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- PDB-5a08: X-ray structure of the mannosyltransferase Ktr4p from S. cerevisiae -
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Open data
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Basic information
Entry | Database: PDB / ID: 5a08 | ||||||
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Title | X-ray structure of the mannosyltransferase Ktr4p from S. cerevisiae | ||||||
![]() | PROBABLE MANNOSYLTRANSFERASE KTR4 | ||||||
![]() | TRANSFERASE / GOLGI APPARATUS / MANNOSYLTRANSFERASES / GT-A / MEMBRANE PROTEINS | ||||||
Function / homology | ![]() alpha-1,2-mannosyltransferase activity / mannosylation / mannosyltransferase activity / cell wall mannoprotein biosynthetic process / fungal-type vacuole / protein O-linked glycosylation / protein N-linked glycosylation / Transferases; Glycosyltransferases; Hexosyltransferases / Golgi apparatus / membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Possner, D.D.D. / Guy, J.E. | ||||||
![]() | ![]() Title: Structure of the Glycosyltransferase Ktr4P from Saccharomyces Cerevisiae Authors: Possner, D.D.D. / Claesson, M. / Guy, J.E. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 185.1 KB | Display | ![]() |
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PDB format | ![]() | 146.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 445.5 KB | Display | ![]() |
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Full document | ![]() | 451.5 KB | Display | |
Data in XML | ![]() | 33.9 KB | Display | |
Data in CIF | ![]() | 49.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5a07C ![]() 1s4nS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: HIS / Beg label comp-ID: HIS / End auth comp-ID: TYR / End label comp-ID: TYR / Refine code: _ / Auth seq-ID: 71 - 464 / Label seq-ID: 41 - 434
NCS oper: (Code: given Matrix: (0.7453, 0.6631, 0.0689), Vector: |
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Components
#1: Protein | Mass: 51226.426 Da / Num. of mol.: 2 / Fragment: LUMENAL PART, RESIDUES 33-464 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: S288C / Plasmid: PNIC28-BSA4 / Production host: ![]() ![]() References: UniProt: P38131, Transferases; Glycosyltransferases; Hexosyltransferases #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.36 Å3/Da / Density % sol: 47.95 % / Description: NONE |
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Crystal grow | pH: 6.5 Details: 0.1M NA-CACODYLATE, PH 6.5 0.2M CAOAC 18% (W/V) PEG8000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PIXEL / Detector: PIXEL / Date: May 17, 2014 / Details: KB MIRROR |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8726 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. obs: 49674 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 7.8 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 13.8 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 8 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 3 / % possible all: 97 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1S4N Resolution: 2.21→85.74 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.933 / SU B: 4.68 / SU ML: 0.117 / Cross valid method: THROUGHOUT / ESU R: 0.225 / ESU R Free: 0.176 / Stereochemistry target values: MAXIMUM LIKELIHOOD 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.972 Å2
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Refinement step | Cycle: LAST / Resolution: 2.21→85.74 Å
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Refine LS restraints |
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