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- PDB-1rh9: Family GH5 endo-beta-mannanase from Lycopersicon esculentum (tomato) -
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Open data
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Basic information
Entry | Database: PDB / ID: 1rh9 | ||||||
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Title | Family GH5 endo-beta-mannanase from Lycopersicon esculentum (tomato) | ||||||
![]() | endo-beta-mannanase | ||||||
![]() | HYDROLASE / ENDO-BETA-MANNASE / Retaining / Glycoside Hydrolase Family 5 / mannan | ||||||
Function / homology | ![]() : / mannan endo-1,4-beta-mannosidase / mannan endo-1,4-beta-mannosidase activity / extracellular region Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Oakley, A.J. / Bourgault, R. / Bewley, J.D. / Wilce, M.C.J. | ||||||
![]() | ![]() Title: Three-dimensional structure of (1,4)-beta-D-mannan mannanohydrolase from tomato fruit. Authors: Bourgault, R. / Oakley, A.J. / Bewley, J.D. / Wilce, M.C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 87.5 KB | Display | ![]() |
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PDB format | ![]() | 66.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 402 KB | Display | ![]() |
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Full document | ![]() | 402.3 KB | Display | |
Data in XML | ![]() | 9.1 KB | Display | |
Data in CIF | ![]() | 13 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1qnpS 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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1 |
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Unit cell |
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Details | The asymmetric unit contains the biological assembly (a monomer). |
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Components
#1: Protein | Mass: 42435.910 Da / Num. of mol.: 1 / Fragment: residues 27-399 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q93WT4, UniProt: Q8L5J1*PLUS, mannan endo-1,4-beta-mannosidase |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.99 Å3/Da / Density % sol: 37.76 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 30% PEG 4000, 0.1M Na Citrate, 0.2M NH4 Acetate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 1, 2003 / Details: BEAMLINE OPTICS |
Radiation | Monochromator: BEAMLINE OPTICS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→54.233 Å / Num. all: 56178 / Num. obs: 56178 / % possible obs: 98.4 % / Observed criterion σ(F): -1 / Observed criterion σ(I): -1 / Rmerge(I) obs: 0.08 / Net I/σ(I): 12.1 |
Reflection shell | Resolution: 1.5→1.55 Å / Rmerge(I) obs: 0.743 / Mean I/σ(I) obs: 1.2 / % possible all: 99.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1QNP Resolution: 1.5→20 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.962 / SU B: 1.977 / SU ML: 0.068 / Cross valid method: THROUGHOUT / σ(F): -1 / ESU R: 0.084 / ESU R Free: 0.081 / 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.865 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.539 Å / Total num. of bins used: 20 /
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