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- PDB-8rin: Crystal structure of EccC5 DUF domain of Mycobacterium tuberculosis -

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Basic information

Entry
Database: PDB / ID: 8rin
TitleCrystal structure of EccC5 DUF domain of Mycobacterium tuberculosis
ComponentsESX-5 secretion system protein EccC5
KeywordsUNKNOWN FUNCTION / Type VII secretion systems / DUF / ESX5
Function / homology
Function and homology information


peptidoglycan-based cell wall / ATP hydrolysis activity / DNA binding / ATP binding / plasma membrane
Similarity search - Function
EccCa-like, Actinobacteria / EccCb-like, Actinobacteria / : / FtsK domain / FtsK/SpoIIIE family / FtsK domain profile. / 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 EccC5
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsCeballos-Zuniga, F. / Perez-Dorado, I.
Funding support Spain, 1items
OrganizationGrant numberCountry
Comunidad de Madrid2019-T1/BMD-14774 Spain
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2024
Title: New insights into the domain of unknown function (DUF) of EccC 5 , the pivotal ATPase providing the secretion driving force to the ESX-5 secretion system.
Authors: Ceballos-Zuniga, F. / Menendez, M. / Perez-Dorado, I.
History
DepositionDec 19, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 27, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ESX-5 secretion system protein EccC5
B: ESX-5 secretion system protein EccC5


Theoretical massNumber of molelcules
Total (without water)65,3622
Polymers65,3622
Non-polymers00
Water5,170287
1
A: ESX-5 secretion system protein EccC5


Theoretical massNumber of molelcules
Total (without water)32,6811
Polymers32,6811
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ESX-5 secretion system protein EccC5


Theoretical massNumber of molelcules
Total (without water)32,6811
Polymers32,6811
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.301, 52.236, 57.441
Angle α, β, γ (deg.)88.39, 84.6, 80.17
Int Tables number1
Space group name H-MP1

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Components

#1: Protein ESX-5 secretion system protein EccC5 / ESX conserved component C5 / Type VII secretion system protein EccC5 / T7SS protein EccC5


Mass: 32680.775 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: DUF domain (aminoacids 1-417) N-terminal GP- Residues from PreScission protease cleavage site. Aminoacids 17-118 replaced by GSSG Aminoacids 167-198 replaced by GSG (numbered in pdb as 166a- ...Details: DUF domain (aminoacids 1-417) N-terminal GP- Residues from PreScission protease cleavage site. Aminoacids 17-118 replaced by GSSG Aminoacids 167-198 replaced by GSG (numbered in pdb as 166a-166b-166c) Sample sequence scheme: GP-1-16-GSSG-119-166-GSG-199-417 GP+(aminoacids 1-123) - Unobserved region Aminoacids 275-283 - Unobserved region Aminoacids 311-315 - Unobserved region
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Gene: eccC5, Rv1783 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P9WNA5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 287 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.17 Å3/Da / Density % sol: 43.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 25% PEG MME 2000, 0.3 M Trimethylamine N-oxide dihydrate, 0.1 M Tris pH 8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 25, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.05→57.18 Å / Num. obs: 32869 / % possible obs: 95.1 % / Redundancy: 3.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.055 / Rpim(I) all: 0.035 / Rrim(I) all: 0.065 / Net I/σ(I): 9.6
Reflection shellResolution: 2.05→2.11 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.354 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 2122 / CC1/2: 0.869 / Rpim(I) all: 0.242 / Rrim(I) all: 0.432

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Processing

Software
NameVersionClassification
BUSTER2.10.4refinement
PHENIX1.20-4459refinement
Cootmodel building
autoPROCdata processing
Aimless0.7.4data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.05→57.18 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.916 / SU R Cruickshank DPI: 0.199 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.198 / SU Rfree Blow DPI: 0.166 / SU Rfree Cruickshank DPI: 0.168
RfactorNum. reflection% reflectionSelection details
Rfree0.2242 1645 -RANDOM
Rwork0.1846 ---
obs0.1866 32862 95.1 %-
Displacement parametersBiso mean: 34.59 Å2
Baniso -1Baniso -2Baniso -3
1-5.7297 Å2-3.9873 Å25.8561 Å2
2---9.8938 Å2-4.6486 Å2
3---4.1641 Å2
Refine analyzeLuzzati coordinate error obs: 0.23 Å
Refinement stepCycle: LAST / Resolution: 2.05→57.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3932 0 0 287 4219
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0084088HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.885587HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1333SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes701HARMONIC5
X-RAY DIFFRACTIONt_it4088HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion522SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact3536SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.4
X-RAY DIFFRACTIONt_other_torsion15.35
LS refinement shellResolution: 2.05→2.11 Å
RfactorNum. reflection% reflection
Rfree0.2448 36 -
Rwork0.2308 --
obs--69.45 %

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