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- PDB-6j17: ATPase -

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Basic information

Entry
Database: PDB / ID: 6j17
TitleATPase
ComponentsESX-3 secretion system protein EccC3
KeywordsMOTOR PROTEIN / ATPase
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
ADENOSINE-5'-TRIPHOSPHATE / ESX-3 secretion system protein EccC3
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.975 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-3 secretion system protein EccC3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,4833
Polymers34,9511
Non-polymers5312
Water2,666148
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area960 Å2
ΔGint-11 kcal/mol
Surface area11730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.363, 56.628, 93.532
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein ESX-3 secretion system protein EccC3 / ESX conserved component C3 / Type VII secretion system protein EccC3 / T7SS protein EccC3


Mass: 34951.094 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: eccC3, Rv0284 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P9WNA9
#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.: 148 / 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: 2.02 Å3/Da / Density % sol: 39.16 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Hepes/sodium hydroxide pH 7.5, 0.2 M sodium chloride, 20% (w/v) PEG3000

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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: Oct 12, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97776 Å / Relative weight: 1
ReflectionResolution: 1.97→50 Å / Num. obs: 19248 / % possible obs: 93.2 % / Redundancy: 5.5 % / Biso Wilson estimate: 30.23 Å2 / Rmerge(I) obs: 0.116 / Rpim(I) all: 0.051 / Rrim(I) all: 0.127 / Χ2: 0.778 / Net I/σ(I): 4.2 / Num. measured all: 106252
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.97-23.70.4486790.7770.2490.5170.59667.3
2-2.044.10.3887970.8560.2010.440.59978.1
2.04-2.084.40.3918080.8460.2030.4440.60581.1
2.08-2.124.40.3948570.8430.2010.4460.65283.8
2.12-2.174.60.3648790.8820.1830.410.62786.9
2.17-2.224.60.3468790.8860.1710.3870.66486.4
2.22-2.274.70.369260.7620.180.4050.7690.5
2.27-2.344.70.3139400.9180.1530.350.74893.3
2.34-2.45.20.3059880.9240.1440.3390.71897.5
2.4-2.485.70.32410160.9350.1480.3570.71798.4
2.48-2.575.90.30710160.9360.1380.3380.69399.6
2.57-2.676.10.29710300.9510.1310.3250.72899.8
2.67-2.860.25610170.9480.1140.2810.78899.9
2.8-2.946.40.2110300.9710.0890.2290.80699.7
2.94-3.136.70.17110350.980.0710.1850.9299.6
3.13-3.376.60.13510350.9890.0570.1470.92299.9
3.37-3.716.20.10910400.990.0470.1191.08299.9
3.71-4.246.50.08810490.9910.0370.0960.965100
4.24-5.356.20.07110720.9950.030.0770.863100
5.35-505.90.05211550.9980.0230.0570.55699.8

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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: 4NH0

4nh0


Resolution: 1.975→46.35 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 25.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2275 930 4.85 %
Rwork0.1811 18242 -
obs0.1835 19172 93.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 139.95 Å2 / Biso mean: 44.3764 Å2 / Biso min: 18.04 Å2
Refinement stepCycle: final / Resolution: 1.975→46.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1955 0 32 148 2135
Biso mean--25.94 44.38 -
Num. residues----254
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0152029
X-RAY DIFFRACTIONf_angle_d1.3282776
X-RAY DIFFRACTIONf_chiral_restr0.08324
X-RAY DIFFRACTIONf_plane_restr0.008359
X-RAY DIFFRACTIONf_dihedral_angle_d10.3141231
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9754-2.07950.30211000.21692105220577
2.0795-2.20980.25281310.20522330246185
2.2098-2.38040.23991270.19232545267292
2.3804-2.620.22411480.19492726287499
2.62-2.9990.2351070.198728142921100
2.999-3.77820.23471530.177427932946100
3.7782-46.36270.20851640.163929293093100
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)
11.4779-0.3071.17551.8747-0.44745.2404-0.0963-0.17540.09930.68110.02840.3745-0.6215-0.59020.06030.4840.07390.11770.34770.00330.293612.56263.605633.0364
21.9087-0.43140.90863.2663-0.78124.09120.0940.1367-0.2021-0.3240.00020.58460.2594-0.4705-0.09310.21440.0142-0.02940.249-0.03420.299110.5102-4.432113.8259
33.70961.1478-1.60682.0664-0.91173.13690.22760.34961.2409-0.51720.41521.0165-1.0008-0.92840.36240.63120.1942-0.04180.53910.10470.6676.06613.46966.316
42.5106-0.32111.11651.60370.60313.51660.26680.3472-0.1049-0.5425-0.24870.1081-0.0320.2279-0.16430.40260.08850.01660.3011-0.00040.234220.098-2.85372.5564
52.9479-0.62161.63914.0044-0.7915.5034-0.1010.17590.1854-0.4942-0.0627-0.4697-0.25250.34360.14290.2434-0.00290.06680.22140.01370.242524.21222.757713.3932
64.24990.54980.27445.9765-0.60255.8853-0.0789-0.11520.03890.3552-0.0342-0.5716-0.07020.34080.09370.2860.0115-0.00630.1756-0.00420.209626.60560.707527.4666
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1060 through 1096 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 1097 through 1176 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 1177 through 1201 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 1202 through 1235 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 1236 through 1271 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 1272 through 1313 )A0

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