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Open data
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Basic information
Entry | Database: PDB / ID: 3a0f | ||||||
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Title | The crystal structure of Geotrichum sp. M128 xyloglucanase | ||||||
![]() | Xyloglucanase | ||||||
![]() | HYDROLASE / BETA-PROPELLER | ||||||
Function / homology | BNR-Asp box repeat / BNR repeat / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / WD40/YVTN repeat-like-containing domain superfamily / Mainly Beta / Xyloglucanase![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Yaoi, K. / Kondo, H. / Hiyoshi, A. / Noro, N. / Sugimoto, H. / Tsuda, S. / Miyazaki, K. | ||||||
![]() | ![]() Title: The crystal structure of a xyloglucan-specific endo-beta-1,4-glucanase from Geotrichum sp. M128 xyloglucanase reveals a key amino acid residue for substrate specificity Authors: Yaoi, K. / Kondo, H. / Hiyoshi, A. / Noro, N. / Sugimoto, H. / Tsuda, S. / Miyazaki, K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 153.2 KB | Display | ![]() |
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PDB format | ![]() | 118.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 428.6 KB | Display | ![]() |
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Full document | ![]() | 442.9 KB | Display | |
Data in XML | ![]() | 28.6 KB | Display | |
Data in CIF | ![]() | 39.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1sqjS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 81557.078 Da / Num. of mol.: 1 / Fragment: residues in UNP 21-776 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q764N8, xyloglucan-specific endo-beta-1,4-glucanase |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.92 Å3/Da / Density % sol: 68.66 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.8 Details: 0.1M MES, 6% PEG 8000, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 14, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→20 Å / Num. all: 43425 / Num. obs: 43425 / % possible obs: 98.4 % / Redundancy: 6.2 % / Biso Wilson estimate: 30.2 Å2 / Rmerge(I) obs: 0.096 / Net I/σ(I): 19.9 |
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 6 % / Rmerge(I) obs: 0.199 / Mean I/σ(I) obs: 8.6 / Num. unique all: 4042 / % possible all: 93.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1SQJ Resolution: 2.5→20 Å / Cor.coef. Fo:Fc: 0.882 / Cor.coef. Fo:Fc free: 0.847 / SU B: 8.154 / SU ML: 0.19 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R: 0.341 / ESU R Free: 0.264 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.283 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.564 Å / Total num. of bins used: 20
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