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Yorodumi- PDB-1e19: Structure of the carbamate kinase-like carbamoyl phosphate synthe... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1.0E+19 | ||||||
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Title | Structure of the carbamate kinase-like carbamoyl phosphate synthetase from the hyperthermophilic archaeon Pyrococcus furiosus bound to ADP | ||||||
Components | CARBAMATE KINASE | ||||||
Keywords | TRANSFERASE / HYPERTHERMOPHILES / ADP SITE / ARGININE METABOLISM PHOSPHORYL GROUP TRANSFER | ||||||
Function / homology | Function and homology information carbamate kinase / carbamate kinase activity / arginine metabolic process / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | PYROCOCCUS FURIOSUS (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Ramon-Maiques, S. / Marina, A. / Uriarte, M. / Fita, I. / Rubio, V. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2000 Title: The 1.5-A Resolution Crystal Structure of the Carbamate Kinase-Like Carbamoyl Phosphate Synthetase from the Hyperthermophilic Archaeon Pyrococcus Furiosus, Bound to Adp, Confirms that This ...Title: The 1.5-A Resolution Crystal Structure of the Carbamate Kinase-Like Carbamoyl Phosphate Synthetase from the Hyperthermophilic Archaeon Pyrococcus Furiosus, Bound to Adp, Confirms that This Thermoestable Enzyme is a Carbamate Kinase, and Provides Insights Into Substrate Binding and Stability in Carbamate Kinases Authors: Ramon-Maiques, S. / Marina, A. / Uriarte, M. / Fita, I. / Rubio, V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1e19.cif.gz | 154.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1e19.ent.gz | 119.9 KB | Display | PDB format |
PDBx/mmJSON format | 1e19.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e1/1e19 ftp://data.pdbj.org/pub/pdb/validation_reports/e1/1e19 | HTTPS FTP |
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-Related structure data
Related structure data | 1b7bS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.958996, -0.047676, 0.279105), Vector: |
-Components
#1: Protein | Mass: 34475.582 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) PYROCOCCUS FURIOSUS (archaea) / References: UniProt: P95474, carbamate kinase #2: Chemical | #3: Chemical | #4: 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: 2.5 Å3/Da / Density % sol: 50 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 8 Details: 1.3M SODIUM CITRATE 0.1M TRIS-HCL, PH=8.5, 0-10% ETHYLENE GLYCOL PROTEIN SOLUTION: 10MG/ML OF PROTEIN IN 10MM TRIS-HCL CONTAINING 20MM ATP AND MGCL2, pH 8.00 | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 22 ℃ / Method: vapor diffusion, hanging drop / pH: 8.5 | ||||||||||||||||||||||||||||||||||||||||||
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 / Type: ESRF / Wavelength: 0.93 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Sep 15, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.93 Å / Relative weight: 1 |
Reflection | Resolution: 1.43→76.67 Å / Num. obs: 116569 / % possible obs: 97.3 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.067 / Rsym value: 0.067 / Net I/σ(I): 5.2 |
Reflection shell | Resolution: 1.5→1.59 Å / Rmerge(I) obs: 0.355 / Mean I/σ(I) obs: 1.9 / Rsym value: 0.355 / % possible all: 98.6 |
Reflection | *PLUS Num. measured all: 448640 |
Reflection shell | *PLUS Highest resolution: 1.5 Å / % possible obs: 98.6 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1B7B Resolution: 1.5→15 Å / Cross valid method: THROUGHOUT / σ(F): 0
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Refinement step | Cycle: LAST / Resolution: 1.5→15 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.183 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 1.5 Å / Lowest resolution: 1.66 Å / Rfactor Rfree: 0.267 / Num. reflection Rfree: 1593 / Num. reflection obs: 24677 / Rfactor obs: 0.229 |