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Yorodumi- PDB-2z71: Structure of truncated mutant CYS1GLY of penicillin V acylase fro... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2z71 | ||||||
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Title | Structure of truncated mutant CYS1GLY of penicillin V acylase from bacillus sphaericus co-crystallized with penicillin V | ||||||
Components | Penicillin acylase | ||||||
Keywords | HYDROLASE / ZYMOGEN / PRECURSOR / PENICILLIN / AUTOPROTEOLYSIS / ANTIBIOTIC RESISTANCE / CATALYSIS / PENICILLIN V ACYLASE | ||||||
Function / homology | Function and homology information penicillin amidase / penicillin amidase activity / response to antibiotic Similarity search - Function | ||||||
Biological species | Bacillus sphaericus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Pathak, M.C. / Brannigan, J. / Dodson, G.G. / Suresh, C.G. | ||||||
Citation | Journal: To be published Title: Studies on the catalysis and post translational processing of penicillin V acylase Authors: Pathak, M.C. / Brannigan, J. / Dodson, G.G. / Suresh, C.G. #1: Journal: To be Published Title: Auto-proteolytic processing of Penicillin V Acylase is simpler than of other related Ntn hydrolases Authors: Pathak, M.C. / Brannigan, J. / Dodson, G.G. / Suresh, C.G. #2: Journal: To be Published Title: Co-crystal structure of Penicillin V Acylase with substrate Penicillin V: Insight in to catalytic specificity Authors: Pathak, M.C. / Brannigan, J. / Dodson, G.G. / Suresh, C.G. #3: Journal: To be Published Title: Polymorphism shown by the crystals of Penicillin V Acyalse from Bacillus sphaericus Authors: Pathak, M.C. / Brannigan, J. / Dodson, G.G. / Suresh, C.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2z71.cif.gz | 140.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2z71.ent.gz | 111.1 KB | Display | PDB format |
PDBx/mmJSON format | 2z71.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2z71_validation.pdf.gz | 510.6 KB | Display | wwPDB validaton report |
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Full document | 2z71_full_validation.pdf.gz | 559.5 KB | Display | |
Data in XML | 2z71_validation.xml.gz | 21.4 KB | Display | |
Data in CIF | 2z71_validation.cif.gz | 30.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z7/2z71 ftp://data.pdbj.org/pub/pdb/validation_reports/z7/2z71 | HTTPS FTP |
-Related structure data
Related structure data | 2pvaS 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: 37199.105 Da / Num. of mol.: 2 / Mutation: C1G Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus sphaericus (bacteria) / Strain: NCIM 2478 / Production host: Escherichia coli (E. coli) / References: UniProt: P12256, penicillin amidase #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.14 Å3/Da / Density % sol: 60.86 % |
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 6.4 / Details: pH 6.4, VAPOR DIFFUSION, HANGING DROP |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.933 Å |
Detector | Date: Mar 8, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→20 Å / Num. all: 78639 / Num. obs: 28157 / % possible obs: 89.6 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2PVA Resolution: 2.6→20 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.914 / SU B: 13.545 / SU ML: 0.28 / Cross valid method: THROUGHOUT / ESU R: 0.743 / ESU R Free: 0.339 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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 WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 46.447 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.666 Å / Total num. of bins used: 20 /
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