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Yorodumi- PDB-1s4o: Crystal structure of yeast alpha1,2-mannosyltransferase Kre2p/Mnt... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1s4o | |||||||||
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Title | Crystal structure of yeast alpha1,2-mannosyltransferase Kre2p/Mnt1p: binary complex with GDP/Mn | |||||||||
Components | Glycolipid 2-alpha-mannosyltransferase | |||||||||
Keywords | TRANSFERASE / ALPHA/BETA FOLD / NUCLEOTIDE-BINDING DOMAIN / ROSSMANN FOLD / BINARY COMPLEX WITH GDP-MN2+ | |||||||||
Function / homology | Function and homology information alpha-1,2-mannosyltransferase activity / mannosylation / cell wall mannoprotein biosynthetic process / N-glycan processing / protein O-linked glycosylation / protein N-linked glycosylation / fungal-type vacuole membrane / Transferases; Glycosyltransferases; Hexosyltransferases / Golgi medial cisterna / Golgi membrane / Golgi apparatus Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.01 Å | |||||||||
Authors | Lobsanov, Y.D. / Romero, P.A. / Sleno, B. / Yu, B. / Yip, P. / Herscovics, A. / Howell, P.L. | |||||||||
Citation | Journal: J.Biol.Chem. / Year: 2004 Title: Structure of Kre2p/Mnt1p: A YEAST {alpha}1,2-MANNOSYLTRANSFERASE INVOLVED IN MANNOPROTEIN BIOSYNTHESIS Authors: Lobsanov, Y.D. / Romero, P.A. / Sleno, B. / Yu, B. / Yip, P. / Herscovics, A. / Howell, P.L. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1s4o.cif.gz | 172.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1s4o.ent.gz | 133.3 KB | Display | PDB format |
PDBx/mmJSON format | 1s4o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1s4o_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 1s4o_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 1s4o_validation.xml.gz | 33.1 KB | Display | |
Data in CIF | 1s4o_validation.cif.gz | 49 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s4/1s4o ftp://data.pdbj.org/pub/pdb/validation_reports/s4/1s4o | HTTPS FTP |
-Related structure data
Related structure data | 1s4nSC 1s4pC 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
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 41349.199 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: KRE2, MNT1, YDR483W, D8035.26 / Plasmid: pPICZaA / Production host: Pichia pastoris (fungus) / Strain (production host): KM71 / References: UniProt: P27809, EC: 2.4.1.131 |
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-Sugars , 2 types, 2 molecules
#2: Polysaccharide | alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
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#3: Polysaccharide | 2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
-Non-polymers , 5 types, 571 molecules
#4: Chemical | #5: Chemical | ChemComp-CL / #6: Chemical | #7: Chemical | #8: Water | ChemComp-HOH / | |
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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: 2.28 Å3/Da / Density % sol: 46 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: GDP, manganese chloride, PEG 2000 MME, HEPES, SODIUM CHLORIDE, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Dec 27, 2002 / Details: MIRRORS |
Radiation | Monochromator: OSMIC CONFOCAL MULTILAYER MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.01→100 Å / Num. all: 49240 / Num. obs: 49240 / % possible obs: 96.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.11 % / Biso Wilson estimate: 23.8 Å2 / Rmerge(I) obs: 0.056 / Rsym value: 0.056 / Net I/σ(I): 15 |
Reflection shell | Resolution: 2.01→2.08 Å / Rmerge(I) obs: 0.251 / Mean I/σ(I) obs: 3.7 / Rsym value: 0.251 / % possible all: 98.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1S4N Resolution: 2.01→52.42 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 276317.8 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 45.7221 Å2 / ksol: 0.333736 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.01→52.42 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.01→2.14 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
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Xplor file |
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