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- PDB-6jd5: ATPase -

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Basic information

Entry
Database: PDB / ID: 6jd5
TitleATPase
ComponentsESX conserved component EccC2. ESX-2 type VII secretion system protein. Possible membrane protein
KeywordsMOTOR PROTEIN / ATPase
Function / homology
Function and homology information


peptidoglycan-based cell wall / DNA binding / ATP binding / metal ion binding / plasma membrane
Similarity search - Function
EccCa-like, Actinobacteria / EccCb-like, Actinobacteria / : / FtsK domain / FtsK/SpoIIIE family / FtsK domain profile. / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / ESX conserved component EccC2. ESX-2 type VII secretion system protein. Possible membrane protein
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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
DepositionJan 31, 2019Deposition 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ESX conserved component EccC2. ESX-2 type VII secretion system protein. Possible membrane protein
B: ESX conserved component EccC2. ESX-2 type VII secretion system protein. Possible membrane protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,1956
Polymers60,1322
Non-polymers1,0634
Water3,891216
1
A: ESX conserved component EccC2. ESX-2 type VII secretion system protein. Possible membrane protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,5983
Polymers30,0661
Non-polymers5312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area70 Å2
ΔGint-5 kcal/mol
Surface area13260 Å2
MethodPISA
2
B: ESX conserved component EccC2. ESX-2 type VII secretion system protein. Possible membrane protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,5983
Polymers30,0661
Non-polymers5312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area80 Å2
ΔGint-5 kcal/mol
Surface area13230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.449, 69.691, 75.963
Angle α, β, γ (deg.)90.000, 100.570, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein ESX conserved component EccC2. ESX-2 type VII secretion system protein. Possible membrane protein


Mass: 30066.225 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: eccC2, Rv3894c / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O05450
#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / 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.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 216 / 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: 2.23 Å3/Da / Density % sol: 44.75 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / Details: 0.1 M BIS-TRIS pH 6.5, 45% (v/v) PEG400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9789 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 24, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 2.2→74.674 Å / Num. all: 26929 / Num. obs: 26929 / % possible obs: 99.9 % / Redundancy: 6.9 % / Rpim(I) all: 0.037 / Rrim(I) all: 0.099 / Rsym value: 0.091 / Net I/av σ(I): 7.3 / Net I/σ(I): 13.5 / Num. measured all: 184657
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
2.2-2.3270.6421.22744539330.2610.6940.6422.8100
2.32-2.4670.4361.82576137020.1780.4710.4364100
2.46-2.636.60.3192.42294634570.1330.3460.3195.299.7
2.63-2.847.10.2173.52301832510.0870.2340.2177.8100
2.84-3.116.70.1455.12016329950.060.1570.1451199.8
3.11-3.486.90.0927.81864726990.0380.0990.09217.599.7
3.48-4.026.80.05712.21634323890.0230.0620.05726.699.9
4.02-4.926.90.042151391420310.0170.0450.04233.999.9
4.92-6.966.70.04315.11055015850.0180.0470.0433099.8
6.96-40.9336.60.0316.758708870.0130.0320.0338.499.2

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
SCALA3.3.22data scaling
PDB_EXTRACT3.24data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4NH0

4nh0


Resolution: 2.2→38.707 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2251 1322 4.92 %
Rwork0.1757 25558 -
obs0.1781 26880 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 80.55 Å2 / Biso mean: 40.4184 Å2 / Biso min: 22.18 Å2
Refinement stepCycle: final / Resolution: 2.2→38.707 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4037 0 64 216 4317
Biso mean--34.7 40.35 -
Num. residues----519
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074193
X-RAY DIFFRACTIONf_angle_d0.9765719
X-RAY DIFFRACTIONf_chiral_restr0.055631
X-RAY DIFFRACTIONf_plane_restr0.006749
X-RAY DIFFRACTIONf_dihedral_angle_d8.762567
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 (%)
2.2-2.28810.33021630.239328242987100
2.2881-2.39220.24461680.214727902958100
2.3922-2.51830.26391330.204528402973100
2.5183-2.67610.29161450.199328082953100
2.6761-2.88260.26941520.197328623014100
2.8826-3.17260.26971230.18822824294799
3.1726-3.63140.23071470.170228643011100
3.6314-4.5740.17681510.145428372988100
4.574-38.71330.1821400.16082909304999

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