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Yorodumi- PDB-1e3a: A slow processing precursor penicillin acylase from Escherichia coli -
+Open data
-Basic information
Entry | Database: PDB / ID: 1e3a | ||||||
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Title | A slow processing precursor penicillin acylase from Escherichia coli | ||||||
Components | (PENICILLIN AMIDASE ...) x 2 | ||||||
Keywords | ANTIBIOTIC RESISTANCE / AMIDASE / NTN-HYDROLASE / HYDROLYSIS OF PENICILLIN G ACYLASE | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Hewitt, L. / Kasche, V. / Lummer, K. / Lewis, R.J. / Murshudov, G.N. / Verma, C.S. / Dodson, G.G. / Wilson, K.S. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2000 Title: Structure of a Slow Processing Precursor Penicillin Acylase from Escherichia Coli Reveals the Linker Peptide Blocking the Active-Site Cleft Authors: Hewitt, L. / Kasche, V. / Lummer, K. / Lewis, R.J. / Murshudov, G.N. / Verma, C.S. / Dodson, G.G. / Wilson, K.S. #1: Journal: Acta Crystallogr.,Sect.D / Year: 1999 Title: Crystallisation of a Precursor Penicillin Acylase from Escherichia Coli Authors: Hewitt, L. / Kasche, V. / Lummer, K. / Rieks, A. / Wilson, K.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1e3a.cif.gz | 202.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1e3a.ent.gz | 156.8 KB | Display | PDB format |
PDBx/mmJSON format | 1e3a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1e3a_validation.pdf.gz | 436 KB | Display | wwPDB validaton report |
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Full document | 1e3a_full_validation.pdf.gz | 449.1 KB | Display | |
Data in XML | 1e3a_validation.xml.gz | 43.9 KB | Display | |
Data in CIF | 1e3a_validation.cif.gz | 69.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e3/1e3a ftp://data.pdbj.org/pub/pdb/validation_reports/e3/1e3a | HTTPS FTP |
-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
-PENICILLIN AMIDASE ... , 2 types, 2 molecules AB
#1: Protein | Mass: 28963.695 Da / Num. of mol.: 1 / Fragment: PENICILLIN AMIDASE RESIDUES 29-286 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: HB101 / Cellular location: PERIPLASM / Gene: PAC / Plasmid: PHM12 / Gene (production host): PAC / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): K5 / References: UniProt: P06875, penicillin amidase |
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#2: Protein | Mass: 62684.770 Da / Num. of mol.: 1 / Fragment: PENICILLIN AMIDASE RESIDUES 287-846 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: HB101 / Cellular location: PERIPLASM / Gene: PAC / Plasmid: PHM12 / Gene (production host): PAC / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): K5 / References: UniProt: P06875, penicillin amidase |
-Non-polymers , 4 types, 1198 molecules
#3: Chemical | ChemComp-CA / | ||
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#4: Chemical | ChemComp-CL / | ||
#5: Chemical | #6: Water | ChemComp-HOH / | |
-Details
Compound details | CHAIN B ENGINEEREDSequence details | SWISS-PROT SEQ: SIGNAL REMOVED ON TRANSLOCAT | |
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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: 2.17 Å3/Da / Density % sol: 43 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.2 Details: 50MM MOPS PH7.2, 18-20% PEG 5KME, 10MM CACL2, pH 7.20 | |||||||||||||||||||||||||||||||||||
Crystal | *PLUS Density % sol: 43 % | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 18 ℃ / Method: vapor diffusion, hanging drop / pH: 7.2 | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.9096 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 15, 1997 / Details: SEGMENTED MIRROR |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9096 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→20 Å / Num. obs: 70642 / % possible obs: 96.9 % / Redundancy: 1.9 % / Biso Wilson estimate: 12.2 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 10.3 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.216 / Mean I/σ(I) obs: 3.16 / % possible all: 89.1 |
Reflection | *PLUS Num. measured all: 133678 |
Reflection shell | *PLUS % possible obs: 89.1 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1PNK Resolution: 1.8→20 Å / SU B: 2.5 / SU ML: 0.08 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.13 / ESU R Free: 0.12
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Displacement parameters | Biso mean: 15.1 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→20 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 20 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: p_bond_d / Dev ideal: 0.009 |