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Yorodumi- PDB-1mqq: THE CRYSTAL STRUCTURE OF ALPHA-D-GLUCURONIDASE FROM BACILLUS STEA... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1mqq | ||||||
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Title | THE CRYSTAL STRUCTURE OF ALPHA-D-GLUCURONIDASE FROM BACILLUS STEAROTHERMOPHILUS T-1 COMPLEXED WITH GLUCURONIC ACID | ||||||
Components | ALPHA-D-GLUCURONIDASE | ||||||
Keywords | HYDROLASE | ||||||
Function / homology | Function and homology information xylan alpha-1,2-glucuronosidase / xylan alpha-1,2-glucuronosidase activity / alpha-glucuronidase activity / xylan catabolic process / extracellular region Similarity search - Function | ||||||
Biological species | Geobacillus stearothermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / AB INITIO / Resolution: 1.65 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 | 1mqq.cif.gz | 168.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1mqq.ent.gz | 133.1 KB | Display | PDB format |
PDBx/mmJSON format | 1mqq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1mqq_validation.pdf.gz | 402.6 KB | Display | wwPDB validaton report |
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Full document | 1mqq_full_validation.pdf.gz | 413.3 KB | Display | |
Data in XML | 1mqq_validation.xml.gz | 16.5 KB | Display | |
Data in CIF | 1mqq_validation.cif.gz | 29.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mq/1mqq ftp://data.pdbj.org/pub/pdb/validation_reports/mq/1mqq | HTTPS FTP |
-Related structure data
Related structure data | 1k9dSC 1k9eC 1k9fC 1l8nC 1mqpC 1mqrC 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 78579.234 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Geobacillus stearothermophilus (bacteria) Strain: T-1 / Gene: AGUA / Plasmid: PET9D / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q8VVD2, EC: 3.2.1.139 | ||
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#2: Sugar | ChemComp-GCU / | ||
#3: Chemical | ChemComp-GOL / #4: 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: 2.88 Å3/Da / Density % sol: 57.54 % |
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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: 95 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å |
Detector | Type: BRANDEIS - B4 / Detector: CCD / Date: Jul 12, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→40 Å / Num. obs: 111221 / % possible obs: 98.9 % / Redundancy: 10 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 7.9 |
Reflection shell | Resolution: 1.65→1.68 Å / Redundancy: 10 % / Rmerge(I) obs: 0.452 / Num. unique all: 4995 / % possible all: 91 |
-Processing
Software |
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Refinement | Method to determine structure: AB INITIO Starting model: PDB CODE 1K9D Resolution: 1.65→40 Å / Num. parameters: 25802 / Num. restraintsaints: 24044 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
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Refine analyze | Luzzati coordinate error obs: 0.15 Å / Num. disordered residues: 44 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 6237.05 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.65→40 Å
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Refine LS restraints |
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