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

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Basic information

Entry
Database: PDB / ID: 6ajj
TitleCrystal structure of mycolic acid transporter MmpL3 from Mycobacterium smegmatis complexed with ICA38
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 / viral release from host cell by cytolysis / peptidoglycan catabolic process / phosphatidylinositol binding / regulation of membrane potential / cell wall organization / cell wall macromolecule catabolic process / lysozyme / lysozyme 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 / Endolysin T4 type / T4-type lysozyme / : / Glycoside hydrolase, family 24 / Phage lysozyme / Lysozyme domain superfamily / Lysozyme-like domain superfamily
Similarity search - Domain/homology
Chem-J9E / Chem-L6T / (CARBAMOYLMETHYL-CARBOXYMETHYL-AMINO)-ACETIC ACID / Trehalose monomycolate exporter MmpL3 / Endolysin / Trehalose monomycolate exporter MmpL3
Similarity search - Component
Biological speciesMycobacterium smegmatis (bacteria)
Enterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.794 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 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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)107,2879
Polymers104,0081
Non-polymers3,2808
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area300 Å2
ΔGint0 kcal/mol
Surface area39400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.386, 139.731, 140.713
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 / MmpL3 transporter / 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 (strain ATCC 700084 / mc(2)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.: 5 / Source method: obtained synthetically / Formula: C24H46O11
#4: Chemical ChemComp-J9E / 4,6-difluoro-N-(spiro[5.5]undecan-3-yl)-1H-indole-2-carboxamide


Mass: 346.414 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H24F2N2O

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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: 4.13 Å3/Da / Density % sol: 70.22 %
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), 7.5%-17.5% (v/v) polyethylene glycol 2000 (PEG 2000)
PH range: 6.0-7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97891 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 30, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97891 Å / Relative weight: 1
ReflectionResolution: 2.794→50 Å / Num. obs: 43398 / % possible obs: 100 % / Redundancy: 13.1 % / Biso Wilson estimate: 77.28 Å2 / Rmerge(I) obs: 0.079 / Rpim(I) all: 0.023 / Rrim(I) all: 0.082 / Χ2: 0.575 / Net I/σ(I): 4.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.8-2.8513.30.96221300.90.27110.44100
2.85-2.913.20.79421330.9240.2250.8250.457100
2.9-2.9613.10.69921340.9420.1990.7270.452100
2.96-3.0212.90.57121630.9590.1640.5950.468100
3.02-3.0812.70.46521090.9670.1340.4840.483100
3.08-3.1512.10.39621560.9760.1190.4140.487100
3.15-3.2312.70.31821350.9850.0920.3310.509100
3.23-3.3213.80.26121400.9890.0720.2710.545100
3.32-3.4213.80.21521500.9910.0590.2230.554100
3.42-3.5313.70.17521620.9930.0490.1820.592100
3.53-3.6513.70.14421450.9960.040.150.622100
3.65-3.813.50.11921790.9960.0330.1240.664100
3.8-3.9713.20.10121530.9970.0290.1050.712100
3.97-4.1812.10.08721690.9970.0260.0910.751100
4.18-4.4413.60.07421520.9980.0210.0770.761100
4.44-4.7913.80.06621830.9980.0180.0680.757100
4.79-5.2713.50.05921850.9980.0170.0610.672100
5.27-6.0312.40.05622270.9990.0160.0580.553100
6.03-7.5912.90.04422290.9990.0130.0460.481100
7.59-5011.50.03423640.9990.010.0360.599.7

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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: 6AJF

6ajf


Resolution: 2.794→44.466 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 28.12
RfactorNum. reflection% reflection
Rfree0.2527 1996 4.63 %
Rwork0.2182 --
obs0.2198 43136 99.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 250.14 Å2 / Biso mean: 89.4345 Å2 / Biso min: 37.38 Å2
Refinement stepCycle: final / Resolution: 2.794→44.466 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6955 0 226 0 7181
Biso mean--104.17 --
Num. residues----901
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0067334
X-RAY DIFFRACTIONf_angle_d0.9189949
X-RAY DIFFRACTIONf_chiral_restr0.0491130
X-RAY DIFFRACTIONf_plane_restr0.0061230
X-RAY DIFFRACTIONf_dihedral_angle_d18.1584555
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7941-2.86390.32791400.28662820296098
2.8639-2.94130.31311430.276729083051100
2.9413-3.02790.30231370.266829173054100
3.0279-3.12560.34081420.263729343076100
3.1256-3.23730.29151440.252429243068100
3.2373-3.36680.28321410.234529083049100
3.3668-3.520.27481430.224729303073100
3.52-3.70550.2341390.222429183057100
3.7055-3.93750.26971440.214329723116100
3.9375-4.24130.23991390.208629643103100
4.2413-4.66780.23451450.182829523097100
4.6678-5.34220.22821470.197429873134100
5.3422-6.72690.27241450.23130193164100
6.7269-44.47160.22361470.21212987313495
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)
10.98050.1182-0.10831.77071.82243.02270.05410.1833-0.08740.08030.0607-0.27370.37530.0371-0.10570.49820.0655-0.00240.45480.02590.45635.7838-20.91432.3699
21.3509-0.2468-0.45422.69711.77784.04570.0256-0.17290.445-0.11180.2087-0.4277-0.65580.495-0.14420.4901-0.03220.03510.3812-0.08580.60167.18724.253920.2529
31.32750.31860.17471.51451.54733.2011-0.08370.47990.1911-0.56160.147-0.0185-0.6937-0.0888-0.07060.69580.0160.05790.58910.17820.56891.5181-5.4793-14.3643
42.60440.75360.40681.98651.11633.43520.0457-0.78741.09520.07980.0889-0.2413-1.1197-0.0087-0.27170.9060.00380.02010.8209-0.32261.010210.360411.953418.5659
51.58870.3264-0.21590.486-0.54463.34090.2069-0.41350.5050.5722-0.2369-0.0205-1.12010.2614-0.49791.0492-0.17280.0360.7948-0.26080.846612.685213.504511.8629
61.4770.06950.76073.4010.19270.64880.18590.2585-0.1794-0.1935-0.00480.24570.3986-0.0635-0.03310.54150.0298-0.01950.7239-0.09180.5768-14.779125.536652.1384
74.09980.63090.3972.34040.59032.10150.17620.6229-0.2770.270.0690.00910.06090.0483-0.20890.52460.0435-0.02240.5998-0.03480.5688-3.967324.329558.5141
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid -4 through 234 )A-4 - 234
2X-RAY DIFFRACTION2chain 'A' and (resid 235 through 428 )A235 - 428
3X-RAY DIFFRACTION3chain 'A' and (resid 429 through 628 )A429 - 628
4X-RAY DIFFRACTION4chain 'A' and (resid 629 through 695 )A629 - 695
5X-RAY DIFFRACTION5chain 'A' and (resid 696 through 739 )A696 - 739
6X-RAY DIFFRACTION6chain 'A' and (resid 740 through 787 )A740 - 787
7X-RAY DIFFRACTION7chain 'A' and (resid 788 through 928 )A788 - 928

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