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Yorodumi- PDB-6pnl: Structure of Epimerase Mth375 from the thermophilic pseudomurein-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6pnl | ||||||
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Title | Structure of Epimerase Mth375 from the thermophilic pseudomurein-containing methanogen Methanothermobacter thermautotrophicus | ||||||
Components | UDP-glucose 4-epimerase related protein | ||||||
Keywords | ISOMERASE / Pseudomurein / UDP-N-acetylglucosamine / epimerase / cell wall / Methanothermobacter | ||||||
Function / homology | NAD-dependent epimerase/dehydratase / NAD dependent epimerase/dehydratase family / NAD(P)-binding domain superfamily / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / URIDINE-5'-DIPHOSPHATE / UDP-glucose 4-epimerase related protein Function and homology information | ||||||
Biological species | Methanothermobacter thermautotrophicus (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.01 Å | ||||||
Authors | Carbone, V. / Schofield, L.R. / Sutherland-Smith, A.J. / Ronimus, R.S. | ||||||
Funding support | New Zealand, 1items
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Citation | Journal: To Be Published Title: Structure of a UDP-GALE 4-epimerase (Mth375) from the thermophilic pseudomurein-containing methanogen Methanothermobacter thermautotrophicus Authors: Carbone, V. / Schofield, L.R. / Sutherland-Smith, A.J. / Ronimus, R.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6pnl.cif.gz | 95.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6pnl.ent.gz | 68 KB | Display | PDB format |
PDBx/mmJSON format | 6pnl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6pnl_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 6pnl_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 6pnl_validation.xml.gz | 17.1 KB | Display | |
Data in CIF | 6pnl_validation.cif.gz | 24.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pn/6pnl ftp://data.pdbj.org/pub/pdb/validation_reports/pn/6pnl | HTTPS FTP |
-Related structure data
Related structure data | 6pmhSC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 42049.320 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanothermobacter thermautotrophicus (archaea) Production host: Escherichia coli (E. coli) / References: UniProt: O26475 |
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-Non-polymers , 5 types, 245 molecules
#2: Chemical | ChemComp-NAD / | ||||
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#3: Chemical | ChemComp-UDP / | ||||
#4: Chemical | #5: Chemical | ChemComp-SO4 / | #6: Water | ChemComp-HOH / | |
-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: 2.4 Å3/Da / Density % sol: 48.78 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.1 M Sodium chloride, 1.6 M Ammonium sulfate 0.1 M Sodium HEPES, 3.0% w/v 1,8-Diaminooctane |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.953653 Å | ||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 23, 2017 | ||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.953653 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 2.01→46.52 Å / Num. obs: 28060 / % possible obs: 99.7 % / Redundancy: 19.3 % / CC1/2: 0.996 / Rmerge(I) obs: 0.192 / Net I/σ(I): 16.1 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | ||||||
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Phasing MR | R rigid body: 0.351
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6PMH Resolution: 2.01→46.52 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.944 / SU B: 3.015 / SU ML: 0.083 / SU R Cruickshank DPI: 0.1551 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.155 / ESU R Free: 0.133 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 68.01 Å2 / Biso mean: 22.501 Å2 / Biso min: 10.38 Å2
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Refinement step | Cycle: final / Resolution: 2.01→46.52 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.014→2.066 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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