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Yorodumi- PDB-1gk1: Structure-based prediction of modifications in glutarylamidase to... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1gk1 | ||||||
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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 / MOLECULAR REPLACEMENT / Resolution: 2.4 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.P. / 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 | 1gk1.cif.gz | 282.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1gk1.ent.gz | 228.3 KB | Display | PDB format |
PDBx/mmJSON format | 1gk1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gk/1gk1 ftp://data.pdbj.org/pub/pdb/validation_reports/gk/1gk1 | HTTPS FTP |
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-Related structure data
Related structure data | 1gk0SC S: Starting model for refinement C: citing same article (ref.) |
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Similar 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: 16941.619 Da / Num. of mol.: 2 / Fragment: RESIDUES 36-188 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: 58339.941 Da / Num. of mol.: 2 / Fragment: RESIDUES 199-720 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: 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 | ||||||||||||||||||||||||||||||
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: ROTATING ANODE / Type: ENRAF-NONIUS FR571 / Wavelength: 1.5418 |
Detector | Type: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Feb 15, 1997 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→14.63 Å / Num. obs: 67222 / % possible obs: 94.1 % / Redundancy: 1.9 % / Biso Wilson estimate: 16.7 Å2 / Rmerge(I) obs: 0.09 |
Reflection shell | Resolution: 2.4→2.5 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.262 / % possible all: 92.7 |
Reflection | *PLUS Lowest resolution: 15 Å / % possible obs: 93.7 % / Rmerge(I) obs: 0.093 |
Reflection shell | *PLUS % possible obs: 92.7 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1GK0 Resolution: 2.4→14.63 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 6897765.46 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / ksol: 0.33435 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.4→14.63 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.55 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: 15 Å / Rfactor obs: 0.18 / Rfactor Rwork: 0.18 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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