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Yorodumi- PDB-1gk0: Structure-based prediction of modifications in glutarylamidase to... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1gk0 | ||||||
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Title | Structure-based prediction of modifications in glutarylamidase to allow single-step enzymatic production of 7-aminocephalosporanic acid from cephalosporin C | ||||||
Components | (CEPHALOSPORIN ACYLASE) x 2 | ||||||
Keywords | HYDROLASE / CEPHALOSPORIN ACYLASE / GLUTARYL ACYLASE / CEPHALOSPORIN C / CATALYTIC TRIAD / NTN-HYDROLASE / X-RAZ STRUCTURE | ||||||
Function / homology | Function and homology information glutaryl-7-aminocephalosporanic-acid acylase / glutaryl-7-aminocephalosporanic-acid acylase activity / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides / antibiotic biosynthetic process / periplasmic space / response to antibiotic / metal ion binding Similarity search - Function | ||||||
Biological species | PSEUDOMONAS SP. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å | ||||||
Authors | Fritz-Wolf, K. / Koller, K.P. / Lange, G. / Liesum, A. / Sauber, K. / Schreuder, H. / Aretz, W. / Kabsch, W. | ||||||
Citation | Journal: Protein Sci. / Year: 2002 Title: Structure-Based Prediction of Modifications in Glutarylamidase to Allow Single-Step Enzymatic Production of 7-Aminocephalosporanic Acid from Cephalosporin C. Authors: Fritz-Wolf, K. / Koller, K. / Lange, G. / Liesum, A. / Sauber, K. / Schreuder, H. / Aretz, W. / Kabsch, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1gk0.cif.gz | 279.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1gk0.ent.gz | 236.1 KB | Display | PDB format |
PDBx/mmJSON format | 1gk0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gk/1gk0 ftp://data.pdbj.org/pub/pdb/validation_reports/gk/1gk0 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 16988.514 Da / Num. of mol.: 2 / Fragment: RESIDUES A8-A160 Source method: isolated from a genetically manipulated source Source: (gene. exp.) PSEUDOMONAS SP. (bacteria) / Production host: ESCHERICHIA COLI (E. coli) References: UniProt: O86089, UniProt: P07662*PLUS, penicillin amidase #2: Protein | Mass: 58855.785 Da / Num. of mol.: 2 / Fragment: RESIDUES B1-B522 Source method: isolated from a genetically manipulated source Source: (gene. exp.) PSEUDOMONAS SP. (bacteria) / Production host: ESCHERICHIA COLI (E. coli) References: UniProt: O86089, UniProt: P07662*PLUS, penicillin amidase #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Compound details | CATALYTICLLY ACTIVE CEPHALOSPORIN ACYLASE IS FORMED BY A TWO-STEP AUTOCATALYTIC PROCESS FROM THE ...CATALYTICL | |
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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 Å3/Da / Density % sol: 58 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8 Details: CRYSTALS GROWN AT 18 C, HANGING DROP PRECIPITATION AGENT: 1.5-2.0 M POTASSIUM PHOSPHATE PH:7.0 -9.0, pH 8.00 | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 18 ℃ / pH: 7.5 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.8854,0.9776,0.9779 | ||||||||||||
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE | ||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.5→20 Å / Num. obs: 118686 / % possible obs: 96.8 % / Redundancy: 2.05 % / Biso Wilson estimate: 20.4 Å2 / Rmerge(I) obs: 0.045 | ||||||||||||
Reflection shell | Resolution: 2.5→2.6 Å / Redundancy: 1.63 % / Rmerge(I) obs: 0.095 / % possible all: 79.4 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.5→19.48 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 8082389.02 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / ksol: 0.36922 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→19.48 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.66 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 20 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor obs: 0.256 |