+Open data
-Basic information
Entry | Database: PDB / ID: 5ylh | ||||||
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Title | Structure of GH113 beta-1,4-mannanase | ||||||
Components | beta-1,4-mannanase | ||||||
Keywords | HYDROLASE / beta-1 / 4-mannanase | ||||||
Function / homology | Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta / 1,4-beta-xylanase Function and homology information | ||||||
Biological species | Amphibacillus xylanus NBRC 15112 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.29 Å | ||||||
Authors | Jiang, Z.Q. / You, X. / Yang, S.Q. / Huang, P. / Ma, J.W. | ||||||
Citation | Journal: J. Biol. Chem. / Year: 2018 Title: Structural insights into the catalytic mechanism of a novel glycoside hydrolase family 113 beta-1,4-mannanase from Amphibacillus xylanus Authors: You, X. / Qin, Z. / Yan, Q. / Yang, S. / Li, Y. / Jiang, Z. #1: Journal: To Be Published Title: Structure of GH113 beta-1,4-mannanase at 2.3 Angstroms resolution Authors: Jiang, Z.Q. / You, X. / Yang, S.Q. / Huang, P. / Ma, J.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ylh.cif.gz | 138.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ylh.ent.gz | 108.2 KB | Display | PDB format |
PDBx/mmJSON format | 5ylh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5ylh_validation.pdf.gz | 437.5 KB | Display | wwPDB validaton report |
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Full document | 5ylh_full_validation.pdf.gz | 445.6 KB | Display | |
Data in XML | 5ylh_validation.xml.gz | 24.9 KB | Display | |
Data in CIF | 5ylh_validation.cif.gz | 34.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yl/5ylh ftp://data.pdbj.org/pub/pdb/validation_reports/yl/5ylh | HTTPS FTP |
-Related structure data
Related structure data | 5yliC 5ylkC 5yllC 5z4tC 3civS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 36281.508 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Amphibacillus xylanus NBRC 15112 (bacteria) Strain: NBRC 15112 / Gene: AXY_22370 / Production host: Escherichia coli (E. coli) / References: UniProt: K0J0N5 #2: 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: 2.48 Å3/Da / Density % sol: 50.31 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG4000, HEPES Na, 2-Propylalcohol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.978 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 3, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978 Å / Relative weight: 1 |
Reflection | Resolution: 2.29→30.38 Å / Num. obs: 29076 / % possible obs: 88 % / Observed criterion σ(I): 1 / Redundancy: 3.7 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 9.8 |
Reflection shell | Resolution: 2.29→30.383 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.122 / Mean I/σ(I) obs: 4.6 / Rsym value: 0.118 / % possible all: 88 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3CIV Resolution: 2.29→2.38 Å / Cross valid method: FREE R-VALUE
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Refinement step | Cycle: LAST / Resolution: 2.29→2.38 Å
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LS refinement shell | Highest resolution: 2.29 Å |