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- PDB-5a07: X-ray structure of the mannosyltransferase Ktr4p from S. cerevisi... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5a07 | ||||||
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Title | X-ray structure of the mannosyltransferase Ktr4p from S. cerevisiae in complex with GDP | ||||||
![]() | 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 | ![]() | 192.2 KB | Display | ![]() |
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PDB format | ![]() | 150.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 35.6 KB | Display | |
Data in CIF | ![]() | 53 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5a08SC S: Starting model for refinement C: citing same article ( |
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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: MET / End label comp-ID: MET / Refine code: _ / Auth seq-ID: 71 - 463 / Label seq-ID: 41 - 433
NCS oper: (Code: given Matrix: (0.7457, 0.6628, 0.06883), 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: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50.75 % / 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: Jun 18, 2014 / Details: TOROIDAL MIRROR |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.972422 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. obs: 81509 / % possible obs: 99.1 % / Observed criterion σ(I): 2 / Redundancy: 9.8 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 15.5 |
Reflection shell | Resolution: 1.9→1.94 Å / Redundancy: 9.2 % / Rmerge(I) obs: 0.87 / Mean I/σ(I) obs: 2.3 / % possible all: 98.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 5A08 Resolution: 1.9→86.79 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.95 / SU B: 2.919 / SU ML: 0.083 / Cross valid method: THROUGHOUT / ESU R: 0.118 / ESU R Free: 0.114 / 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: 26.426 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→86.79 Å
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Refine LS restraints |
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