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Yorodumi- PDB-2wlt: The crystal structure of Helicobacter pylori L-asparaginase at 1.... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2wlt | ||||||
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Title | The crystal structure of Helicobacter pylori L-asparaginase at 1.4 A resolution | ||||||
Components | L-ASPARAGINASEAsparaginase | ||||||
Keywords | HYDROLASE | ||||||
Function / homology | Function and homology information asparagine metabolic process / asparaginase / asparaginase activity / cytosol Similarity search - Function | ||||||
Biological species | HELICOBACTER PYLORI (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å | ||||||
Authors | Dhavala, P. / Papageorgiou, A.C. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2009 Title: Structure of Helicobacter Pylori L-Asparaginase at 1.4 A Resolution Authors: Dhavala, P. / Papageorgiou, A.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2wlt.cif.gz | 156.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2wlt.ent.gz | 122.2 KB | Display | PDB format |
PDBx/mmJSON format | 2wlt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wl/2wlt ftp://data.pdbj.org/pub/pdb/validation_reports/wl/2wlt | HTTPS FTP |
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-Related structure data
Related structure data | 2wt4C 1wsaS 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: 35607.449 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HELICOBACTER PYLORI (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q9ZLB9, asparaginase |
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#2: Chemical | ChemComp-ASP / |
#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: 2.1 Å3/Da / Density % sol: 41 % / Description: NONE |
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Crystal grow | pH: 7 Details: PROTEIN WAS CRYSTALLIZED FROM 17.5% W/V PEG 4000, 0.1 M MG FORMATE, 0.1 M HEPES-NAOH, PH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.8081 |
Detector | Type: MARRESEARCH SX-165 / Detector: CCD / Date: Aug 17, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8081 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→20 Å / Num. obs: 59013 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 7.1 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 22.8 |
Reflection shell | Resolution: 1.4→1.42 Å / Redundancy: 8.2 % / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 7.2 / % possible all: 99.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1WSA Resolution: 1.4→20 Å / Num. parameters: 26187 / Num. restraintsaints: 32640 / Cross valid method: FREE R-VALUE / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
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Refine analyze | Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 2780.35 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.4→20 Å
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Refine LS restraints |
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