+Open data
-Basic information
Entry | Database: PDB / ID: 1ajp | ||||||
---|---|---|---|---|---|---|---|
Title | PENICILLIN ACYLASE COMPLEXED WITH 2,5-DIHYDROXYPHENYLACETIC 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 / ISOMORPHOUS TO NATIVE / Resolution: 2.31 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 | 1ajp.cif.gz | 182 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1ajp.ent.gz | 140 KB | Display | PDB format |
PDBx/mmJSON format | 1ajp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ajp_validation.pdf.gz | 461.2 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1ajp_full_validation.pdf.gz | 483.8 KB | Display | |
Data in XML | 1ajp_validation.xml.gz | 38.4 KB | Display | |
Data in CIF | 1ajp_validation.cif.gz | 57.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/aj/1ajp ftp://data.pdbj.org/pub/pdb/validation_reports/aj/1ajp | HTTPS FTP |
-Related structure data
Related structure data | 1ai4C 1ai5C 1ai6C 1ai7C 1ajnC 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-OMD / |
#4: Chemical | ChemComp-CA / |
#5: Water | ChemComp-HOH / |
Nonpolymer details | THERE IS DISORDER IN THE LIGAND WHICH IS ONLY 50% OCCUPIED. |
-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 10MM 2,5-DIHYDROXYPHENYLACETIC 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: Jul 1, 1995 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.31→26.81 Å / Num. obs: 33820 / % possible obs: 96.1 % / Redundancy: 2 % / Biso Wilson estimate: 19.46 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 7.2 |
Reflection shell | Resolution: 2.31→2.44 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.179 / Mean I/σ(I) obs: 3.7 / % possible all: 84.7 |
Reflection | *PLUS Num. measured all: 67021 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ISOMORPHOUS TO NATIVE / Resolution: 2.31→26.81 Å / Cross valid method: FREE R Details: ISOMORPHOUS TO NATIVE THERE IS DISORDER IN A 145 AND A 146, BOTH HAVING DUAL CONFORMATIONS AS A RESULT OF LIGAND BINDING.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.45 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.31→26.81 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor all: 0.146 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |