+Open data
-Basic information
Entry | Database: PDB / ID: 5x6a | ||||||
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Title | Crystal structure of an endoglucanase PMO-5 | ||||||
Components | Endoglucanase, putative | ||||||
Keywords | HYDROLASE / endoglucanase | ||||||
Function / homology | Function and homology information cellulose binding / cellulase / cellulase activity / cellulose catabolic process / extracellular region Similarity search - Function | ||||||
Biological species | Neosartorya fumigata Af293 (mold) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Shen, Q. | ||||||
Citation | Journal: To Be Published Title: Crystal structure of an endoglucanase PMO-5 Authors: Shen, Q. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5x6a.cif.gz | 109.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5x6a.ent.gz | 82.7 KB | Display | PDB format |
PDBx/mmJSON format | 5x6a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5x6a_validation.pdf.gz | 432.3 KB | Display | wwPDB validaton report |
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Full document | 5x6a_full_validation.pdf.gz | 434.7 KB | Display | |
Data in XML | 5x6a_validation.xml.gz | 23.5 KB | Display | |
Data in CIF | 5x6a_validation.cif.gz | 36.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x6/5x6a ftp://data.pdbj.org/pub/pdb/validation_reports/x6/5x6a | HTTPS FTP |
-Related structure data
Related structure data | 3zudS S: Starting model for refinement |
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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: 24171.695 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Neosartorya fumigata Af293 (mold) / Strain: Af293 / Gene: AFUA_4G07850 / Production host: Escherichia coli (E. coli) References: UniProt: Q4WP32, Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds #2: Chemical | #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: 2.27 Å3/Da / Density % sol: 45.91 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.2M Magnesium chloride hexahydrate, 25% w/v Polyethylene glycol 3350, 0.1M BIS-TRIS pH 6.0 |
-Data collection
Diffraction | Mean temperature: 77 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9791 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jan 10, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→27.5 Å / Num. obs: 46666 / % possible obs: 95.9 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.117 / Rpim(I) all: 0.062 / Rsym value: 0.099 / Net I/σ(I): 37.3 |
Reflection shell | Resolution: 1.7→1.73 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.476 / Mean I/σ(I) obs: 16.5 / Num. unique obs: 2194 / Rpim(I) all: 0.242 / Rsym value: 0.409 / % possible all: 95.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3zud Resolution: 1.7→27.5 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.949 / SU B: 1.5 / SU ML: 0.051 / Cross valid method: THROUGHOUT / ESU R: 0.091 / ESU R Free: 0.088 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 12.114 Å2
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Refinement step | Cycle: 1 / Resolution: 1.7→27.5 Å
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Refine LS restraints |
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