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Yorodumi- PDB-1mqr: THE CRYSTAL STRUCTURE OF ALPHA-D-GLUCURONIDASE (E386Q) FROM BACIL... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1mqr | ||||||
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Title | THE CRYSTAL STRUCTURE OF ALPHA-D-GLUCURONIDASE (E386Q) FROM BACILLUS STEAROTHERMOPHILUS T-6 | ||||||
Components | ALPHA-D-GLUCURONIDASE | ||||||
Keywords | HYDROLASE | ||||||
Function / homology | Function and homology information glucuronoxylan catabolic process / xylan alpha-1,2-glucuronosidase / xylan alpha-1,2-glucuronosidase activity / alpha-glucuronidase activity / extracellular region Similarity search - Function | ||||||
Biological species | Geobacillus stearothermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 2 Å | ||||||
Authors | Golan, G. / Shallom, D. / Teplitsky, A. / Zaide, G. / Shulami, S. / Baasov, T. / Stojanoff, V. / Thompson, A. / Shoham, Y. / Shoham, G. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2004 Title: Crystal Structures of Geobacillus stearothermophilus {alpha}-Glucuronidase Complexed with Its Substrate and Products: MECHANISTIC IMPLICATIONS. Authors: Golan, G. / Shallom, D. / Teplitsky, A. / Zaide, G. / Shulami, S. / Baasov, T. / Stojanoff, V. / Thompson, A. / Shoham, Y. / Shoham, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1mqr.cif.gz | 160.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1mqr.ent.gz | 126.5 KB | Display | PDB format |
PDBx/mmJSON format | 1mqr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1mqr_validation.pdf.gz | 381.2 KB | Display | wwPDB validaton report |
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Full document | 1mqr_full_validation.pdf.gz | 389.2 KB | Display | |
Data in XML | 1mqr_validation.xml.gz | 15.2 KB | Display | |
Data in CIF | 1mqr_validation.cif.gz | 25.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mq/1mqr ftp://data.pdbj.org/pub/pdb/validation_reports/mq/1mqr | HTTPS FTP |
-Related structure data
Related structure data | 1k9dC 1k9eC 1k9fC 1l8nC 1mqpSC 1mqqC 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
#1: Protein | Mass: 78577.289 Da / Num. of mol.: 1 / Mutation: E386Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Geobacillus stearothermophilus (bacteria) Strain: T-6 / Gene: AGUA / Plasmid: PET9D / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 References: UniProt: Q9ZFM3, UniProt: Q09LY5*PLUS, EC: 3.2.1.139 | ||
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#2: Chemical | ChemComp-GOL / #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: 2.83 Å3/Da / Density % sol: 56.51 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 12% ISOPROPANOL, 14% PEG 4K, 0.1M NA-CITRATE, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 203.4 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.913 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Jul 8, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.913 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. obs: 62425 / % possible obs: 99.8 % / Redundancy: 5.5 % / Biso Wilson estimate: 11.6 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 10.2 |
Reflection shell | Resolution: 2→2.03 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.317 / Num. unique all: 3055 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: AB INITIO PHASING Starting model: pdb entry 1mqp Resolution: 2→49.03 Å / Rfactor Rfree error: 0.003 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 42.4492 Å2 / ksol: 0.370989 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→49.03 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.007 / Total num. of bins used: 6
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Xplor file |
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