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- PDB-6j18: ATPase -

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Basic information

Entry
Database: PDB / ID: 6j18
TitleATPase
ComponentsESX-5 secretion system protein EccC5
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-5 secretion system protein EccC5
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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-5 secretion system protein EccC5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9033
Polymers34,3711
Non-polymers5312
Water3,855214
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area920 Å2
ΔGint-11 kcal/mol
Surface area12790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.161, 89.161, 62.637
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65

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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: 34371.281 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: eccC5, Rv1783 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P9WNA5
#2: 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
#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 / Water


Mass: 18.015 Da / Num. of mol.: 214 / 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: 2.09 Å3/Da / Density % sol: 41.18 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 0.2 M sodium dihydrogen phosphate monohydrate pH 4.5, 20% (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: Dec 23, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97776 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 19280 / % possible obs: 100 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.123 / Rpim(I) all: 0.062 / Rrim(I) all: 0.138 / Χ2: 1.229 / Net I/σ(I): 4.7 / Num. measured all: 94374
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2-2.034.60.449670.8410.2260.4950.578100
2.03-2.074.50.4149380.8460.2170.4690.628100
2.07-2.114.70.3659570.8830.1870.4110.656100
2.11-2.1550.3429590.90.1690.3820.66100
2.15-2.250.3169550.9160.1560.3530.714100
2.2-2.2550.2759610.9290.1360.3080.756100
2.25-2.3150.2529670.9410.1250.2820.813100
2.31-2.374.90.2369620.9440.1180.2640.844100
2.37-2.444.80.2129410.9490.1070.2380.85100
2.44-2.524.60.1949760.9550.1010.2190.9699.9
2.52-2.614.90.189520.9630.090.2020.98699.9
2.61-2.715.10.1669650.9660.0810.1851.095100
2.71-2.845.10.1449640.9770.0710.1611.19599.9
2.84-2.995.10.1379550.9760.0670.1531.3399.9
2.99-3.174.80.1269590.9810.0630.1411.51199.9
3.17-3.424.80.1129810.9850.0570.1261.82299.9
3.42-3.765.20.1079680.9860.0520.1192.158100
3.76-4.315.10.1039640.9850.0510.1152.312100
4.31-5.434.70.0939770.9870.0470.1042.27100
5.43-504.90.09110120.990.0460.1022.19899.9

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
SCALEPACKdata scaling
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4NH0

4nh0


Resolution: 2→38.608 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 18.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1999 934 4.85 %
Rwork0.1668 18323 -
obs0.1684 19257 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 87.56 Å2 / Biso mean: 34.6042 Å2 / Biso min: 17.69 Å2
Refinement stepCycle: final / Resolution: 2→38.608 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2063 0 32 214 2309
Biso mean--24.85 39.88 -
Num. residues----272
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032174
X-RAY DIFFRACTIONf_angle_d0.812968
X-RAY DIFFRACTIONf_chiral_restr0.03322
X-RAY DIFFRACTIONf_plane_restr0.004391
X-RAY DIFFRACTIONf_dihedral_angle_d14.991812
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.0002-2.10570.22091320.200126122744
2.1057-2.23760.20561400.196225942734
2.2376-2.41030.21951270.190126092736
2.4103-2.65280.22191520.19325782730
2.6528-3.03650.21781180.180626272745
3.0365-3.82520.20931310.162726232754
3.8252-38.6150.1691340.138126802814
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)
11.8278-0.1867-0.29250.7508-0.52350.6816-0.0604-0.2613-0.1170.2030.04820.0337-0.00190.01730.00310.21660.0717-0.00280.31710.01110.242835.439234.6779-7.7266
21.7357-0.06721.08731.07350.13291.44-0.01530.21130.0127-0.104-0.0148-0.0195-0.08530.05550.03250.20480.05340.01460.28970.00280.215335.106340.3146-28.375
32.6795-0.17291.59340.4929-0.35261.9987-0.12960.0580.29360.0253-0.0152-0.0231-0.28350.070.10080.24410.03390.01910.2166-0.02010.253537.240449.9027-22.1573
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1125 through 1165 )A1125 - 1165
2X-RAY DIFFRACTION2chain 'A' and (resid 1166 through 1258 )A1166 - 1258
3X-RAY DIFFRACTION3chain 'A' and (resid 1259 through 1396)A1259 - 1396

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