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Yorodumi- PDB-4lyp: Crystal Structure of Glycoside Hydrolase Family 5 Mannosidase fro... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4lyp | ||||||
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Title | Crystal Structure of Glycoside Hydrolase Family 5 Mannosidase from Rhizomucor miehei | ||||||
Components | Exo-beta-1,4-mannosidase | ||||||
Keywords | HYDROLASE / Tim Barrel / extracellular protein | ||||||
Function / homology | Glycosidases / TIM Barrel / Alpha-Beta Barrel / Alpha Beta / GUANIDINE Function and homology information | ||||||
Biological species | Rhizomucor miehei (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.28 Å | ||||||
Authors | Jiang, Z.Q. / Zhou, P. / Yang, S.Q. / Liu, Y. / Yan, Q.J. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2014 Title: Structural insights into the substrate specificity and transglycosylation activity of a fungal glycoside hydrolase family 5 beta-mannosidase. Authors: Zhou, P. / Liu, Y. / Yan, Q. / Chen, Z. / Qin, Z. / Jiang, Z. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4lyp.cif.gz | 393 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4lyp.ent.gz | 333.8 KB | Display | PDB format |
PDBx/mmJSON format | 4lyp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ly/4lyp ftp://data.pdbj.org/pub/pdb/validation_reports/ly/4lyp | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 51297.961 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhizomucor miehei (fungus) / Production host: Escherichia coli (E. coli) / References: beta-mannosidase #2: Chemical | ChemComp-GAI / #3: Chemical | #4: Water | ChemComp-HOH / | Sequence details | A SEQUENCE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST. | |
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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: 2.27 Å3/Da / Density % sol: 45.7 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 16% PEG 4000, 0.2 M guanidine hydrochloride, 0.1M HEPES buffer pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 0.9794 Å | |||||||||
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: May 21, 2012 | |||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 | |||||||||
Reflection | Resolution: 1.28→86 Å / Num. all: 235043 / Num. obs: 205153 / % possible obs: 87.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 9.9 % / Rmerge(I) obs: 0.052 | |||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.28→20 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.966 / SU B: 0.983 / SU ML: 0.019 / Cross valid method: THROUGHOUT / ESU R: 0.043 / ESU R Free: 0.043 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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: 14.159 Å2
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Refinement step | Cycle: LAST / Resolution: 1.28→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.277→1.311 Å / Total num. of bins used: 20
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