+Open data
-Basic information
Entry | Database: PDB / ID: 2zai | ||||||
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Title | Crystal structure of the soluble domain of STT3 from P. furiosus | ||||||
Components | Oligosaccharyl transferase stt3 subunit related protein | ||||||
Keywords | TRANSFERASE / Multi-domain proteins (alpha and beta) | ||||||
Function / homology | Function and homology information dolichyl-phosphooligosaccharide-protein glycotransferase / dolichyl-diphosphooligosaccharide-protein glycotransferase activity / protein N-linked glycosylation via asparagine / post-translational protein modification / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | Pyrococcus furiosus (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Maita, N. | ||||||
Citation | Journal: Embo J. / Year: 2008 Title: Structure-guided identification of a new catalytic motif of oligosaccharyltransferase Authors: Igura, M. / Maita, N. / Kamishikiryo, J. / Yamada, M. / Obita, T. / Maenaka, K. / Kohda, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2zai.cif.gz | 372.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2zai.ent.gz | 303.6 KB | Display | PDB format |
PDBx/mmJSON format | 2zai.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2zai_validation.pdf.gz | 470.7 KB | Display | wwPDB validaton report |
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Full document | 2zai_full_validation.pdf.gz | 527.4 KB | Display | |
Data in XML | 2zai_validation.xml.gz | 68.7 KB | Display | |
Data in CIF | 2zai_validation.cif.gz | 93.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/za/2zai ftp://data.pdbj.org/pub/pdb/validation_reports/za/2zai | HTTPS FTP |
-Related structure data
Related structure data | 2zagSC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
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Unit cell |
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-Components
#1: Protein | Mass: 55976.117 Da / Num. of mol.: 4 / Fragment: Soluble domain, UNP residues 471-967 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus furiosus (archaea) / Strain: DSM 3638 / Gene: PF0156 / Plasmid: pET21d / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q8U4D2 #2: Chemical | ChemComp-CA / #3: Chemical | ChemComp-CL / #4: 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: 3.01 Å3/Da / Density % sol: 59.1 % |
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Crystal grow | Temperature: 303 K / Method: vapor diffusion, hanging drop / pH: 9 Details: 22% PEG 4000, 0.3M NaCOOH, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 303K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.96419 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 5, 2005 / Details: mirrors |
Radiation | Monochromator: silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.96419 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→40 Å / Num. all: 75298 / Num. obs: 75226 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.1 % / Biso Wilson estimate: 57.6 Å2 / Rmerge(I) obs: 0.081 / Net I/σ(I): 12.4 |
Reflection shell | Resolution: 2.7→2.8 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.443 / Mean I/σ(I) obs: 3.5 / Num. unique all: 7371 / % possible all: 99.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2ZAG Resolution: 2.7→20 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 44.15 Å2
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Refinement step | Cycle: LAST / Resolution: 2.7→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.8 Å
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