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Basic information

Entry
Database: PDB / ID: 6jd4
TitleATPase
ComponentsESX-1 secretion system protein EccCb1
KeywordsMOTOR PROTEIN / ATPase
Function / homology
Function and homology information


protein secretion by the type VII secretion system / evasion of host immune response / biological process involved in interaction with host / peptidoglycan-based cell wall / DNA binding / ATP binding / plasma membrane / cytoplasm
Similarity search - Function
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
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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

Downloads & links

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Assembly

Deposited unit
A: ESX-1 secretion system protein EccCb1
B: ESX-1 secretion system protein EccCb1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,6026
Polymers60,5392
Non-polymers1,0634
Water6,954386
1
A: ESX-1 secretion system protein EccCb1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,8013
Polymers30,2701
Non-polymers5312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area930 Å2
ΔGint-11 kcal/mol
Surface area12220 Å2
MethodPISA
2
B: ESX-1 secretion system protein EccCb1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,8013
Polymers30,2701
Non-polymers5312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area930 Å2
ΔGint-11 kcal/mol
Surface area12200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.220, 77.314, 106.011
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-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.: 2
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: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 386 / 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: 2.07 Å3/Da / Density % sol: 40.64 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 0.49 M sodium phosphate monobasic monohydrate, 0.91 M potassium phosphate dibasic, pH 6.9

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 17, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→62.466 Å / Num. all: 30107 / Num. obs: 30107 / % possible obs: 100 % / Redundancy: 12.9 % / Biso Wilson estimate: 16.5 Å2 / Rpim(I) all: 0.039 / Rrim(I) all: 0.14 / Rsym value: 0.134 / Net I/av σ(I): 3.6 / Net I/σ(I): 17.9 / Num. measured all: 388582
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
2.1-2.2112.90.3311.85573643130.0980.3460.3319.6100
2.21-2.3512.60.29125199941180.0880.3050.29110.699.9
2.35-2.5113.20.2492.25050938190.0740.260.24912.2100
2.51-2.71130.2022.64685136060.060.2110.20214.7100
2.71-2.9712.50.16534169333480.050.1720.16517.499.9
2.97-3.3213.10.1453.33980730330.0410.1510.14522.2100
3.32-3.8313.40.14.83622526940.0280.1040.127.7100
3.83-4.713.20.0796.23045923010.0220.0820.07930.9100
4.7-6.6412.50.0746.32250018070.0220.0770.07428.599.8
6.64-43.723120.058.41280310680.0150.0520.053199.7

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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: 2.1→43.723 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 31.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2464 1431 4.78 %
Rwork0.2015 28532 -
obs0.2036 29963 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 135.24 Å2 / Biso mean: 22.5091 Å2 / Biso min: 2.81 Å2
Refinement stepCycle: final / Resolution: 2.1→43.723 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3986 0 64 386 4436
Biso mean--12.76 27.01 -
Num. residues----522
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034162
X-RAY DIFFRACTIONf_angle_d0.7155690
X-RAY DIFFRACTIONf_chiral_restr0.045630
X-RAY DIFFRACTIONf_plane_restr0.006736
X-RAY DIFFRACTIONf_dihedral_angle_d12.5992514
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1-2.17510.29691430.215827922935100
2.1751-2.26220.25861660.242427972963100
2.2622-2.36510.28771540.24732771292599
2.3651-2.48980.34921230.252828382961100
2.4898-2.64580.27741250.236728462971100
2.6458-2.850.26371370.24628442981100
2.85-3.13670.23631400.201528392979100
3.1367-3.59050.23771460.177928743020100
3.5905-4.52290.18521380.152529123050100
4.5229-43.73250.22161590.178930193178100
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)
10.13630.02260.02810.13020.04570.2514-0.00210.0183-0.00620.00820.0316-0.0746-0.03190.02440.08390.0530.00360.01030.07180.00110.116337.31850.0693-27.1335
20.1729-0.1005-0.05140.17980.09750.02660.00820.057-0.0098-0.0122-0.0347-0.0293-0.038-0.0461-0.12440.05220.0068-0.0050.080.01360.063420.8272-2.6932-21.8178
30.00860.01660.00870.05290.02620.0432-0.0338-0.1295-0.13330.10090.0190.26230.1384-0.1361-0.00510.1681-0.02160.01530.11620.03650.113916.4835-12.2-8.3595
40.46480.0912-0.03660.2208-0.08250.4314-0.1047-0.2391-0.03380.1353-0.02170.01890.09610.1982-0.20180.11930.04760.00660.1530.04730.034230.8363-17.1345-11.3485
50.0386-0.016-0.02130.0140.00750.0131-0.157-0.010.00170.0586-0.06340.0503-0.0905-0.1289-0.00180.17760.01460.0140.1558-0.02670.10216.47593.1212-5.1865
60.6989-0.0104-0.21110.2111-0.19910.24540.166-0.13080.27280.2304-0.1848-0.10950.02630.15290.16490.18210.0061-0.04490.0889-0.0210.041226.568-1.0142-7.6432
70.4004-0.1537-0.51520.08810.27070.87890.18010.00720.0158-0.08910.032-0.0528-0.17110.18640.24070.0711-0.0126-0.03480.0697-0.00150.103630.95897.4592-9.071
80.01420.0197-0.04270.0479-0.01030.12960.00070.07290.1474-0.01550.04260.1253-0.0834-0.1858-0.01060.11330.07060.0031-0.32270.13130.090834.959816.1198-13.3918
90.04980.0235-0.07030.38940.07650.1104-0.0569-0.0875-0.1261-0.12810.0409-0.05520.0388-0.06430.00550.04250.00550.01640.08210.0050.138735.78077.5176-21.1765
100.2986-0.1314-0.04520.13860.06640.2643-0.026-0.004-0.02930.03370.00830.1733-0.0588-0.0284-0.04510.09940.0019-0.00280.0718-0.00420.125524.893911.777529.6836
110.1196-0.0448-0.00430.3012-0.08520.1542-0.02320.0252-0.01-0.0234-0.01310.0696-0.01230.0382-0.17040.0461-0.0103-0.00970.0723-0.00850.057135.94729.567621.7591
120.1395-0.14320.11430.67220.53850.94120.10390.17760.0575-0.09120.0417-0.2325-0.11570.3690.07370.07190.0693-0.02050.07450.00670.089844.8979-0.6848.5469
130.2992-0.0710.11650.03150.02120.1413-0.07340.10720.1383-0.14110.0030.1190.0047-0.0952-0.05690.1105-0.0463-0.00830.0791-0.03440.043530.4315-5.969611.4535
140.0295-0.0097-0.00690.0048-0.00520.0011-0.139-0.1307-0.0472-0.09160.0605-0.0595-0.06890.0953-0.03090.2369-0.00660.03150.14190.00750.179844.807214.64895.3123
150.56890.0497-0.31530.25920.31510.63440.18820.1170.1515-0.2009-0.09670.1627-0.0909-0.24870.22340.1535-0.0187-0.05520.03430.02560.070934.565810.30477.6031
160.1402-0.0544-0.10530.2290.08980.1047-0.01940.22850.0037-0.116-0.10940.2112-0.1597-0.18870.00310.13110.0062-0.04420.12930.00430.12430.222818.71359.106
170.1576-0.0496-0.10141.4926-0.28010.17090.160.27180.0969-0.27320.07840.3261-0.0106-0.01080.01440.14220.0115-0.04110.16870.03460.193425.632427.508113.1249
180.1874-0.07-0.18110.03770.06430.1528-0.07430.1111-0.17080.0508-0.01160.2040.096-0.1305-0.1570.0483-0.0322-0.00690.0304-0.02840.135825.407719.06221.1056
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 318 through 371 )A318 - 371
2X-RAY DIFFRACTION2chain 'A' and (resid 372 through 431 )A372 - 431
3X-RAY DIFFRACTION3chain 'A' and (resid 432 through 449 )A432 - 449
4X-RAY DIFFRACTION4chain 'A' and (resid 450 through 477 )A450 - 477
5X-RAY DIFFRACTION5chain 'A' and (resid 478 through 491 )A478 - 491
6X-RAY DIFFRACTION6chain 'A' and (resid 492 through 522 )A492 - 522
7X-RAY DIFFRACTION7chain 'A' and (resid 523 through 545 )A523 - 545
8X-RAY DIFFRACTION8chain 'A' and (resid 546 through 559 )A546 - 559
9X-RAY DIFFRACTION9chain 'A' and (resid 560 through 578 )A560 - 578
10X-RAY DIFFRACTION10chain 'B' and (resid 318 through 354 )B318 - 354
11X-RAY DIFFRACTION11chain 'B' and (resid 355 through 431 )B355 - 431
12X-RAY DIFFRACTION12chain 'B' and (resid 432 through 449 )B432 - 449
13X-RAY DIFFRACTION13chain 'B' and (resid 450 through 477 )B450 - 477
14X-RAY DIFFRACTION14chain 'B' and (resid 478 through 491 )B478 - 491
15X-RAY DIFFRACTION15chain 'B' and (resid 492 through 522 )B492 - 522
16X-RAY DIFFRACTION16chain 'B' and (resid 523 through 545 )B523 - 545
17X-RAY DIFFRACTION17chain 'B' and (resid 546 through 559 )B546 - 559
18X-RAY DIFFRACTION18chain 'B' and (resid 560 through 578 )B560 - 578

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