+Open data
-Basic information
Entry | Database: PDB / ID: 1ai5 | ||||||
---|---|---|---|---|---|---|---|
Title | PENICILLIN ACYLASE COMPLEXED WITH M-NITROPHENYLACETIC ACID | ||||||
Components | (PENICILLIN AMIDOHYDROLASE) x 2 | ||||||
Keywords | ANTIBIOTIC RESISTANCE / LIGAND INDUCED CONFORMATIONAL CHANGE / HYDROLASE | ||||||
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 / STRUCTURE ISOMORPHOUS TO NATIVE / Resolution: 2.36 Å | ||||||
Authors | Done, S.H. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1998 Title: Ligand-induced conformational change in penicillin acylase. Authors: Done, S.H. / Brannigan, J.A. / Moody, P.C.E. / Hubbard, R.E. #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. #3: Journal: Protein Eng. / Year: 1990 Title: Expression, Purification and Crystallization 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. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1ai5.cif.gz | 180.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1ai5.ent.gz | 139.3 KB | Display | PDB format |
PDBx/mmJSON format | 1ai5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ai5_validation.pdf.gz | 458.6 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1ai5_full_validation.pdf.gz | 481.4 KB | Display | |
Data in XML | 1ai5_validation.xml.gz | 38.2 KB | Display | |
Data in CIF | 1ai5_validation.cif.gz | 57.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ai/1ai5 ftp://data.pdbj.org/pub/pdb/validation_reports/ai/1ai5 | HTTPS FTP |
-Related structure data
Related structure data | 1ai4C 1ai6C 1ai7C 1ajnC 1ajpC 1ajqC C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 23838.824 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P06875, penicillin amidase |
---|---|
#2: Protein | Mass: 62428.512 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P06875, penicillin amidase |
#3: Chemical | ChemComp-CA / |
#4: Chemical | ChemComp-MNP / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.06 Å3/Da / Density % sol: 59.5 % | ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Method: streak seeded / pH: 7.2 Details: CRYSTALLIZED FROM 10% PEG 8000, 50MM MOPS, PH 7.2, STREAK SEEDED. SOAKED IN 5MM M-NITROPHENYLACETIC ACID, streak seeded | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 300 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X31 / Wavelength: 0.98 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 1, 1995 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.36→26.12 Å / Num. obs: 34287 / % possible obs: 97.4 % / Redundancy: 2.1 % / Biso Wilson estimate: 19.02 Å2 / Rmerge(I) obs: 0.091 / Net I/σ(I): 8.2 |
Reflection shell | Resolution: 2.35→2.48 Å / Redundancy: 2 % / Rmerge(I) obs: 0.331 / Mean I/σ(I) obs: 2.3 / % possible all: 93.4 |
Reflection | *PLUS Num. measured all: 71097 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: STRUCTURE ISOMORPHOUS TO NATIVE Resolution: 2.36→26.12 Å / Cross valid method: FREE_R / σ(F): 0
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.47 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.36→26.12 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Num. reflection all: 34287 / Rfactor all: 0.1493 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |