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Yorodumi- PDB-1jvz: Structure of cephalosporin acylase in complex with glutaryl-7-ami... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1jvz | ||||||
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Title | Structure of cephalosporin acylase in complex with glutaryl-7-aminocephalosporanic acid | ||||||
Components |
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Keywords | HYDROLASE / cephalosporin acylase / glutaryl-7-aminocephalosporanic acid | ||||||
Function / homology | Function and homology information glutaryl-7-aminocephalosporanic-acid acylase / glutaryl-7-aminocephalosporanic-acid acylase activity / antibiotic biosynthetic process / periplasmic space / response to antibiotic Similarity search - Function | ||||||
Biological species | Brevundimonas diminuta (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.6 Å | ||||||
Authors | Kim, Y. / Hol, W.G.J. | ||||||
Citation | Journal: CHEM.BIOL. / Year: 2001 Title: Structure of cephalosporin acylase in complex with glutaryl-7-aminocephalosporanic acid and glutarate: insight into the basis of its substrate specificity Authors: Kim, Y. / Hol, W.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1jvz.cif.gz | 150.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1jvz.ent.gz | 122.7 KB | Display | PDB format |
PDBx/mmJSON format | 1jvz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jv/1jvz ftp://data.pdbj.org/pub/pdb/validation_reports/jv/1jvz | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | heterodimer of one alpha and one beta chains |
-Components
#1: Protein | Mass: 17472.033 Da / Num. of mol.: 1 / Fragment: RESIDUES 30-187 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Brevundimonas diminuta (bacteria) / Plasmid: pET24d(+) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9L5D6 |
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#2: Protein | Mass: 58686.363 Da / Num. of mol.: 1 / Fragment: RESIDUES 199-718 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Brevundimonas diminuta (bacteria) / Plasmid: pET24d(+) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9L5D6 |
#3: Chemical | ChemComp-CEN / |
#4: 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: 3.42 Å3/Da / Density % sol: 64.08 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: PEG8000, MgAcetate, NaCacodylate, DTT, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 21 ℃ / pH: 7 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 125 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 1.0332 Å |
Detector | Type: CUSTOM-MADE / Detector: CCD / Date: Jun 24, 2000 |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→20 Å / Num. all: 33008 / Num. obs: 32457 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1.98 / Redundancy: 6 % / Biso Wilson estimate: 35 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 22.9 |
Reflection shell | Resolution: 2.6→2.69 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.587 / % possible all: 92.1 |
Reflection | *PLUS Lowest resolution: 20 Å / % possible obs: 98.3 % / Num. measured all: 196351 / Rmerge(I) obs: 0.06 |
Reflection shell | *PLUS Highest resolution: 2.6 Å / % possible obs: 92.1 % / Mean I/σ(I) obs: 1.98 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 2.6→20 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.6→20 Å
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Refine LS restraints |
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Refinement | *PLUS Lowest resolution: 20 Å / Rfactor Rfree: 0.213 / Rfactor Rwork: 0.19 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: c_bond_d / Dev ideal: 0.006 |