+Open data
-Basic information
Entry | Database: PDB / ID: 4m29 | ||||||
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Title | Structure of a GH39 Beta-xylosidase from Caulobacter crescentus | ||||||
Components | Beta-xylosidase | ||||||
Keywords | HYDROLASE / family GH39 / beta-xylosidase | ||||||
Function / homology | Function and homology information hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process Similarity search - Function | ||||||
Biological species | Caulobacter crescentus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Polo, C.C. / Santos, C.R. / Correa, J.M. / Simao, R.C.G. / Seixas, F.A.V. / Murakami, M.T. | ||||||
Citation | Journal: Thesis Title: Structure of a GH39 Beta-xylosidase from Caulobacter crescentus Authors: Polo, C.C. / Santos, C.R. / Correa, J.M. / Simao, R.C.G. / Seixas, F.A.V. / Murakami, M.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4m29.cif.gz | 183.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4m29.ent.gz | 145.9 KB | Display | PDB format |
PDBx/mmJSON format | 4m29.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4m29_validation.pdf.gz | 443.1 KB | Display | wwPDB validaton report |
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Full document | 4m29_full_validation.pdf.gz | 452.8 KB | Display | |
Data in XML | 4m29_validation.xml.gz | 19.9 KB | Display | |
Data in CIF | 4m29_validation.cif.gz | 28 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m2/4m29 ftp://data.pdbj.org/pub/pdb/validation_reports/m2/4m29 | HTTPS FTP |
-Related structure data
Related structure data | 4ekjS 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
#1: Protein | Mass: 56305.574 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Caulobacter crescentus (bacteria) / Strain: ATCC 19089 / CB15 / Gene: Itgav, CC_2357 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9A5U0 |
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#2: Chemical | ChemComp-MES / |
#3: 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: 2.02 Å3/Da / Density % sol: 39.25 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 0.1 M MES, 12% PEG6000, 0.05 M NaCl, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.6 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 5, 2012 |
Radiation | Monochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.6 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→17.4 Å / Num. all: 25413 / Num. obs: 25082 / % possible obs: 96.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 |
Reflection shell | Resolution: 2.1→2.14 Å / % possible all: 96.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 4EKJ Resolution: 2.1→17.4 Å / Cor.coef. Fo:Fc: 0.895 / Cor.coef. Fo:Fc free: 0.846 / SU B: 11.983 / SU ML: 0.163 / Cross valid method: THROUGHOUT / ESU R: 0.313 / ESU R Free: 0.243 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 16.78 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→17.4 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.155 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: -10.2259 Å / Origin y: -3.0899 Å / Origin z: -23.8065 Å
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