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- PDB-6ajf: Crystal structure of mycolic acid transporter MmpL3 from Mycobact... -

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Basic information

Entry
Database: PDB / ID: 6ajf
TitleCrystal structure of mycolic acid transporter MmpL3 from Mycobacterium smegmatis
ComponentsDrug exporters of the RND superfamily-like protein,Endolysin
KeywordsMEMBRANE PROTEIN / HYDROLASE / transporter / RND family / cell wall biosynthesis / drug target
Function / homology
Function and homology information


phosphatidylethanolamine transfer activity / phosphatidylglycerol binding / trehalose transmembrane transporter activity / trehalose transport / mycolate cell wall layer assembly / cell wall biogenesis / diacylglycerol binding / cell pole / cell tip / mycolic acid biosynthetic process ...phosphatidylethanolamine transfer activity / phosphatidylglycerol binding / trehalose transmembrane transporter activity / trehalose transport / mycolate cell wall layer assembly / cell wall biogenesis / diacylglycerol binding / cell pole / cell tip / mycolic acid biosynthetic process / cell septum / phospholipid transport / cardiolipin binding / phosphatidylethanolamine binding / D-mannose binding / viral release from host cell by cytolysis / peptidoglycan catabolic process / phosphatidylinositol binding / regulation of membrane potential / cell wall organization / defense response / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / toxin activity / host cell cytoplasm / defense response to bacterium / response to xenobiotic stimulus / response to antibiotic / plasma membrane
Similarity search - Function
: / Membrane transport protein MMPL domain / MMPL family / Legume lectin / Legume lectin, alpha chain, conserved site / Legume lectins alpha-chain signature. / Legume lectins beta-chain signature. / Legume lectin domain / Legume lectin, beta chain, Mn/Ca-binding site / Legume lectin domain ...: / Membrane transport protein MMPL domain / MMPL family / Legume lectin / Legume lectin, alpha chain, conserved site / Legume lectins alpha-chain signature. / Legume lectins beta-chain signature. / Legume lectin domain / Legume lectin, beta chain, Mn/Ca-binding site / Legume lectin domain / : / Endolysin T4 type / T4-type lysozyme / : / Glycoside hydrolase, family 24 / Phage lysozyme / Lysozyme domain superfamily / Lysozyme-like domain superfamily / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
Chem-L6T / (CARBAMOYLMETHYL-CARBOXYMETHYL-AMINO)-ACETIC ACID / Leucoagglutinating phytohemagglutinin / Endolysin / Trehalose monomycolate exporter MmpL3
Similarity search - Component
Biological speciesMycobacterium smegmatis str. MC2 155 (bacteria)
Enterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.698 Å
AuthorsZhang, B. / Li, J. / Yang, X.L. / Wu, L.J. / Yang, H.T. / 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 Science Foundation (China)813300237 China
National Science Foundation (China)31500607 China
National Science Foundation (China)81520108019 China
CitationJournal: Cell / Year: 2019
Title: Crystal Structures of Membrane Transporter MmpL3, an Anti-TB Drug Target.
Authors: Zhang, B. / Li, J. / Yang, X. / Wu, L. / Zhang, J. / Yang, Y. / Zhao, Y. / Zhang, L. / Yang, X. / Yang, X. / Cheng, X. / Liu, Z. / Jiang, B. / Jiang, H. / Guddat, L.W. / Yang, H. / Rao, Z.
History
DepositionAug 27, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 26, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 13, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Drug exporters of the RND superfamily-like protein,Endolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,4307
Polymers104,0081
Non-polymers2,4236
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area310 Å2
ΔGint0 kcal/mol
Surface area38730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.320, 138.338, 139.950
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 Drug exporters of the RND superfamily-like protein,Endolysin / Lysis protein / Lysozyme / Muramidase


Mass: 104007.633 Da / Num. of mol.: 1 / Mutation: C54T, C97A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium smegmatis str. MC2 155 (bacteria), (gene. exp.) Enterobacteria phage T4 (virus)
Strain: ATCC 700084 / mc(2)155 / Gene: mmpL3, MSMEI_0243, e, T4Tp126
Production host: Mycobacterium smegmatis str. MC2 155 (bacteria)
References: UniProt: I7G2R2, UniProt: D9IEF7, UniProt: A0QP27*PLUS, lysozyme
#2: Chemical ChemComp-MHA / (CARBAMOYLMETHYL-CARBOXYMETHYL-AMINO)-ACETIC ACID / N-(2-ACETAMIDO)IMINODIACETIC ACID


Mass: 190.154 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H10N2O5 / Comment: pH buffer*YM
#3: Sugar
ChemComp-L6T / alpha-D-glucopyranosyl 6-O-dodecyl-alpha-D-glucopyranoside


Type: saccharide / Mass: 510.615 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C24H46O11

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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: 4.02 Å3/Da / Density % sol: 69.38 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 10%-20% (v/v) polyethylene glycol monomethyl ether 350 (PEGMME 350), 50 mM ADA (N-(2-Acetamido) iminodiacetic acid) (pH 6.0-7.0) and 7.5%-17.5% (v/v) polyethylene glycol 2000 (PEG2000)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 27, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.698→98.385 Å / Num. obs: 46808 / % possible obs: 99.8 % / Redundancy: 13.3 % / Biso Wilson estimate: 76.16 Å2 / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.019 / Rrim(I) all: 0.068 / Rsym value: 0.066 / Net I/σ(I): 23.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRpim(I) allRrim(I) allRsym value% possible all
2.7-2.8413.40.739166580.2070.7680.73999.1
2.84-3.0213.40.4281.863860.120.4440.428100
3.02-3.2313.10.2343.260550.0670.2430.234100
3.23-3.4813.90.1365.356090.0380.1410.136100
3.48-3.8213.70.0877.951830.0240.090.087100
3.82-4.2712.90.06210.547120.0180.0640.062100
4.27-4.9313.80.05112.241890.0140.0530.051100
4.93-6.0312.70.05112.135730.0150.0530.051100
6.03-8.5313.10.0431228070.0120.0450.043100
8.53-49.19211.50.0419.516360.0130.0430.04199.3

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
HKL-2000data scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.698→41.243 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 27.06
RfactorNum. reflection% reflection
Rfree0.2489 2320 4.97 %
Rwork0.2232 --
obs0.2244 46708 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 232.14 Å2 / Biso mean: 89.6693 Å2 / Biso min: 41.28 Å2
Refinement stepCycle: final / Resolution: 2.698→41.243 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6955 0 166 0 7121
Biso mean--112.2 --
Num. residues----901
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0047267
X-RAY DIFFRACTIONf_angle_d1.0099861
X-RAY DIFFRACTIONf_chiral_restr0.0351129
X-RAY DIFFRACTIONf_plane_restr0.0041228
X-RAY DIFFRACTIONf_dihedral_angle_d21.432825
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6983-2.75340.37011470.3122473262098
2.7534-2.81320.34961480.287225812729100
2.8132-2.87870.30971290.26925842713100
2.8787-2.95060.3341750.278625192694100
2.9506-3.03040.31021300.272425972727100
3.0304-3.11950.28781380.276125932731100
3.1195-3.22020.30541530.253825682721100
3.2202-3.33520.28561330.239825982731100
3.3352-3.46870.2589910.237526342725100
3.4687-3.62650.26761290.233426232752100
3.6265-3.81760.25691330.215226002733100
3.8176-4.05650.22581340.209326172751100
4.0565-4.36940.25711270.198326282755100
4.3694-4.80850.20631510.181626352786100
4.8085-5.5030.22621360.209226382774100
5.503-6.92780.29591300.229826992829100
6.9278-41.24810.19861360.22132801293799
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)
10.75630.1391-0.06573.22942.16242.2281-0.0381-0.0292-0.1097-0.3353-0.12830.16-0.138-0.30950.1920.48520.0164-0.05220.50450.00050.545815.7995-34.4124-57.2939
21.3580.44190.17383.28951.71312.14960.0003-0.43560.03810.3166-0.25240.54930.0867-0.27870.19640.3785-0.00570.02140.5565-0.05320.450915.6761-21.7292-36.7726
31.5075-0.0105-0.25043.55822.11992.7539-0.2484-0.0705-0.53670.7526-0.0206-0.01521.1470.18070.00360.85840.0582-0.02960.58920.20110.692126.2179-53.5677-41.3866
40.7530.0070.23053.09591.49992.08820.245-0.48150.26050.9289-0.73590.70030.3955-0.71360.41110.7482-0.21810.12290.8083-0.14680.53359.4183-22.7796-25.9513
50.30810.3126-0.0412.12380.63342.84880.00990.33290.0192-0.1289-0.1093-0.0614-0.1650.19560.10140.43640.01750.01250.6765-0.02530.603628.103920.133-9.8299
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid -4 through 207 )A-4 - 207
2X-RAY DIFFRACTION2chain 'A' and (resid 208 through 470 )A208 - 470
3X-RAY DIFFRACTION3chain 'A' and (resid 471 through 583 )A471 - 583
4X-RAY DIFFRACTION4chain 'A' and (resid 584 through 734 )A584 - 734
5X-RAY DIFFRACTION5chain 'A' and (resid 735 through 928 )A735 - 928

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