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- PDB-4haq: Crystal Structure of a GH7 family cellobiohydrolase from Limnoria... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4haq | ||||||||||||
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Title | Crystal Structure of a GH7 family cellobiohydrolase from Limnoria quadripunctata in complex with cellobiose and cellotriose | ||||||||||||
![]() | GH7 family protein | ||||||||||||
![]() | HYDROLASE / cellobiohydrolase | ||||||||||||
Function / homology | ![]() cellulose 1,4-beta-cellobiosidase (non-reducing end) / cellulose 1,4-beta-cellobiosidase activity / cellulose catabolic process / extracellular region Similarity search - Function | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | ![]() ![]() ![]() ![]() | ||||||||||||
![]() | Martin, R.N.A. / McGeehan, J.E. / Streeter, S.D. / Cragg, S.M. / Guille, M.J. / Schnorr, K.M. / Kern, M. / Bruce, N.C. / McQueen-Mason, S.J. | ||||||||||||
![]() | ![]() Title: Structural characterization of a unique marine animal family 7 cellobiohydrolase suggests a mechanism of cellulase salt tolerance Authors: Kern, M. / McGeehan, J.E. / Streeter, S.D. / Martin, R.N. / Besser, K. / Elias, L. / Eborall, W. / Malyon, G.P. / Payne, C.M. / Himmel, M.E. / Schnorr, K. / Beckham, G.T. / Cragg, S.M. / ...Authors: Kern, M. / McGeehan, J.E. / Streeter, S.D. / Martin, R.N. / Besser, K. / Elias, L. / Eborall, W. / Malyon, G.P. / Payne, C.M. / Himmel, M.E. / Schnorr, K. / Beckham, G.T. / Cragg, S.M. / Bruce, N.C. / McQueen-Mason, S.J. #1: Journal: Proc.Natl.Acad.Sci.USA / Year: 2010 Title: Molecular insight into lignocellulose digestion by a marine isopod in the absence of gut microbes. Authors: King, A.J. / Cragg, S.M. / Li, Y. / Dymond, J. / Guille, M.J. / Bowles, D.J. / Bruce, N.C. / Graham, I.A. / McQueen-Mason, S.J. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 191 KB | Display | ![]() |
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PDB format | ![]() | 147.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.4 MB | Display | ![]() |
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Full document | ![]() | 1.4 MB | Display | |
Data in XML | ![]() | 38.6 KB | Display | |
Data in CIF | ![]() | 57.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4gwaSC ![]() 4hapC ![]() 4ipmC S: Starting model for refinement C: citing same article ( |
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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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2 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 46535.949 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 19-448 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: D4HRL0, cellulose 1,4-beta-cellobiosidase (non-reducing end) |
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-Sugars , 2 types, 3 molecules
#2: Polysaccharide | #3: Polysaccharide | beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-cellotriose | |
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-Non-polymers , 4 types, 568 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/TRS.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/TRS.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-MG / | ||
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#5: Chemical | ChemComp-TRS / | ||
#6: Chemical | #7: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.19 Å3/Da / Density % sol: 43.83 % / Mosaicity: 0.64 ° |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion / pH: 8 Details: 0.2M MAGNESIUM CHLORIDE, 0.1M BIS-TRIS, 25% w/v PEG 3350, PH 8.0, VAPOUR DIFFUSION, SITTING DROP, TEMPERATURE 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 6, 2012 |
Radiation | Monochromator: SI(111)DUAL CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9173 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→45.04 Å / Num. obs: 59787 / % possible obs: 96 % / Redundancy: 3.4 % / Rsym value: 0.146 / Net I/σ(I): 6.7 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.513 / Mean I/σ(I) obs: 1.3 / Rsym value: 0.513 / % possible all: 95.4 |
-Phasing
Phasing | Method: ![]() | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4GWA Resolution: 1.9→44.62 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.916 / WRfactor Rfree: 0.2062 / WRfactor Rwork: 0.1569 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8883 / SU B: 3.327 / SU ML: 0.098 / SU R Cruickshank DPI: 0.1597 / SU Rfree: 0.1475 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.165 / ESU R Free: 0.151 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES
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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: MASK | |||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 92.18 Å2 / Biso mean: 13.627 Å2 / Biso min: 3.11 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→44.62 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.949 Å / Total num. of bins used: 20
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