGint-30 kcal/mol
Surface area13900 Å2
Unit cell
Length a, b, c (Å)57.236, 65.645, 98.204
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein ESX-5 secretion system protein EccA5 / ESX conserved component A5 / Type VII secretion system protein EccA5 / T7SS protein EccA5


Mass: 30931.049 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: eccA5, Rv1798, MTV049.20 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: P9WPI1
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 150 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.8 Å3/Da / Density % sol: 56.02 % / Description: 3D rod shaped crystals
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: Lithium sulfate, sodium citrate 5.6, Ammonium sulfate, glycerol as additive

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: RRCAT INDUS-2 / Beamline: PX-BL21 / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 17, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.15→43.14 Å / Num. obs: 20585 / % possible obs: 99.2 % / Redundancy: 5.3 % / CC1/2: 0.997 / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.067 / Rrim(I) all: 0.116 / Χ2: 1.03 / Net I/av σ(I): 13.4 / Net I/σ(I): 2.3
Reflection shellResolution: 2.15→2.2 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.631 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 1717 / CC1/2: 0.715 / Rpim(I) all: 0.474 / Rrim(I) all: 0.793 / Χ2: 1.02 / % possible all: 98.3

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
Aimless7.0.072data scaling
PDB_EXTRACT3.27data extraction
XDS0.7data reduction
PHENIX2.8.2phasing
RefinementMethod to determine structure: SAD / Resolution: 2.15→39.319 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2164 993 4.84 %
Rwork0.1861 19543 -
obs0.1877 20536 98.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 85.35 Å2 / Biso mean: 34.0412 Å2 / Biso min: 15.81 Å2
Refinement stepCycle: final / Resolution: 2.15→39.319 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2106 0 43 150 2299
Biso mean--52.69 40.9 -
Num. residues----274
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.15-2.26330.27291260.2332270298
2.2633-2.40510.28791400.2195274899
2.4051-2.59080.23621280.2276499
2.5908-2.85150.24361330.1986277699
2.8515-3.26390.25111470.1935279099
3.2639-4.11150.18951550.1587282299
4.1115-39.30.18181640.17672941100

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