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Yorodumi- PDB-1bul: 6ALPHA-(HYDROXYPROPYL)PENICILLANATE ACYLATED ON NMC-A BETA-LACTAM... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1bul | ||||||
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Title | 6ALPHA-(HYDROXYPROPYL)PENICILLANATE ACYLATED ON NMC-A BETA-LACTAMASE FROM ENTEROBACTER CLOACAE | ||||||
Components | NMC-A BETA-LACTAMASE | ||||||
Keywords | HYDROLASE / ANTIBIOTIC RESISTANCE / CLASS A CARBAPENEMASE | ||||||
Function / homology | Function and homology information beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic Similarity search - Function | ||||||
Biological species | Enterobacter cloacae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å | ||||||
Authors | Mourey, L. / Swaren, P. / Miyashita, K. / Bulychev, A. / Mobashery, S. / Samama, J.P. | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 1998 Title: Inhibition of the Nmc-A B-Lactamase by a Penicillanic Acid Derivative, and the Structural Bases for the Increase in Substrate Profile of This Antibiotic Resistance Enzyme Authors: Mourey, L. / Swaren, P. / Miyashita, K. / Bulychev, A. / Mobashery, S. / Samama, J.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1bul.cif.gz | 70.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1bul.ent.gz | 50.3 KB | Display | PDB format |
PDBx/mmJSON format | 1bul.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1bul_validation.pdf.gz | 821 KB | Display | wwPDB validaton report |
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Full document | 1bul_full_validation.pdf.gz | 827.5 KB | Display | |
Data in XML | 1bul_validation.xml.gz | 14.6 KB | Display | |
Data in CIF | 1bul_validation.cif.gz | 21 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bu/1bul ftp://data.pdbj.org/pub/pdb/validation_reports/bu/1bul | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 29137.596 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: ACYL-ENZYME COMPLEX / Source: (natural) Enterobacter cloacae (bacteria) / Strain: NOR-1 / References: UniProt: P52663, beta-lactamase | ||||
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#2: Chemical | ChemComp-AP3 / | ||||
#3: Chemical | #4: Water | ChemComp-HOH / | Compound details | THE STRUCTURE DEPOSITED IS AN ACYL-ENZYME COMPLEX BETWEEN 6 ALPHA-(HYDROXYPROPYL)PENICILLANIC ACID ...THE STRUCTURE DEPOSITED IS AN ACYL-ENZYME COMPLEX BETWEEN 6 ALPHA-(HYDROXYPRO | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47.2 % |
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Crystal grow | pH: 7.5 Details: 20% (W/V)PEG 1500, 0.200 M MES PH 5.25, 6% (V/V) N-PROPANOL, pH 7.5 |
Crystal grow | *PLUS Method: unknown |
-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: SYNCHROTRON / Site: LURE / Beamline: DW32 / Wavelength: 0.97 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 15, 1997 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 1.89→18.6 Å / Num. obs: 22025 / % possible obs: 98.6 % / Redundancy: 3.7 % / Biso Wilson estimate: 8 Å2 / Rmerge(I) obs: 0.046 / Net I/σ(I): 9 |
Reflection shell | Resolution: 1.89→1.96 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.098 / Mean I/σ(I) obs: 5.9 / % possible all: 95 |
Reflection | *PLUS Num. measured all: 81088 |
Reflection shell | *PLUS % possible obs: 95 % / Num. unique obs: 2019 / Num. measured obs: 6594 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: THE NMC-A BETA-LACTAMASE STRUCTURE Resolution: 1.89→18.6 Å / Rfactor Rfree error: 0.0064 / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Cross valid method: THROUGHOUT / σ(F): 0 Details: BULK SOLVENT CORRECTION USED WITH A DENSITY OF 0.33 E-/A**3, SOLVENT RADIUS OF 0.25 ANGSTROMS AND B VALUES OF 50 A**2.
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Displacement parameters | Biso mean: 13.1 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati d res low obs: 18.6 Å / Luzzati sigma a obs: 0.21 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.89→18.6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.89→1.98 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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