+Open data
-Basic information
Entry | Database: PDB / ID: 1h2g | ||||||
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Title | Altered substrate specificity mutant of penicillin acylase | ||||||
Components |
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Keywords | HYDROLASE / AMIDOHYDROLASE / ANTIBIOTIC RESISTANCE / ALTERED SPECIFICITY / ZYMOGEN | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | McVey, C.E. / Morillas, M. / Brannigan, J.A. / Ladurner, A.G. / Forney, L.J. / Virden, R. | ||||||
Citation | Journal: Biochem.J. / Year: 2003 Title: Mutations of Penicillin Acylase Residue B71 Extend Substrate Specificity by Decreasing Steric Constraints for Substrate Binding Authors: Morillas, M. / Mcvey, C.E. / Brannigan, J.A. / Ladurner, A.G. / Forney, L.J. / Virden, R. #1: 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. #2: 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. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1h2g.cif.gz | 177.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1h2g.ent.gz | 137.4 KB | Display | PDB format |
PDBx/mmJSON format | 1h2g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h2/1h2g ftp://data.pdbj.org/pub/pdb/validation_reports/h2/1h2g | HTTPS FTP |
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-Related structure data
Related structure data | 1pnkS 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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Unit cell |
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-Components
#1: Protein | Mass: 23838.824 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Plasmid: PACYC184PAC / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P06875, penicillin amidase | ||||
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#2: Protein | Mass: 62395.480 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Details: ENGINEERED MUTATION PHE 360 LEU / Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Plasmid: PACYC184PAC / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P06875, penicillin amidase | ||||
#3: Chemical | ChemComp-EDO / #4: Chemical | ChemComp-CA / | #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: 48.9 % | ||||||||||||||||||||||||
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Crystal grow | pH: 7.2 / Details: 50MM MOPS PH 7.2, 12% MME PEG2K, STREAK-SEEDING | ||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.2 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→20 Å / Num. obs: 50677 / % possible obs: 93 % / Redundancy: 2 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 14.8 |
Reflection shell | Resolution: 2→2.43 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.101 / Mean I/σ(I) obs: 7.1 / % possible all: 80 |
Reflection | *PLUS Highest resolution: 2 Å / Lowest resolution: 19.8 Å / % possible obs: 93 % / Num. measured all: 102704 / Rmerge(I) obs: 0.04 |
Reflection shell | *PLUS % possible obs: 80 % / Rmerge(I) obs: 0.101 / Mean I/σ(I) obs: 7.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1PNK Resolution: 2→19.8 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.935 / SU B: 10.31 / SU ML: 0.292 / Cross valid method: THROUGHOUT / ESU R: 0.173 / ESU R Free: 0.147 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL PLUS MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.47 Å2
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Refinement step | Cycle: LAST / Resolution: 2→19.8 Å
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Refine LS restraints |
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