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- PDB-7c2n: Crystal structure of mycolic acid transporter MmpL3 from Mycobact... -

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Basic information

Entry
Database: PDB / ID: 7c2n
TitleCrystal structure of mycolic acid transporter MmpL3 from Mycobacterium smegmatis complexed with SPIRO
ComponentsDrug exporters of the RND superfamily-like protein,Endolysin
KeywordsMEMBRANE PROTEIN
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-FG0 / Chem-L6T / (CARBAMOYLMETHYL-CARBOXYMETHYL-AMINO)-ACETIC ACID / Endolysin / Trehalose monomycolate exporter MmpL3 / Trehalose monomycolate exporter MmpL3
Similarity search - Component
Biological speciesMycolicibacterium smegmatis MC2 155 (bacteria)
Enterobacteria phage RB59 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.82 Å
AuthorsZhang, B. / Yang, X. / Hu, T. / Rao, Z.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)81520108019 China
Chinese Academy of Sciences2017YFC0840300 China
CitationJournal: J.Mol.Biol. / Year: 2020
Title: Structural Basis for the Inhibition of Mycobacterial MmpL3 by NITD-349 and SPIRO.
Authors: Yang, X. / Hu, T. / Yang, X. / Xu, W. / Yang, H. / Guddat, L.W. / Zhang, B. / Rao, Z.
History
DepositionMay 8, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 2, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 16, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 29, 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

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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)106,2979
Polymers103,0071
Non-polymers3,2918
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area290 Å2
ΔGint1 kcal/mol
Surface area39620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.490, 140.386, 145.229
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: 103006.500 Da / Num. of mol.: 1 / Mutation: C803T,C846A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycolicibacterium smegmatis MC2 155 (bacteria), (gene. exp.) Enterobacteria phage RB59 (virus)
Strain: MC2 155 / Gene: mmpL3, MSMEI_0243, e, RB59_126 / Plasmid: pM261
Production host: Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: I7G2R2, UniProt: A0A097J809, UniProt: A0QP27*PLUS, lysozyme
#2: Sugar
ChemComp-L6T / alpha-D-glucopyranosyl 6-O-dodecyl-alpha-D-glucopyranoside


Type: saccharide / Mass: 510.615 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Formula: C24H46O11
#3: 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
#4: Chemical ChemComp-FG0 / 1'-(2,3-dihydro-1,4-benzodioxin-6-ylmethyl)spiro[6,7-dihydrothieno[3,2-c]pyran-4,4'-piperidine]


Mass: 357.467 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H23NO3S
Has ligand of interestN

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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: 4.46 Å3/Da / Density % sol: 72.43 %
Crystal growTemperature: 293 K / Method: evaporation / pH: 6.5
Details: 15% (v/v) polyethylene glycol monomethyl ether 350 (PEGMME 350), 50 mM ADA (N-(2-Acetamido) iminodiacetic acid) (pH 6.5) and 12.5% (v/v) polyethylene glycol 2000 (PEG2000), protein ...Details: 15% (v/v) polyethylene glycol monomethyl ether 350 (PEGMME 350), 50 mM ADA (N-(2-Acetamido) iminodiacetic acid) (pH 6.5) and 12.5% (v/v) polyethylene glycol 2000 (PEG2000), protein concentration 5mg/ml, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NFPSS / Beamline: BL19U1 / Wavelength: 0.978 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 18, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.82→44.54 Å / Num. obs: 43256 / % possible obs: 99.4 % / Redundancy: 5.422 % / Biso Wilson estimate: 81.978 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.077 / Rrim(I) all: 0.085 / Χ2: 1.057 / Net I/σ(I): 15.18 / Num. measured all: 234546 / Scaling rejects: 10
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.82-2.895.4441.31.3816622319630530.6241.43495.5
2.89-2.975.61.0541.8217311309430910.7361.15999.9
2.97-3.065.4820.7992.3316418299829950.8190.88299.9
3.06-3.155.1360.589314817289728850.8610.65599.6
3.15-3.255.4760.4384.1615541284228380.9260.48499.9
3.25-3.375.760.3475.5315945277327680.9640.38199.8
3.37-3.495.7290.2447.5515085263626330.9810.26899.9
3.49-3.645.6730.1879.7214495255725550.9890.20599.9
3.64-3.85.5880.1313.4913742246124590.9930.14499.9
3.8-3.985.3840.09916.6412646235223490.9950.1199.9
3.98-4.24.9410.07420.0111024224422310.9960.08399.4
4.2-4.455.5950.0625.5611984214421420.9980.06699.9
4.45-4.765.5190.0529.6410961198919860.9980.05599.8
4.76-5.145.4460.04530.8410277188918870.9980.0599.9
5.14-5.635.3040.05129.489207173917360.9980.05799.8
5.63-6.34.7950.04728.67476157115590.9980.05299.2
6.3-7.275.4680.03637.417677140414040.9990.04100
7.27-8.915.3020.02744.396363120212000.9990.0399.8
8.91-12.64.6820.02546.3744399549480.9990.02899.4
12.6-44.544.6850.02446.5125165625370.9980.02995.6

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XSCALEdata scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6AJH

6ajh


Resolution: 2.82→44.54 Å / SU ML: 0.46 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 31.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2734 2001 4.63 %
Rwork0.2324 41238 -
obs0.2343 43239 99.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 204.09 Å2 / Biso mean: 88.3065 Å2 / Biso min: 36.35 Å2
Refinement stepCycle: final / Resolution: 2.82→44.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6952 0 226 0 7178
Biso mean--102.08 --
Num. residues----900
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 (%)
2.82-2.890.45041400.36892804294495
2.89-2.970.39441400.325629053045100
2.97-3.050.35551400.317429233063100
3.05-3.150.34341440.296428823026100
3.15-3.260.33141430.274829303073100
3.26-3.390.30611400.247429253065100
3.39-3.550.31131380.238929433081100
3.55-3.740.26381500.230429283078100
3.74-3.970.27621350.216229593094100
3.97-4.280.20431480.20522934308299
4.28-4.710.28031440.197229723116100
4.71-5.390.22611420.197429953137100
5.39-6.780.28031450.24729983143100
6.78-44.540.25511520.22943140329299

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