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Yorodumi- PDB-1gm8: Crystal structures of penicillin acylase enzyme-substrate complex... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1gm8 | ||||||
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Title | Crystal structures of penicillin acylase enzyme-substrate complexes: Structural insights into the catalytic mechanism | ||||||
Components |
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Keywords | HYDROLASE / ANTIBIOTIC RESISTANCE | ||||||
Function / homology | Function and homology information penicillin amidase / penicillin amidase activity / antibiotic biosynthetic process / periplasmic space / response to antibiotic / metal ion binding Similarity search - Function | ||||||
Biological species | ESCHERICHIA COLI (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2 Å | ||||||
Authors | McVey, C.E. / Walsh, M.A. / Dodson, G.G. / Wilson, K.S. / Brannigan, J.A. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2001 Title: Crystal Structures of Penicillin Acylase Enzyme- Substrate Complexes: Structural Insights Into the Catalytic Mechanism Authors: Mcvey, C.E. / Walsh, M.A. / Dodson, G.G. / Wilson, K.S. / Brannigan, J.A. #1: Journal: Protein Eng. / Year: 1990 Title: Expression, Purification and Crystallisation of Penicillin G Acylase from Escherichia Coli Atcc 11105 Authors: Hunt, P.D. / Tolley, S.P. / Ward, R.J. / Hill, C.P. / Dodson, G.G. #2: Journal: Nature / Year: 1995 Title: Penicillin Acylase Has a Single-Amino-Acid Catalytic Centre Authors: Duggleby, H.J. / Tolley, S.P. / Hill, C.P. / Dodson, E.J. / Dodson, G. / Moody, P.C.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1gm8.cif.gz | 179.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1gm8.ent.gz | 139.7 KB | Display | PDB format |
PDBx/mmJSON format | 1gm8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gm/1gm8 ftp://data.pdbj.org/pub/pdb/validation_reports/gm/1gm8 | 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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-Components
#1: Protein | Mass: 23838.824 Da / Num. of mol.: 1 / Fragment: RESIDUES 27-235 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Cellular location: PERIPLASM / Gene: PAC / Plasmid: PACYC184PAC / Cellular location (production host): PERIPLASM / Gene (production host): PAC / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P06875, penicillin amidase |
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#2: Protein | Mass: 62386.473 Da / Num. of mol.: 1 / Fragment: RESIDUES 290-846 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Cellular location: PERIPLASM / Gene: PAC / Plasmid: PACYC184PAC / Cellular location (production host): PERIPLASM / Gene (production host): PAC / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P06875, penicillin amidase |
#3: Chemical | ChemComp-CA / |
#4: Chemical | ChemComp-SOX / |
#5: 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: 2.4 Å3/Da / Density % sol: 41.8 % |
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Crystal grow | pH: 7.5 / Details: pH 7.50 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.89 |
Detector | Type: MAR scanner 300 mm plate / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.89 Å / Relative weight: 1 |
Reflection | Resolution: 2→15 Å / Num. obs: 50974 / % possible obs: 93.4 % / Redundancy: 1.9 % / Biso Wilson estimate: 15.9 Å2 / Rmerge(I) obs: 0.086 / Net I/σ(I): 7.2 |
Reflection shell | Resolution: 2→2.03 Å / Rmerge(I) obs: 0.321 / Mean I/σ(I) obs: 1.7 / % possible all: 77.8 |
-Processing
Software |
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Refinement | Method to determine structure: OTHER / Resolution: 2→15 Å / SU B: 4.44 / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.182 / ESU R Free: 0.179
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Displacement parameters | Biso mean: 18.2 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→15 Å
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Refine LS restraints |
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