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- PDB-9jv8: Crystal structure of M. tuberculosis EccCb1-D2 domain -

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Basic information

Entry
Database: PDB / ID: 9jv8
TitleCrystal structure of M. tuberculosis EccCb1-D2 domain
ComponentsESX-1 secretion system protein EccCb1
KeywordsTRANSPORT PROTEIN / M. tuberculosis ESX-1 / EccC1 / EsxAB / Molecular docking / Dynamics simulation
Function / homology
Function and homology information


protein secretion by the type VII secretion system / symbiont-mediated evasion of host immune response / biological process involved in interaction with host / peptidoglycan-based cell wall / ATP hydrolysis activity / DNA binding / ATP binding / plasma membrane / cytoplasm
Similarity search - Function
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
ADENOSINE-5'-TRIPHOSPHATE / ESX-1 secretion system protein EccCb1
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsSaxena, A.K.
Funding support India, 1items
OrganizationGrant numberCountry
Science and Engineering Research Board (SERB)EMR/2016/000867 India
CitationJournal: To Be Published
Title: M. tuberculosis EccCb1-D2 domain
Authors: Saxena, A.K.
History
DepositionOct 8, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 8, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ESX-1 secretion system protein EccCb1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9503
Polymers34,4181
Non-polymers5312
Water2,774154
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area910 Å2
ΔGint-11 kcal/mol
Surface area12540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.389, 75.642, 102.524
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein ESX-1 secretion system protein EccCb1 / ESX conserved component Cb1 / Snm2 secretory protein / Type VII secretion system protein EccCb1 / ...ESX conserved component Cb1 / Snm2 secretory protein / Type VII secretion system protein EccCb1 / T7SS protein EccCb1


Mass: 34418.121 Da / Num. of mol.: 1 / Fragment: D2 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Gene: eccCb1, snm2, Rv3871 / Plasmid: pET23a(+)
Details (production host): vectors carry an N-terminal T7Tag sequence plus an optional C-terminal HisTagsequence.
Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): pLys / References: UniProt: P9WNB1
#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 154 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.21 Å3/Da / Density % sol: 43.86 %
Description: Rectangular shaped crystals dimension 0.3 x 0.2 x 0.1 mm3
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.1M Sodium citrate tribasic dihydrate pH 5.6, 20% (v/v) PEG 4000 and 20% (v/v) 2-Propanol
PH range: 5.6-6.4 / Temp details: Stabe at 4 degree

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Liquid nitrogen temperature / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER TURBO X-RAY SOURCE / Wavelength: 1.5418 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: May 4, 2020
RadiationMonochromator: Ni / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→35 Å / Num. obs: 15346 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.9 % / Biso Wilson estimate: 22 Å2 / CC1/2: 0.99 / CC star: 0.99 / Rmerge(I) obs: 0.089 / Rpim(I) all: 0.025 / Rrim(I) all: 0.092 / Rsym value: 0.02 / Χ2: 0.91 / Net I/av σ(I): 23.7 / Net I/σ(I): 14.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.2-2.2813.20.24514280.9860.9970.070.2551.20695.6
2.28-2.3714.10.21215080.9920.9980.0590.2210.923100
2.37-2.4814.20.17715080.9940.9980.0490.1840.914100
2.48-2.6114.20.15115110.9950.9990.0420.1570.918100
2.61-2.7714.20.13115290.9960.9990.0360.1360.926100
2.77-2.9914.30.10915150.9970.9990.030.1130.953100
2.99-3.2914.20.08715410.9980.9990.0240.0910.863100
3.29-3.7613.90.07515640.9980.9990.0210.0780.927100
3.76-4.7413.90.06515770.99810.0180.0680.874100
4.74-3513.20.05216650.99910.0150.0540.64399.6

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
SCALEPACK2.3.10data scaling
PHASER1.20.1-4487phasing
HKL-30002.3.10data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→28.05 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.27 / Stereochemistry target values: ML
Details: Phenix refinement, individual B factor refinement, Electron density fitting with COOT
RfactorNum. reflection% reflectionSelection details
Rfree0.2285 1528 10 %0.1
Rwork0.1767 ---
obs0.1819 15284 99.45 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 30.1 Å2 / ksol: 0.33 e/Å3
Displacement parametersBiso mean: 31 Å2
Refinement stepCycle: LAST / Resolution: 2.2→28.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2160 0 32 154 2346
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072237
X-RAY DIFFRACTIONf_angle_d1.0093042
X-RAY DIFFRACTIONf_dihedral_angle_d10.439320
X-RAY DIFFRACTIONf_chiral_restr0.061334
X-RAY DIFFRACTIONf_plane_restr0.006402
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.270.26131280.20911156X-RAY DIFFRACTION95
2.27-2.350.26011370.19561233X-RAY DIFFRACTION99
2.35-2.450.25871360.17791222X-RAY DIFFRACTION100
2.45-2.560.24881380.19071241X-RAY DIFFRACTION100
2.56-2.690.24151380.19111243X-RAY DIFFRACTION100
2.69-2.860.26841380.20771239X-RAY DIFFRACTION100
2.86-3.080.28711390.20071252X-RAY DIFFRACTION100
3.08-3.390.24781410.19541270X-RAY DIFFRACTION100
3.39-3.880.22531380.16371251X-RAY DIFFRACTION100
3.88-4.880.17861430.14471283X-RAY DIFFRACTION100
4.89-28.050.17531520.14941366X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -14.0013 Å / Origin y: -3.3207 Å / Origin z: 20.7818 Å
111213212223313233
T0.0826 Å2-0.011 Å2-0.0121 Å2-0.0944 Å2-0.0078 Å2--0.1102 Å2
L1.3139 °20.2111 °2-0.6255 °2-1.1257 °2-0.3917 °2--1.4857 °2
S-0.0529 Å °0.0609 Å °-0.0348 Å °-0.0291 Å °0.0324 Å °0.0103 Å °0.075 Å °-0.0764 Å °0.0147 Å °
Refinement TLS groupSelection details: all

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