+Open data
-Basic information
Entry | Database: PDB / ID: 1jgt | ||||||
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Title | CRYSTAL STRUCTURE OF BETA-LACTAM SYNTHETASE | ||||||
Components | BETA-LACTAM SYNTHETASE | ||||||
Keywords | HYDROLASE / BETA-LACTAM SYNTHETASE / ASPARAGINE SYNTHETASE / CLAVULANIC ACID / AMPCPP / CEA / CARBOXYETHYLARGININE | ||||||
Function / homology | Function and homology information (carboxyethyl)arginine beta-lactam-synthase / (carboxyethyl)arginine beta-lactam-synthase activity / asparagine synthase (glutamine-hydrolyzing) activity / asparagine biosynthetic process / clavulanic acid biosynthetic process / ATP binding / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Streptomyces clavuligerus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.95 Å | ||||||
Authors | Miller, M.T. / Bachmann, B.O. / Townsend, C.A. / Rosenzweig, A.C. | ||||||
Citation | Journal: Nat.Struct.Biol. / Year: 2001 Title: Structure of beta-lactam synthetase reveals how to synthesize antibiotics instead of asparagine. Authors: Miller, M.T. / Bachmann, B.O. / Townsend, C.A. / Rosenzweig, A.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1jgt.cif.gz | 216.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1jgt.ent.gz | 168.5 KB | Display | PDB format |
PDBx/mmJSON format | 1jgt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1jgt_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 1jgt_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 1jgt_validation.xml.gz | 45.4 KB | Display | |
Data in CIF | 1jgt_validation.cif.gz | 64.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jg/1jgt ftp://data.pdbj.org/pub/pdb/validation_reports/jg/1jgt | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 54601.562 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces clavuligerus (bacteria) / Gene: 1901 / Plasmid: pET24a(+) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): bl21(DE3) / References: UniProt: Q9R8E3, UniProt: P0DJQ7*PLUS |
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-Non-polymers , 5 types, 633 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-GOL / #6: Water | ChemComp-HOH / | |
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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: 2.22 Å3/Da / Density % sol: 44.71 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop / pH: 8 Details: POLYETHYLENEGLYCOL 4000, GLYCEROL, TRIS, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 296K | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.5 / Details: Miller, M.T., (2001) Nature Struct. Biol., 8, 684. | |||||||||||||||||||||||||||||||||||||||||||||||||
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: APS / Beamline: 5ID-B / Wavelength: 1 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Nov 18, 2000 |
Radiation | Monochromator: GRAPHITE / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→19.97 Å / Num. all: 69641 / Num. obs: 68300 / % possible obs: 94.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 6.8 % / Biso Wilson estimate: 15.1 Å2 / Limit h max: 31 / Limit h min: -31 / Limit k max: 50 / Limit k min: -31 / Limit l max: 41 / Limit l min: 0 / Observed criterion F max: 569036.55 / Observed criterion F min: 0.32 / Rmerge(I) obs: 0.194 / Net I/σ(I): 10.4 |
Reflection shell | Resolution: 1.95→2.02 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.23 / % possible all: 98.1 |
Reflection | *PLUS Lowest resolution: 20 Å / % possible obs: 98.3 % / Num. measured all: 465261 / Rmerge(I) obs: 0.062 |
Reflection shell | *PLUS % possible obs: 98.1 % / Rmerge(I) obs: 0.231 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.95→19.89 Å / Rfactor Rfree error: 0.003 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 2 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: CNS bulk solvent model used / Bsol: 55.1407 Å2 / ksol: 0.386944 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 77.68 Å2 / Biso mean: 30.4 Å2 / Biso min: 11.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.95→19.89 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 20 Å / σ(F): 0 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 30.4 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.254 / % reflection Rfree: 7 % / Rfactor Rwork: 0.253 |