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- PDB-6j19: ATPase -

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Basic information

Entry
Database: PDB / ID: 6j19
TitleATPase
Components
  • ESAT-6-like protein EsxB
  • ESX-1 secretion system protein EccCb1
KeywordsMOTOR PROTEIN / ATPase
Function / homology
Function and homology information


protein secretion by the type VII secretion system / host cell surface binding / evasion of host immune response / biological process involved in interaction with host / host cell endoplasmic reticulum / peptidoglycan-based cell wall / host cell surface / DNA binding / extracellular region / ATP binding ...protein secretion by the type VII secretion system / host cell surface binding / evasion of host immune response / biological process involved in interaction with host / host cell endoplasmic reticulum / peptidoglycan-based cell wall / host cell surface / DNA binding / extracellular region / ATP binding / plasma membrane / cytoplasm
Similarity search - Function
ESAT-6-like superfamily / Type VII secretion system ESAT-6-like / Proteins of 100 residues with WXG / EccCb-like, Actinobacteria / FtsK domain / FtsK/SpoIIIE family / FtsK domain profile. / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain ...ESAT-6-like superfamily / Type VII secretion system ESAT-6-like / Proteins of 100 residues with WXG / EccCb-like, Actinobacteria / FtsK domain / FtsK/SpoIIIE family / FtsK domain profile. / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / ESX-1 secretion system protein EccCb1 / ESAT-6-like protein EsxB
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.978 Å
AuthorsWang, S.H. / Li, J. / Rao, Z.H.
Funding support China, 7items
OrganizationGrant numberCountry
Ministry of Science and Technology (China)2017YFC0840300 China
Chinese Academy of SciencesXDB08020200 China
Ministry of Science and Technology (China)2014CB542800 China
Ministry of Science and Technology (China)2014CBA02003 China
National Natural Science Foundation of China813300237 China
National Natural Science Foundation of China31500607 China
National Natural Science Foundation of China81520108019 China
CitationJournal: Protein Cell / Year: 2020
Title: Structural insights into substrate recognition by the type VII secretion system.
Authors: Wang, S. / Zhou, K. / Yang, X. / Zhang, B. / Zhao, Y. / Xiao, Y. / Yang, X. / Yang, H. / Guddat, L.W. / Li, J. / Rao, Z.
History
DepositionDec 28, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 4, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 29, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ESX-1 secretion system protein EccCb1
B: ESAT-6-like protein EsxB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,9024
Polymers41,3712
Non-polymers5312
Water3,981221
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1810 Å2
ΔGint-19 kcal/mol
Surface area12780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.580, 129.647, 64.195
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-322-

ARG

21A-902-

HOH

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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: 30269.658 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: eccCb1, snm2, Rv3871 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P9WNB1
#2: Protein ESAT-6-like protein EsxB / 10 kDa culture filtrate antigen CFP-10 / CFP-10 / Secreted antigenic protein MTSA-10


Mass: 11101.037 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: esxB, cfp10, lhp, mtsA10, Rv3874, MTV027.09 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P9WNK5
#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine 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
#4: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 221 / Source method: isolated from a natural source / Formula: H2O

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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: 2.05 Å3/Da / Density % sol: 40.04 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 0.1 M MES pH 6.5, 0.2 M sodium chloride, 25% (w/v) PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97776 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 1, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97776 Å / Relative weight: 1
ReflectionResolution: 1.98→50 Å / Num. obs: 23760 / % possible obs: 98 % / Redundancy: 10.5 % / Biso Wilson estimate: 27.9 Å2 / Rmerge(I) obs: 0.189 / Rpim(I) all: 0.057 / Rrim(I) all: 0.197 / Χ2: 0.589 / Net I/σ(I): 2.9 / Num. measured all: 249653
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.98-2.015.50.6749330.7280.2790.7350.45777.5
2.01-2.056.70.67610700.7480.260.7280.47390.5
2.05-2.097.20.65711420.7910.2470.7060.48995
2.09-2.137.70.56611880.8640.2070.6050.48497.8
2.13-2.188.40.56211650.8560.20.5980.48799.2
2.18-2.238.90.55411880.8980.1920.5870.48899.7
2.23-2.299.20.51311910.9230.1760.5430.52699.8
2.29-2.359.50.45212020.9430.1530.4780.533100
2.35-2.4210.70.43912040.9520.1390.4610.54100
2.42-2.4911.10.43312130.9520.1350.4540.535100
2.49-2.5811.30.37211950.9710.1150.390.54599.9
2.58-2.6911.40.34412010.9720.1060.360.577100
2.69-2.8111.10.31211980.9830.0970.3270.599100
2.81-2.9611.90.29312170.9870.0880.3060.627100
2.96-3.14130.27612110.990.0790.2870.649100
3.14-3.3913.20.23512200.9930.0670.2450.678100
3.39-3.7312.50.17512250.9940.0510.1820.719100
3.73-4.2613.40.13512310.9960.0380.140.757100
4.26-5.3712.80.10112480.9980.0290.1050.68100
5.37-5012.30.08613180.9980.0250.090.534100

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
SCALEPACKdata scaling
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6JD4

6jd4


Resolution: 1.978→45.613 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 19.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2082 1218 5.13 %
Rwork0.1697 22526 -
obs0.1716 23744 98.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 129.59 Å2 / Biso mean: 34.1207 Å2 / Biso min: 13.67 Å2
Refinement stepCycle: final / Resolution: 1.978→45.613 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2105 0 32 221 2358
Biso mean--26.94 42.24 -
Num. residues----275
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072193
X-RAY DIFFRACTIONf_angle_d0.8572992
X-RAY DIFFRACTIONf_chiral_restr0.052329
X-RAY DIFFRACTIONf_plane_restr0.006389
X-RAY DIFFRACTIONf_dihedral_angle_d10.4171327
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9778-2.0570.27071160.2452163227986
2.057-2.15060.26411300.22122444257497
2.1506-2.2640.28361640.200624902654100
2.264-2.40590.23221290.193225322661100
2.4059-2.59160.251240.187325312655100
2.5916-2.85240.20031430.172725332676100
2.8524-3.2650.21991620.168925332695100
3.265-4.11310.16771310.143625872718100
4.1131-45.62540.17391190.152627132832100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.9037-0.73120.56772.95260.13111.50490.31620.1881-0.8286-0.1758-0.07160.17290.34590.0653-0.27370.2921-0.0259-0.07570.16630.0050.277414.9626.8415-3.4024
21.9888-0.21950.41071.71850.05451.12990.05250.0873-0.0136-0.07180.05590.09450.1218-0.034-0.08970.195-0.0087-0.02110.16350.00520.135313.627820.6781-3.7521
33.08860.5894-1.12080.6525-0.39942.26570.0115-0.2212-0.08620.1052-0.0668-0.1083-0.0675-0.05720.04360.14590.01920.00320.18550.02990.2492.057434.97342.1622
43.549-0.44390.8840.99710.18171.4689-0.0262-0.23520.27370.08620.0588-0.0945-0.08920.0484-0.04680.2126-0.02-0.01290.1969-0.01670.189320.843729.65324.4495
50.87010.56541.7613.52513.80325.78730.0372-0.16260.01020.5204-0.14880.04160.48890.11160.01360.2969-0.0242-0.05270.21590.00890.280230.218215.175210.3355
62.56220.1920.43973.031.13383.89530.2423-0.0915-0.1102-0.02960.0788-0.01180.1105-0.2638-0.2890.21610.022-0.03460.14650.02650.201620.98912.97942.928
71.4011-1.01570.53089.38211.11582.39570.1470.1131.4449-0.05210.00230.4764-1.4136-0.2777-0.02990.54850.04440.09470.42780.13170.74035.964849.8335-11.3656
84.42860.1493-0.30835.0667-0.7415.17140.13480.64230.1425-0.31140.24030.4689-0.4893-0.7261-0.38750.25230.0179-0.02940.23960.05780.26783.159738.1787-9.9558
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 320 through 343 )A320 - 343
2X-RAY DIFFRACTION2chain 'A' and (resid 344 through 431 )A344 - 431
3X-RAY DIFFRACTION3chain 'A' and (resid 432 through 469 )A432 - 469
4X-RAY DIFFRACTION4chain 'A' and (resid 470 through 546 )A470 - 546
5X-RAY DIFFRACTION5chain 'A' and (resid 547 through 559 )A547 - 559
6X-RAY DIFFRACTION6chain 'A' and (resid 560 through 580 )A560 - 580
7X-RAY DIFFRACTION7chain 'B' and (resid 87 through 94 )B87 - 94
8X-RAY DIFFRACTION8chain 'B' and (resid 95 through 100 )B95 - 100

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