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- PDB-5xkl: Crystal structure of Rv0289/EspG3 from the ESX-3 type VII secreti... -

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Basic information

Entry
Database: PDB / ID: 5xkl
TitleCrystal structure of Rv0289/EspG3 from the ESX-3 type VII secretion system of M. tuberculosis
ComponentsESX-3 secretion-associated protein EspG3
KeywordsCHAPERONE / new fold
Function / homologyEspG family / EspG family / cytoplasm / ESX-3 secretion-associated protein EspG3
Function and homology information
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.392 Å
AuthorsRaina, R. / Ojha, A. / Arulandu, A.
CitationJournal: To Be Published
Title: To Be Published
Authors: Arulandu, A. / Raina, R.
History
DepositionMay 8, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 16, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ESX-3 secretion-associated protein EspG3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,7712
Polymers31,6751
Non-polymers961
Water27015
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis, Dimer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area170 Å2
ΔGint-12 kcal/mol
Surface area13500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.653, 95.603, 94.989
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein ESX-3 secretion-associated protein EspG3


Mass: 31674.816 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Genomic DNA
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Strain: H37Rv / Gene: espG3, Rv0289 / Plasmid: InfRCo / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2(DE3)pLysS / References: UniProt: P9WJC7
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.71 Å3/Da / Density % sol: 54.63 %
Description: Needle like crystals ranging 0.05 to 0.4 mm in size
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 1M Ammonium Sulphate, 0.5% PEG 3350, 0.1 M Bis-tris pH 5.5, 1mM NAD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.978 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 7, 2014 / Details: bent collimating mirror and toroid
RadiationMonochromator: Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.39→37.83 Å / Num. obs: 13917 / % possible obs: 99.7 % / Redundancy: 7.7 % / Biso Wilson estimate: 53.6 Å2 / CC1/2: 0.798 / Rmerge(I) obs: 0.052 / Rpim(I) all: 0.02 / Χ2: 0.858 / Net I/σ(I): 2.15
Reflection shellResolution: 2.39→2.43 Å / Num. unique obs: 701

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Processing

Software
NameVersionClassification
PHENIX(1.10_2142: ???)refinement
HKL-2000data scaling
HKL-2000data reduction
PHENIXmodel building
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.392→37.826 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 28.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2566 1372 10.01 %
Rwork0.2179 --
obs0.2218 13710 98.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.392→37.826 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1964 0 5 15 1984
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052032
X-RAY DIFFRACTIONf_angle_d0.8342789
X-RAY DIFFRACTIONf_dihedral_angle_d14.6791188
X-RAY DIFFRACTIONf_chiral_restr0.048329
X-RAY DIFFRACTIONf_plane_restr0.008363
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3925-2.4780.35551280.29951155X-RAY DIFFRACTION94
2.478-2.57710.31331350.26811201X-RAY DIFFRACTION97
2.5771-2.69440.32941350.26611198X-RAY DIFFRACTION97
2.6944-2.83640.31091340.24981209X-RAY DIFFRACTION98
2.8364-3.01410.36981380.26291234X-RAY DIFFRACTION99
3.0141-3.24670.2641360.25671239X-RAY DIFFRACTION100
3.2467-3.57320.2611390.23441250X-RAY DIFFRACTION100
3.5732-4.08970.2181400.20061264X-RAY DIFFRACTION100
4.0897-5.15050.20921410.18191271X-RAY DIFFRACTION100
5.1505-37.83120.24931460.20161317X-RAY DIFFRACTION99

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