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Yorodumi- PDB-5mm1: Dolichyl phosphate mannose synthase in complex with GDP and dolic... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5mm1 | ||||||||||||
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Title | Dolichyl phosphate mannose synthase in complex with GDP and dolichyl phosphate mannose | ||||||||||||
Components | Dolichol monophosphate mannose synthase | ||||||||||||
Keywords | MEMBRANE PROTEIN / Dolichol phosphate mannose synthase / enzyme / integral membrane protein / protein glycosylation / product complex / GDP / dolichyl phosphate mannose | ||||||||||||
Function / homology | Function and homology information dolichyl-phosphate beta-D-mannosyltransferase / dolichyl-phosphate beta-D-mannosyltransferase activity / dolichol metabolic process / dolichol-linked oligosaccharide biosynthetic process / GPI anchor biosynthetic process / protein O-linked mannosylation / polysaccharide biosynthetic process / metal ion binding / plasma membrane Similarity search - Function | ||||||||||||
Biological species | Pyrococcus furiosus (archaea) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||||||||
Authors | Gandini, R. / Reichenbach, T. / Tan, T.C. / Divne, C. | ||||||||||||
Funding support | Sweden, 3items
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Citation | Journal: Nat Commun / Year: 2017 Title: Structural basis for dolichylphosphate mannose biosynthesis. Authors: Gandini, R. / Reichenbach, T. / Tan, T.C. / Divne, C. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5mm1.cif.gz | 88.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5mm1.ent.gz | 64.3 KB | Display | PDB format |
PDBx/mmJSON format | 5mm1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5mm1_validation.pdf.gz | 989.4 KB | Display | wwPDB validaton report |
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Full document | 5mm1_full_validation.pdf.gz | 1004 KB | Display | |
Data in XML | 5mm1_validation.xml.gz | 17.3 KB | Display | |
Data in CIF | 5mm1_validation.cif.gz | 21.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mm/5mm1 ftp://data.pdbj.org/pub/pdb/validation_reports/mm/5mm1 | HTTPS FTP |
-Related structure data
Related structure data | 5mlzSC 5mm0C 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
#1: Protein | Mass: 42684.809 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: N-terminal hexa-histdine tag and TEV protease cleavage site precedes the protein sequences Source: (gene. exp.) Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1) (archaea) Gene: PF0058 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8U4M3 |
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#2: Chemical | ChemComp-GDP / |
#3: Chemical | ChemComp-MJC / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.69 Å3/Da / Density % sol: 66.68 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 0.2 M potassium chloride, 0.1 M trisodium citrate (pH 5.5), 37% (v/v) pentaerythritol propoxylate (5/4 PO/OH), 50 mM Hepes (pH 7.5), 150 mM NaCl, 10% (v/v) glycerol, 0.05% LDAO, 5 mM GDP- ...Details: 0.2 M potassium chloride, 0.1 M trisodium citrate (pH 5.5), 37% (v/v) pentaerythritol propoxylate (5/4 PO/OH), 50 mM Hepes (pH 7.5), 150 mM NaCl, 10% (v/v) glycerol, 0.05% LDAO, 5 mM GDP-mannose, 5 mM MgCl2, 0.25 mM C55 dolichyl phosphate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 13, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97857 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→48.385 Å / Num. obs: 19735 / % possible obs: 99.6 % / Redundancy: 12.8 % / Net I/σ(I): 14 |
Reflection shell | Resolution: 2.6→2.7 Å / Mean I/σ(I) obs: 1.1 / Rsym value: 3.535 / % possible all: 99.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5MLZ Resolution: 2.6→48.39 Å / SU ML: 0.52 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 42.41
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→48.39 Å
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Refine LS restraints |
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LS refinement shell |
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