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Yorodumi- PDB-2adv: Crystal Structures Of Glutaryl 7-Aminocephalosporanic Acid Acylas... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2adv | ||||||
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Title | Crystal Structures Of Glutaryl 7-Aminocephalosporanic Acid Acylase: mutational study of activation mechanism | ||||||
Components | (Glutaryl 7- Aminocephalosporanic Acid Acylase) x 3 | ||||||
Keywords | HYDROLASE / autoproteolysis / precursor activation / intermediate structure / cephalosporin acylase | ||||||
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 | Pseudomonas sp. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.244 Å | ||||||
Authors | Kim, J.K. / Yang, I.S. / Shin, H.J. / Cho, K.J. / Ryu, E.K. / Kim, S.H. / Park, S.S. / Kim, K.H. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2006 Title: Insight into autoproteolytic activation from the structure of cephalosporin acylase: a protein with two proteolytic chemistries. Authors: Kim, J.K. / Yang, I.S. / Shin, H.J. / Cho, K.J. / Ryu, E.K. / Kim, S.H. / Park, S.S. / Kim, K.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2adv.cif.gz | 275.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2adv.ent.gz | 222 KB | Display | PDB format |
PDBx/mmJSON format | 2adv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ad/2adv ftp://data.pdbj.org/pub/pdb/validation_reports/ad/2adv | 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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-Components
#1: Protein | Mass: 18205.922 Da / Num. of mol.: 1 / Fragment: alpha domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas sp. (bacteria) / Species: Pseudomonas sp. SY-77-1 / Strain: GK16 / Plasmid: pET23a / Production host: Escherichia coli (E. coli) / References: UniProt: P07662, penicillin amidase |
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#2: Protein/peptide | Mass: 2951.253 Da / Num. of mol.: 1 / Fragment: beta1 domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas sp. (bacteria) / Species: Pseudomonas sp. SY-77-1 / Strain: GK16 / Plasmid: pET23a / Production host: Escherichia coli (E. coli) / References: UniProt: P07662*PLUS, penicillin amidase |
#3: Protein | Mass: 56185.559 Da / Num. of mol.: 1 / Fragment: beta2 domain / Mutation: Y33L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas sp. (bacteria) / Species: Pseudomonas sp. SY-77-1 / Strain: GK16 / Plasmid: pET23a / Production host: Escherichia coli (E. coli) / References: UniProt: P07662*PLUS, penicillin amidase |
#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: 3.4 Å3/Da / Density % sol: 63.5 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: PEG 3350, Tris, magnesium chloride, cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 0.95 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: May 23, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95 Å / Relative weight: 1 |
Reflection | Resolution: 2.24→50 Å / Num. all: 52570 / Num. obs: 49679 / % possible obs: 94.5 % / Rmerge(I) obs: 0.08 / Χ2: 1.02 |
Reflection shell | Resolution: 2.24→2.29 Å / % possible obs: 87.3 % / Num. measured obs: 2995 / Χ2: 0.812 |
-Phasing
Phasing MR | Method rotation: fast direct |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.244→48.22 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.939 / SU B: 4.367 / SU ML: 0.108 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.171 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.343 Å2
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Refinement step | Cycle: LAST / Resolution: 2.244→48.22 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.244→2.302 Å / Total num. of bins used: 20 /
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