+Open data
-Basic information
Entry | Database: PDB / ID: 4zzv | ||||||||||||
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Title | Geotrichum candidum Cel7A apo structure at 1.4A | ||||||||||||
Components | CELLOBIOHYDROLASE ICellulose 1,4-beta-cellobiosidase | ||||||||||||
Keywords | HYDROLASE / CELLOBIOHYDROLASE | ||||||||||||
Function / homology | Function and homology information Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds / cellulose binding / cellulose catabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds / extracellular region Similarity search - Function | ||||||||||||
Biological species | GALACTOMYCES CANDIDUM (yeast) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.37 Å | ||||||||||||
Authors | Borisova, A.S. / Stahlberg, J. | ||||||||||||
Citation | Journal: FEBS J. / Year: 2015 Title: Sequencing, Biochemical Characterization, Crystal Structure and Molecular Dynamics of Cellobiohydrolase Cel7A from Geotrichum Candidum 3C. Authors: Borisova, A.S. / Eneyskaya, E.V. / Bobrov, K.S. / Jana, S. / Logachev, A. / Polev, D.E. / Lapidus, A.L. / Ibatullin, F.M. / Saleem, U. / Sandgren, M. / Payne, C.M. / Kulminskaya, A.A. / Stahlberg, J. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4zzv.cif.gz | 110.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4zzv.ent.gz | 84 KB | Display | PDB format |
PDBx/mmJSON format | 4zzv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zz/4zzv ftp://data.pdbj.org/pub/pdb/validation_reports/zz/4zzv | HTTPS FTP |
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-Related structure data
Related structure data | 4zztC 4zzuC 4zzwC 5ampC 1gpiS C: citing same article (ref.) 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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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 46521.270 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN, RESIDUES 18-455 / Source method: isolated from a natural source / Source: (natural) GALACTOMYCES CANDIDUM (yeast) / Strain: 3C References: UniProt: A0A088T0J9, cellulose 1,4-beta-cellobiosidase (reducing end) |
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-Sugars , 3 types, 4 molecules
#2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source | ||
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#3: Sugar | #4: Sugar | ChemComp-MAN / | |
-Non-polymers , 2 types, 533 molecules
#5: Chemical | ChemComp-MG / |
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#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 3 |
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-Sample preparation
Crystal | Density Matthews: 2.01 Å3/Da / Density % sol: 38.73 % / Description: NONE |
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Crystal grow | pH: 5.9 Details: 0.2M MAGNESIUM CHLORIDE HEXAHYDRATE, 20% PEG 3350, pH 5.9 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9918 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Nov 7, 2013 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9918 Å / Relative weight: 1 |
Reflection | Resolution: 1.37→51.74 Å / Num. obs: 68773 / % possible obs: 93.9 % / Observed criterion σ(I): 7.3 / Redundancy: 3.8 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 7.3 |
Reflection shell | Resolution: 1.37→1.39 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 2.6 / % possible all: 92.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1GPI Resolution: 1.37→51.75 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.956 / SU B: 1.222 / SU ML: 0.049 / Cross valid method: THROUGHOUT / ESU R: 0.072 / ESU R Free: 0.071 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.24 Å2
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Refinement step | Cycle: LAST / Resolution: 1.37→51.75 Å
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Refine LS restraints |
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