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- PDB-7naz: TPR-rich domain of EccA3 from M. smegmatis -

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Basic information

Entry
Database: PDB / ID: 7naz
TitleTPR-rich domain of EccA3 from M. smegmatis
ComponentsESX-3 secretion system protein EccA3
KeywordsUNKNOWN FUNCTION / EccA / Type VII Secretion
Function / homology
Function and homology information


ATP hydrolysis activity / ATP binding / cytoplasm
Similarity search - Function
Type VII secretion system AAA-ATPase, EccA / : / T7SS, ESX-1 secretion system protein EccA1, N-terminal domain / CbbX, AAA lid domain / AAA lid domain / CbxX/CfxQ / : / Tetratricopeptide repeat domain / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core ...Type VII secretion system AAA-ATPase, EccA / : / T7SS, ESX-1 secretion system protein EccA1, N-terminal domain / CbbX, AAA lid domain / AAA lid domain / CbxX/CfxQ / : / Tetratricopeptide repeat domain / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase / Mainly Alpha
Similarity search - Domain/homology
1,4-DIETHYLENE DIOXIDE / ESX-3 secretion system protein EccA3
Similarity search - Component
Biological speciesMycolicibacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 Å
AuthorsCrosskey, T.D. / Wilmanns, M.
CitationJournal: To Be Published
Title: Structure of TPR-rich domain of M. smegmatis EccA3
Authors: Crosskey, T.D. / Wilmanns, M.
History
DepositionJan 25, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 2, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 19, 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-3 secretion system protein EccA3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,74617
Polymers32,2691
Non-polymers1,47716
Water4,143230
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS, Monomeric, SAXS experiments confirmed that it is also monomeric in solution
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2850 Å2
ΔGint-49 kcal/mol
Surface area13740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)159.001, 159.001, 43.364
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein ESX-3 secretion system protein EccA3 / ESX conserved component A3 / Type VII secretion system protein EccA3 / T7SS protein EccA3


Mass: 32268.959 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / Gene: eccA3, MSMEG_0615, MSMEI_0599 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0QQ38
#2: Chemical
ChemComp-DIO / 1,4-DIETHYLENE DIOXIDE


Mass: 88.105 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H8O2
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 230 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.34 Å3/Da / Density % sol: 63.16 %
Crystal growTemperature: 292.15 K / Method: vapor diffusion / pH: 6.5
Details: 0.1 M MES pH6.5, 10 %(v/v) dioxane, 1.6 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.976241 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 13, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976241 Å / Relative weight: 1
ReflectionResolution: 1.42→45.94 Å / Num. obs: 53900 / % possible obs: 100 % / Redundancy: 10 % / Biso Wilson estimate: 22.38 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.027 / Rrim(I) all: 0.071 / Χ2: 0.93 / Net I/av σ(I): 18.7 / Net I/σ(I): 18.7
Reflection shellResolution: 1.42→1.44 Å / Num. unique obs: 75904 / CC1/2: 0.997 / % possible all: 98.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
Aimlessdata scaling
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 1.6→45.94 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.97 / SU B: 3.106 / SU ML: 0.046 / Cross valid method: THROUGHOUT / ESU R: 0.064 / ESU R Free: 0.061 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16994 2810 5.2 %RANDOM
Rwork0.13393 ---
obs0.13575 51088 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.3 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.017 Å2
Baniso -1Baniso -2Baniso -3
1-0.27 Å20.14 Å2-0 Å2
2--0.27 Å2-0 Å2
3----0.89 Å2
Refinement stepCycle: LAST / Resolution: 1.6→45.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2137 0 90 230 2457
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0182295
X-RAY DIFFRACTIONr_bond_other_d0.0010.022084
X-RAY DIFFRACTIONr_angle_refined_deg1.4171.8613126
X-RAY DIFFRACTIONr_angle_other_deg1.2582.8844804
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.4785286
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.91123.429105
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.99115325
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.3451521
X-RAY DIFFRACTIONr_chiral_restr0.1010.2344
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022548
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02477
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.8572.7841132
X-RAY DIFFRACTIONr_mcbond_other1.8442.7811131
X-RAY DIFFRACTIONr_mcangle_it2.4064.1851416
X-RAY DIFFRACTIONr_mcangle_other2.4064.191417
X-RAY DIFFRACTIONr_scbond_it3.1483.3721163
X-RAY DIFFRACTIONr_scbond_other2.8393.3571160
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.5544.8651703
X-RAY DIFFRACTIONr_long_range_B_refined3.93235.9962661
X-RAY DIFFRACTIONr_long_range_B_other3.69135.3812606
X-RAY DIFFRACTIONr_rigid_bond_restr2.43734369
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.28 210 -
Rwork0.213 3727 -
obs--99.95 %

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