+Open data
-Basic information
Entry | Database: PDB / ID: 1q15 | ||||||
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Title | Carbapenam Synthetase | ||||||
Components | CarA | ||||||
Keywords | BIOSYNTHETIC PROTEIN / CMPr / (2S / 5S)-5-carboxymethylproline / b-LS / b-lactam synthetase / AS-B / class B asparagine synthetase / AMP-CPP / a / b-methyleneadenosine 5-triphosphate / CEA / N2-(carboxyethyl)-L-arginine / CMA / N2-(carboxylmethyl)-L-arginine | ||||||
Function / homology | Function and homology information carbapenam-3-carboxylate synthase / asparagine synthase (glutamine-hydrolyzing) activity / asparagine biosynthetic process / antibiotic biosynthetic process / ATP binding / cytosol Similarity search - Function | ||||||
Biological species | Pectobacterium carotovorum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å | ||||||
Authors | Miller, M.T. / Gerratana, B. / Stapon, A. / Townsend, C.A. / Rosenzweig, A.C. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2003 Title: Crystal Structure of Carbapenam Synthetase (CarA) Authors: Miller, M.T. / Gerratana, B. / Stapon, A. / 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 | 1q15.cif.gz | 379.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1q15.ent.gz | 314 KB | Display | PDB format |
PDBx/mmJSON format | 1q15.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1q15_validation.pdf.gz | 455.7 KB | Display | wwPDB validaton report |
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Full document | 1q15_full_validation.pdf.gz | 494.6 KB | Display | |
Data in XML | 1q15_validation.xml.gz | 70.5 KB | Display | |
Data in CIF | 1q15_validation.cif.gz | 96.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q1/1q15 ftp://data.pdbj.org/pub/pdb/validation_reports/q1/1q15 | HTTPS FTP |
-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: 56054.000 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pectobacterium carotovorum (bacteria) / Plasmid: pET24a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9XB61 #2: 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: 2.35 Å3/Da / Density % sol: 47.76 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 23-26 % (w/v) PEG 4000, 100 mM Na citrate, pH 5.6, 210-250 mM ammonium acetate, and 100 mM cesium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 295K | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 7.5 / Method: vapor diffusion, sitting 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: SSRL / Beamline: BL9-1 / Wavelength: 0.9789,0.9417,0.9793 | ||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 26, 2003 / Details: Flat mirror (vertical focusing) | ||||||||||||
Radiation | Monochromator: single crystal Si(311) bent monochromator (horizontal focusing) Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.3→24.22 Å / Num. obs: 91582 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Biso Wilson estimate: 19.2 Å2 / Limit h max: 26 / Limit h min: -26 / Limit k max: 78 / Limit k min: -26 / Limit l max: 42 / Limit l min: 0 / Observed criterion F min: 14 / Rsym value: 0.091 / Net I/σ(I): 7.4 | ||||||||||||
Reflection shell | Resolution: 2.3→2.42 Å / Mean I/σ(I) obs: 2.3 / Rsym value: 0.311 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MAD Starting model: de novo Resolution: 2.3→19.98 Å / Rfactor Rfree error: 0.003 / Occupancy max: 1 / Occupancy min: 1 / Data cutoff high absF: 2498836.12 / Data cutoff low absF: 0 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: CNS bulk solvent model used / Bsol: 31.7287 Å2 / ksol: 0.383535 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 83.26 Å2 / Biso mean: 29.32 Å2 / Biso min: 5.41 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.3→19.98 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION
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Xplor file |
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Software | *PLUS Name: CNS / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.3 Å / Lowest resolution: 20 Å / % reflection Rfree: 10 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |