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Yorodumi- PDB-5ezm: Crystal Structure of ArnT from Cupriavidus metallidurans in the a... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ezm | |||||||||
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Title | Crystal Structure of ArnT from Cupriavidus metallidurans in the apo state | |||||||||
Components | 4-amino-4-deoxy-L-arabinose transferase or related glycosyltransferases of PMT family | |||||||||
Keywords | TRANSFERASE / membrane protein / lipid glycosyltransferase / zinc / GT-C fold / Structural Genomics / PSI-Biology / New York Consortium on Membrane Protein Structure / NYCOMPS | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Cupriavidus metallidurans (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.7 Å | |||||||||
Authors | Petrou, V.I. / Clarke, O.B. / Tomasek, D. / Banerjee, S. / Rajashankar, K.R. / Mancia, F. / New York Consortium on Membrane Protein Structure (NYCOMPS) | |||||||||
Funding support | United States, 2items
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Citation | Journal: Science / Year: 2016 Title: Structures of aminoarabinose transferase ArnT suggest a molecular basis for lipid A glycosylation. Authors: Petrou, V.I. / Herrera, C.M. / Schultz, K.M. / Clarke, O.B. / Vendome, J. / Tomasek, D. / Banerjee, S. / Rajashankar, K.R. / Belcher Dufrisne, M. / Kloss, B. / Kloppmann, E. / Rost, B. / ...Authors: Petrou, V.I. / Herrera, C.M. / Schultz, K.M. / Clarke, O.B. / Vendome, J. / Tomasek, D. / Banerjee, S. / Rajashankar, K.R. / Belcher Dufrisne, M. / Kloss, B. / Kloppmann, E. / Rost, B. / Klug, C.S. / Trent, M.S. / Shapiro, L. / Mancia, F. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ezm.cif.gz | 242.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ezm.ent.gz | 189.4 KB | Display | PDB format |
PDBx/mmJSON format | 5ezm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ez/5ezm ftp://data.pdbj.org/pub/pdb/validation_reports/ez/5ezm | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 63212.332 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Cupriavidus metallidurans (strain ATCC 43123 / DSM 2839 / NBRC 102507 / CH34) (bacteria) Strain: ATCC 43123 / DSM 2839 / NBRC 102507 / CH34 / Gene: Rmet_4828 / Plasmid: pNYCOMPS-N / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q1LDT6, EC: 2.4.2.43 |
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-Non-polymers , 8 types, 90 molecules
#2: Chemical | ChemComp-ZN / | ||||||||||
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#3: Chemical | ChemComp-DSL / | ||||||||||
#4: Chemical | ChemComp-MPG / [( #5: Chemical | #6: Chemical | #7: Chemical | ChemComp-PC / | #8: Chemical | ChemComp-EPE / | #9: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.81 Å3/Da / Density % sol: 56.2 % |
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Crystal grow | Temperature: 295 K / Method: lipidic cubic phase / pH: 6.5 Details: Protein buffer: HEPES, NaCl, DDM, Tcep; Precipitant: MES, PEG500 DME, Manganese chloride, Sodium formate, Tcep; LCP lipids: 99.2% monoolein, 0.8% decaprenyl phosphate |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å | |||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 22, 2014 | |||||||||||||||||||||||||||
Radiation | Monochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 2.7→47.41 Å / Num. obs: 20291 / % possible obs: 100 % / Redundancy: 27.4 % / Biso Wilson estimate: 65.19 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.39 / Rpim(I) all: 0.077 / Net I/σ(I): 63.6 / Num. measured all: 555326 / Scaling rejects: 21936 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: 0
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-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.7→47.405 Å / SU ML: 0.43 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 30.52 / Stereochemistry target values: ML Details: Author's note for MPG: Densities corresponding to partially ordered monoolein molecules (1-MONOOLEOYL-RAC-GLYCEROL) were modelled using alkane chains of varying length (n=4-14). We cannot ...Details: Author's note for MPG: Densities corresponding to partially ordered monoolein molecules (1-MONOOLEOYL-RAC-GLYCEROL) were modelled using alkane chains of varying length (n=4-14). We cannot exclude that a small subset of these densities may correspond to partially ordered detergent or poly-prenyl lipid molecules. For DSL: Only the last three prenyl groups of decaprenyl phosphate appear ordered and have been modelled in the structure.
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 143.6 Å2 / Biso mean: 75.747 Å2 / Biso min: 31.25 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.7→47.405 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14
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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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