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- PDB-1gkf: Crystal structures of penicillin acylase enzyme-substrate complex... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1gkf | ||||||
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Title | Crystal structures of penicillin acylase enzyme-substrate complexes: Structural insights into the catalytic mechanism | ||||||
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![]() | HYDROLASE / ANTIBIOTIC RESISTANCE | ||||||
Function / homology | ![]() penicillin amidase / penicillin amidase activity / antibiotic biosynthetic process / periplasmic space / response to antibiotic / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | McVey, C.E. / Walsh, M.A. / Dodson, G.G. / Wilson, K.S. / Brannigan, J.A. | ||||||
![]() | ![]() 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: ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 188.9 KB | Display | ![]() |
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PDB format | ![]() | 153.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 435.8 KB | Display | ![]() |
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Full document | ![]() | 451.6 KB | Display | |
Data in XML | ![]() | 19.5 KB | Display | |
Data in CIF | ![]() | 34.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 28979.695 Da / Num. of mol.: 1 / Fragment: N-TERMINAL NUCLEOPHILE DOMAIN RESIDUES 29-286 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||||||
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#2: Protein | Mass: 62386.473 Da / Num. of mol.: 1 / Fragment: RESIDUES 287-846 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||||||
#3: Chemical | ChemComp-EDO / #4: Chemical | ChemComp-CA / | #5: Water | ChemComp-HOH / | Compound details | CHAIN B ENGINEERED | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.27 Å3/Da / Density % sol: 45.81 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.5 / Details: pH 7.50 | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 291 K / pH: 7.2 / Method: vapor diffusion, hanging drop / Details: McVey, C.E., (1997) Acta Crystallog., D53, 777. | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
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: 1.4→25 Å / Num. obs: 152163 / % possible obs: 97.4 % / Redundancy: 2.4 % / Biso Wilson estimate: 12.7 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 19.8 |
Reflection shell | Resolution: 1.41→1.43 Å / Rmerge(I) obs: 0.176 / Mean I/σ(I) obs: 4.4 / % possible all: 82.5 |
Reflection | *PLUS Num. measured all: 361905 |
Reflection shell | *PLUS % possible obs: 95.9 % |
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Processing
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Refinement | Method to determine structure: ![]()
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Displacement parameters | Biso mean: 14.4 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.41→25 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 25 Å / Rfactor obs: 0.149 / Rfactor Rfree: 0.169 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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