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Yorodumi- PDB-1o7e: Crystal structure of the class A beta-lactamse L2 from Stenotroph... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1o7e | ||||||
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Title | Crystal structure of the class A beta-lactamse L2 from Stenotrophomonas maltophilia at 1.51 angstrom | ||||||
Components | L2 BETA LACTAMASE | ||||||
Keywords | HYDROLASE / BETA-LACTAMASE / CLASS A / L2 | ||||||
Function / homology | Function and homology information beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic Similarity search - Function | ||||||
Biological species | STENOTROPHOMONAS MALTOPHILIA (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.51 Å | ||||||
Authors | Pernot, L. / Petrella, S. / Sougakoff, W. | ||||||
Citation | Journal: To be Published Title: Role of the Disulfide Bridge Cys69-Cys238 in Class a B-Lactamases : A Structural and Biochemical Investigation on the B-Lactamase L2 from Stenotrophomonas Maltophilia Authors: Petrella, S. / Pernot, L. / Lascoux, D. / Forest, E. / Jarlier, V. / Sougakoff, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1o7e.cif.gz | 132 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1o7e.ent.gz | 102.9 KB | Display | PDB format |
PDBx/mmJSON format | 1o7e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1o7e_validation.pdf.gz | 448.5 KB | Display | wwPDB validaton report |
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Full document | 1o7e_full_validation.pdf.gz | 452.6 KB | Display | |
Data in XML | 1o7e_validation.xml.gz | 29.1 KB | Display | |
Data in CIF | 1o7e_validation.cif.gz | 45.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o7/1o7e ftp://data.pdbj.org/pub/pdb/validation_reports/o7/1o7e | HTTPS FTP |
-Related structure data
Related structure data | 1n4oS 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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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.885043, -0.448562, 0.124462), Vector: |
-Components
#1: Protein | Mass: 29164.059 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) STENOTROPHOMONAS MALTOPHILIA (bacteria) Strain: 405 / Plasmid: PET29-(A+) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q9RBQ1, beta-lactamase #2: Chemical | #3: Chemical | ChemComp-SO4 / #4: Water | ChemComp-HOH / | Sequence details | THE L2 MATURE PROTEIN STARTS AT RESIDUE 28 THERE ARE NO RESIDUES NUMBERED 58 AND 239 | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.57 Å3/Da / Density % sol: 65.23 % |
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Crystal grow | pH: 6.5 Details: AMMONIUM SULFATE 1.5M, SODIUM CACODYLATE 0.1M PH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: LURE / Beamline: DW32 / Wavelength: 0.948 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 25, 2001 |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.948 Å / Relative weight: 1 |
Reflection | Resolution: 1.51→23.9 Å / Num. obs: 131717 / % possible obs: 99.4 % / Observed criterion σ(I): 2.5 / Redundancy: 4.8 % / Biso Wilson estimate: 19.9 Å2 / Rmerge(I) obs: 0.046 / Net I/σ(I): 22.7 |
Reflection shell | Resolution: 1.51→1.59 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.17 / Mean I/σ(I) obs: 4.9 / % possible all: 96 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: THE STARTING MODEL USED WAS THE ONE OF L2 AT 1.85 ANGSTROM, PDB ENTRY 1N4O Resolution: 1.51→23.92 Å / SU B: 0.9034 / SU ML: 0.0346 / Cross valid method: THROUGHOUT / ESU R: 0.14 / ESU R Free: 0.14
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Displacement parameters | Biso mean: 13.9 Å2 | ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.51→23.92 Å
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