[English] 日本語
Yorodumi
- PDB-6ajh: Crystal structure of mycolic acid transporter MmpL3 from Mycobact... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6ajh
TitleCrystal structure of mycolic acid transporter MmpL3 from Mycobacterium smegmatis complexed with AU1235
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-9ZF / 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: 2.818 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) 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)107,45610
Polymers104,0081
Non-polymers3,4489
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area290 Å2
ΔGint1 kcal/mol
Surface area39280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.967, 141.167, 144.214
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
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-9ZF / 1-(2-adamantyl)-3-[2,3,4-tris(fluoranyl)phenyl]urea


Mass: 324.341 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H19F3N2O
#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-MHA / (CARBAMOYLMETHYL-CARBOXYMETHYL-AMINO)-ACETIC ACID / N-(2-ACETAMIDO)IMINODIACETIC ACID


Mass: 190.154 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H10N2O5 / Comment: pH buffer*YM

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 4.26 Å3/Da / Density % sol: 71.1 %
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

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97915 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 16, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 43073 / % possible obs: 99.7 % / Redundancy: 5.9 % / Biso Wilson estimate: 66.99 Å2 / Rmerge(I) obs: 0.095 / Rpim(I) all: 0.042 / Rrim(I) all: 0.096 / Χ2: 1.047 / Net I/σ(I): 7.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allΧ2% possible allRrim(I) all
2.8-2.95.70.95642130.6860.4330.86199.4
2.9-3.025.70.70742270.8070.3190.88599.40.777
3.02-3.155.70.48342600.8940.2180.94999.60.531
3.15-3.325.80.31542480.9520.1411.00499.80.345
3.32-3.535.90.20842710.9760.0931.0841000.228
3.53-3.860.13742980.9880.061.0931000.15
3.8-4.186.10.09443120.9940.0411.0661000.103
4.18-4.7960.07643270.9960.0331.1931000.083
4.79-6.035.90.06643750.9960.0291.2471000.072
6.03-505.80.03145420.9990.0141.05299.20.034

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
SCALEPACKdata scaling
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6AJF

6ajf


Resolution: 2.818→43.484 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.47
RfactorNum. reflection% reflection
Rfree0.2471 2117 4.92 %
Rwork0.2192 --
obs0.2205 42987 98.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 251.31 Å2 / Biso mean: 76.9967 Å2 / Biso min: 25.09 Å2
Refinement stepCycle: final / Resolution: 2.818→43.484 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6952 0 237 0 7189
Biso mean--104.02 --
Num. residues----900
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0047339
X-RAY DIFFRACTIONf_angle_d1.0399961
X-RAY DIFFRACTIONf_chiral_restr0.0321134
X-RAY DIFFRACTIONf_plane_restr0.0061233
X-RAY DIFFRACTIONf_dihedral_angle_d22.8052900
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8185-2.8840.37971450.32282233237884
2.884-2.95610.35631230.294827332856100
2.9561-3.0360.31251390.29052677281699
3.036-3.12540.33711300.270427462876100
3.1254-3.22620.30981360.268827382874100
3.2262-3.34150.31331590.256827062865100
3.3415-3.47520.26931310.238127532884100
3.4752-3.63330.27911270.231127362863100
3.6333-3.82470.24411420.213227552897100
3.8247-4.06420.22111470.208827562903100
4.0642-4.37770.21971330.195627682901100
4.3777-4.81780.24431410.185427752916100
4.8178-5.51370.21381670.194627722939100
5.5137-6.94220.24651590.220327932952100
6.9422-43.48870.19971380.20192929306798
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)
11.8922-0.09280.10990.1136-0.4493.17510.31240.5143-0.04090.1099-0.5028-0.34090.26750.7698-0.0040.55970.0455-0.03480.44440.08490.440149.6379-5.7075-31.3711
20.77040.3163-0.69081.3973-1.11792.2906-0.0834-0.14130.009-0.1184-0.01510.04490.33060.05220.10460.3441-0.038-0.00760.34640.00940.353938.7459-18.1231-5.0419
30.99610.3747-0.42161.3115-0.99440.75930.17050.29470.44870.12810.29040.6191-0.5179-0.6164-0.20670.62480.16490.00690.52960.1070.79326.28273.2455-16.8777
41.2921-0.18160.11741.2019-0.70892.22660.0356-0.28330.24110.34750.15190.1184-0.54720.0796-0.15150.4442-0.02680.07940.3499-0.06860.401938.3473-2.50444.677
50.14090.0587-0.53030.42630.7123.47840.241-0.2145-0.30360.11980.46970.069-0.85430.6080.30570.62670.3557-0.04820.73420.35110.681139.972522.92-29.6287
63.4630.6092-0.24981.7773-0.12831.62690.13640.0015-0.0389-0.11050.0259-0.0952-0.0182-0.0612-0.12420.25010.0152-0.00180.29730.04540.376648.517722.5795-60.2442
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid -4 through 36 )A-4 - 36
2X-RAY DIFFRACTION2chain 'A' and (resid 37 through 330 )A37 - 330
3X-RAY DIFFRACTION3chain 'A' and (resid 331 through 436 )A331 - 436
4X-RAY DIFFRACTION4chain 'A' and (resid 437 through 716 )A437 - 716
5X-RAY DIFFRACTION5chain 'A' and (resid 717 through 760 )A717 - 760
6X-RAY DIFFRACTION6chain 'A' and (resid 761 through 929 )A761 - 929

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more