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Yorodumi- PDB-1ddk: CRYSTAL STRUCTURE OF IMP-1 METALLO BETA-LACTAMASE FROM PSEUDOMONA... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ddk | ||||||
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Title | CRYSTAL STRUCTURE OF IMP-1 METALLO BETA-LACTAMASE FROM PSEUDOMONAS AERUGINOSA | ||||||
Components | IMP-1 METALLO BETA-LACTAMASE | ||||||
Keywords | HYDROLASE / IMP-1 METALLO BETA-LACTAMASE / BINUCLEAR METAL CENTER / ZN BETA-LACTAMASE | ||||||
Function / homology | Function and homology information antibiotic catabolic process / beta-lactamase activity / beta-lactamase / periplasmic space / response to antibiotic / zinc ion binding Similarity search - Function | ||||||
Biological species | Pseudomonas aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 3.1 Å | ||||||
Authors | Concha, N.O. / Janson, C.A. / Rowling, P. / Pearson, S. / Cheever, C.A. / Clarke, B.P. / Lewis, C. / Galleni, M. / Frere, J.M. / Payne, D.J. ...Concha, N.O. / Janson, C.A. / Rowling, P. / Pearson, S. / Cheever, C.A. / Clarke, B.P. / Lewis, C. / Galleni, M. / Frere, J.M. / Payne, D.J. / Bateson, J.H. / Abdel-Meguid, S.S. | ||||||
Citation | Journal: Biochemistry / Year: 2000 Title: Crystal structure of the IMP-1 metallo beta-lactamase from Pseudomonas aeruginosa and its complex with a mercaptocarboxylate inhibitor: binding determinants of a potent, broad-spectrum inhibitor. Authors: Concha, N.O. / Janson, C.A. / Rowling, P. / Pearson, S. / Cheever, C.A. / Clarke, B.P. / Lewis, C. / Galleni, M. / Frere, J.M. / Payne, D.J. / Bateson, J.H. / Abdel-Meguid, S.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ddk.cif.gz | 56.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ddk.ent.gz | 40.5 KB | Display | PDB format |
PDBx/mmJSON format | 1ddk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dd/1ddk ftp://data.pdbj.org/pub/pdb/validation_reports/dd/1ddk | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 24334.750 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 References: UniProt: Q932P5, UniProt: Q79MP6*PLUS, beta-lactamase | ||||
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#2: Chemical | #3: Chemical | ChemComp-ACY / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | *PLUS Density % sol: 60 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: drop contained 5 uL protein (14mg/mL in 20mM HEPES, pH 7.5) with 5 uL reservoir (0.2M sodium acetate, 30% PEG4000, 0.1M sodium citrate pH 5.6). Crystal grew as plates after 2 weeks., pH 6.5, ...Details: drop contained 5 uL protein (14mg/mL in 20mM HEPES, pH 7.5) with 5 uL reservoir (0.2M sodium acetate, 30% PEG4000, 0.1M sodium citrate pH 5.6). Crystal grew as plates after 2 weeks., pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K Temp details: 293-295 | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.5 / Method: vapor diffusion | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 |
Detector | Type: SIEMENS X1000 / Detector: AREA DETECTOR / Date: Feb 20, 1997 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 3→20 Å / Num. obs: 19288 / % possible obs: 90.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 1.6 % / Biso Wilson estimate: 34 Å2 / Rmerge(I) obs: 0.14 |
Reflection shell | Resolution: 3→3.1 Å / Rmerge(I) obs: 0.249 / Num. unique all: 0 / % possible all: 56.6 |
Reflection | *PLUS Num. measured all: 31781 / Rmerge(I) obs: 0.14 |
Reflection shell | *PLUS Highest resolution: 3.1 Å / Lowest resolution: 3.19 Å / % possible obs: 56.6 % |
-Processing
Software |
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Refinement | Resolution: 3.1→20 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 784186.53 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 18.13 Å2 / ksol: 0.294 e/Å3 | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.1→20 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: CONSTR | ||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 3.1→3.29 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 0.5 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 20 Å / σ(F): 0 / % reflection Rfree: 9.9 % | ||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 16.9 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.383 / % reflection Rfree: 9.2 % / Rfactor Rwork: 0.346 |