+Open data
-Basic information
Entry | Database: PDB / ID: 5z4t | |||||||||
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Title | Complex structure - AxMan113A-M3 | |||||||||
Components | beta-1,4-mannanas | |||||||||
Keywords | HYDROLASE / Complex | |||||||||
Function / homology | Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta / 4beta-beta-mannobiose / 1,4-beta-xylanase Function and homology information | |||||||||
Biological species | Amphibacillus xylanus (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.68 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 fromAmphibacillus xylanus Authors: You, X. / Qin, Z. / Yan, Q. / Yang, S. / Li, Y. / Jiang, Z. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5z4t.cif.gz | 163.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5z4t.ent.gz | 125.5 KB | Display | PDB format |
PDBx/mmJSON format | 5z4t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5z4t_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 5z4t_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 5z4t_validation.xml.gz | 35.2 KB | Display | |
Data in CIF | 5z4t_validation.cif.gz | 55.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z4/5z4t ftp://data.pdbj.org/pub/pdb/validation_reports/z4/5z4t | HTTPS FTP |
-Related structure data
Related structure data | 5ylhSC 5yliC 5ylkC 5yllC 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: 36223.473 Da / Num. of mol.: 2 / Mutation: E223A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Amphibacillus xylanus (strain ATCC 51415 / DSM 6626 / JCM 7361 / LMG 17667 / NBRC 15112 / Ep01) (bacteria) Strain: ATCC 51415 / DSM 6626 / JCM 7361 / LMG 17667 / NBRC 15112 / Ep01 Gene: AXY_22370 / Production host: Escherichia coli (E. coli) / References: UniProt: K0J0N5 #2: Polysaccharide | #3: 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: 2.93 Å3/Da / Density % sol: 58.03 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: HEPES sodium pH 7.5, 2-Propanol, PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979 Å |
Detector | Type: RAYONIX MX225-HS / Detector: CCD / Date: Jun 12, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.68→32.92 Å / Num. obs: 91072 / % possible obs: 93 % / Redundancy: 9.3 % / Rmerge(I) obs: 0.198 / Rsym value: 0.196 / Net I/σ(I): 6.8 |
Reflection shell | Resolution: 1.68→1.74 Å / Num. unique obs: 91702 / CC1/2: 0.976 / % possible all: 93 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5YLH Resolution: 1.68→32.92 Å / Cross valid method: FREE R-VALUE
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Refinement step | Cycle: LAST / Resolution: 1.68→32.92 Å
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LS refinement shell | Highest resolution: 1.68 Å |