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Yorodumi- PDB-4ipm: Crystal structure of a GH7 family cellobiohydrolase from Limnoria... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ipm | ||||||||||||
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Title | Crystal structure of a GH7 family cellobiohydrolase from Limnoria quadripunctata in complex with thiocellobiose | ||||||||||||
Components | GH7 family protein | ||||||||||||
Keywords | HYDROLASE / thiocellobiose / cellobiohydrolase | ||||||||||||
Function / homology | Function and homology information cellulose 1,4-beta-cellobiosidase (non-reducing end) / cellulose 1,4-beta-cellobiosidase activity / cellulose catabolic process / extracellular region Similarity search - Function | ||||||||||||
Biological species | Limnoria quadripunctata (crustacean) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.14 Å | ||||||||||||
Authors | McGeehan, J.E. / Martin, R.N.A. / Streeter, S.D. / Cragg, S.M. / Guille, M.J. / Schnorr, K.M. / Kern, M. / Bruce, N.C. / McQueen-Mason, S.J. | ||||||||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2013 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ipm.cif.gz | 347.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ipm.ent.gz | 278.9 KB | Display | PDB format |
PDBx/mmJSON format | 4ipm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ip/4ipm ftp://data.pdbj.org/pub/pdb/validation_reports/ip/4ipm | HTTPS FTP |
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-Related structure data
Related structure data | 4gwaSC 4hapC 4haqC 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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Unit cell |
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-Components
#1: Protein | Mass: 46535.949 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 19-448 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Limnoria quadripunctata (crustacean) / Gene: GH7B / Production host: Aspergillus oryzae (mold) References: UniProt: D4HRL0, cellulose 1,4-beta-cellobiosidase (non-reducing end) |
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#2: Polysaccharide | beta-D-glucopyranose-(1-4)-4-thio-beta-D-glucopyranose / thio-beta-cellobiose |
#3: Chemical | ChemComp-CA / |
#4: Chemical | ChemComp-ACT / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.14 Å3/Da / Density % sol: 42.53 % / Mosaicity: 0.4 ° |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: 100mM sodium acetate pH 4.5, 500mM CaCl2, 15% (w/v) PEG 6000, VAPOR DIFFUSION, HANGING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å | ||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 31, 2012 | ||||||||||||||||||||||||
Radiation | Monochromator: Si (111) Double Crystal Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 1.14→63.559 Å / Num. all: 150535 / Num. obs: 140362 / % possible obs: 96.4 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.084 / Net I/σ(I): 8.4 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4GWA Resolution: 1.14→23 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.975 / WRfactor Rfree: 0.1514 / WRfactor Rwork: 0.1177 / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.9152 / SU B: 0.996 / SU ML: 0.02 / SU R Cruickshank DPI: 0.0291 / SU Rfree: 0.0317 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.029 / ESU R Free: 0.032 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES: REFINED INDIVIDUALLY
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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: 194.46 Å2 / Biso mean: 12.7332 Å2 / Biso min: 3.62 Å2
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Refinement step | Cycle: LAST / Resolution: 1.14→23 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.14→1.17 Å / Total num. of bins used: 20
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