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Yorodumi- PDB-7bvh: Crystal structure of arabinosyltransferase EmbC2-AcpM2 complex fr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7bvh | |||||||||||||||
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Title | Crystal structure of arabinosyltransferase EmbC2-AcpM2 complex from Mycobacterium smegmatis complexed with di-arabinose | |||||||||||||||
Components |
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Keywords | TRANSFERASE / cell wall synthesis / arabinosyltransferase / drug target | |||||||||||||||
Function / homology | Function and homology information indolylacetylinositol arabinosyltransferase / indolylacetylinositol arabinosyltransferase activity / arabinosyltransferase activity / Actinobacterium-type cell wall biogenesis / lipid A biosynthetic process / Transferases; Glycosyltransferases; Pentosyltransferases / acyl binding / acyl carrier activity / cell wall organization / plasma membrane / cytosol Similarity search - Function | |||||||||||||||
Biological species | Mycolicibacterium smegmatis MC2 155 (bacteria) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.3 Å | |||||||||||||||
Authors | Zhao, Y. / Zhang, L. / Wu, L.J. / Wang, Q. / Li, J. / Besra, G.S. / Rao, Z.H. | |||||||||||||||
Funding support | China, United Kingdom, 4items
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Citation | Journal: Science / Year: 2020 Title: Structures of cell wall arabinosyltransferases with the anti-tuberculosis drug ethambutol. Authors: Lu Zhang / Yao Zhao / Yan Gao / Lijie Wu / Ruogu Gao / Qi Zhang / Yinan Wang / Chengyao Wu / Fangyu Wu / Sudagar S Gurcha / Natacha Veerapen / Sarah M Batt / Wei Zhao / Ling Qin / Xiuna Yang ...Authors: Lu Zhang / Yao Zhao / Yan Gao / Lijie Wu / Ruogu Gao / Qi Zhang / Yinan Wang / Chengyao Wu / Fangyu Wu / Sudagar S Gurcha / Natacha Veerapen / Sarah M Batt / Wei Zhao / Ling Qin / Xiuna Yang / Manfu Wang / Yan Zhu / Bing Zhang / Lijun Bi / Xian'en Zhang / Haitao Yang / Luke W Guddat / Wenqing Xu / Quan Wang / Jun Li / Gurdyal S Besra / Zihe Rao / Abstract: The arabinosyltransferases EmbA, EmbB, and EmbC are involved in cell wall synthesis and are recognized as targets for the anti-tuberculosis drug ethambutol. In this study, we determined cryo- ...The arabinosyltransferases EmbA, EmbB, and EmbC are involved in cell wall synthesis and are recognized as targets for the anti-tuberculosis drug ethambutol. In this study, we determined cryo-electron microscopy and x-ray crystal structures of mycobacterial EmbA-EmbB and EmbC-EmbC complexes in the presence of their glycosyl donor and acceptor substrates and with ethambutol. These structures show how the donor and acceptor substrates bind in the active site and how ethambutol inhibits arabinosyltransferases by binding to the same site as both substrates in EmbB and EmbC. Most drug-resistant mutations are located near the ethambutol binding site. Collectively, our work provides a structural basis for understanding the biochemical function and inhibition of arabinosyltransferases and the development of new anti-tuberculosis agents. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7bvh.cif.gz | 892.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7bvh.ent.gz | 743.2 KB | Display | PDB format |
PDBx/mmJSON format | 7bvh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7bvh_validation.pdf.gz | 3.3 MB | Display | wwPDB validaton report |
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Full document | 7bvh_full_validation.pdf.gz | 3.4 MB | Display | |
Data in XML | 7bvh_validation.xml.gz | 82.4 KB | Display | |
Data in CIF | 7bvh_validation.cif.gz | 110.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bv/7bvh ftp://data.pdbj.org/pub/pdb/validation_reports/bv/7bvh | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 2 types, 4 molecules ABCD
#1: Protein | Mass: 119999.414 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycolicibacterium smegmatis MC2 155 (bacteria) Gene: embC, MSMEI_6219 Production host: Mycolicibacterium smegmatis MC2 155 (bacteria) References: UniProt: I7FMU5, UniProt: A0R612*PLUS, indolylacetylinositol arabinosyltransferase #2: Protein | Mass: 10743.876 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria) References: UniProt: A0R0B3 |
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-Sugars , 3 types, 12 molecules
#3: Polysaccharide | #4: Polysaccharide | alpha-D-glucopyranose-(1-4)-beta-D-glucopyranose / beta-maltose #7: Sugar | ChemComp-BXY / |
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-Non-polymers , 2 types, 4 molecules
#5: Chemical | #6: Chemical | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.24 Å3/Da / Density % sol: 71 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop Details: 50mM HEPES (pH 6.8~7.5), 100mM NaCl, 5-10% (v/v) polyethylene glycol 4000, 20-30% (v/v) polyethylene glycol 200 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 6, 2018 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3.3→134.458 Å / Num. all: 67591 / Num. obs: 67591 / % possible obs: 99.9 % / Redundancy: 19.9 % / Rpim(I) all: 0.027 / Rrim(I) all: 0.118 / Rsym value: 0.114 / Net I/av σ(I): 1 / Net I/σ(I): 12.2 / Num. measured all: 1344351 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 3.3→49.67 Å / Cor.coef. Fo:Fc: 0.788 / Cor.coef. Fo:Fc free: 0.73 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 5.608 / SU Rfree Blow DPI: 0.427
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Displacement parameters | Biso max: 230.27 Å2 / Biso mean: 78.18 Å2 / Biso min: 3 Å2
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Refine analyze | Luzzati coordinate error obs: 0.52 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.3→49.67 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.3→3.39 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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