+Open data
-Basic information
Entry | Database: PDB / ID: 2we5 | ||||||
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Title | Carbamate kinase from Enterococcus faecalis bound to MgADP | ||||||
Components | CARBAMATE KINASE 1 | ||||||
Keywords | TRANSFERASE / ARGININE CATABOLISM / ARGININE METABOLISM / ATP SYNTHESYS / KINASE / OPEN ALPHA/BETA SHEET / PHOSPHOTRANSFERASE | ||||||
Function / homology | Function and homology information carbamate kinase / carbamate kinase activity / arginine deiminase pathway / phosphorylation / ATP binding / cytosol Similarity search - Function | ||||||
Biological species | ENTEROCOCCUS FAECALIS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.39 Å | ||||||
Authors | Ramon-Maiques, S. / Marina, A. / Rubio, V. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2010 Title: Substrate Binding and Catalysis in Carbamate Kinase Ascertained by Crystallographic and Site- Directed Mutagenesis Studies. Movements and Significance of a Unique Globular Subdomain of This ...Title: Substrate Binding and Catalysis in Carbamate Kinase Ascertained by Crystallographic and Site- Directed Mutagenesis Studies. Movements and Significance of a Unique Globular Subdomain of This Key Enzyme for Fermentative ATP Production in Bacteria. Authors: Ramon-Maiques, S. / Marina, A. / Guinot, A. / Gil-Ortiz, F. / Uriarte, M. / Fita, I. / Rubio, V. #1: Journal: Protein Sci. / Year: 1999 Title: Carbamate Kinase: New Structural Machinery for Making Carbamoyl Phosphate, the Common Precursor of Pyrimidines and Arginine. Authors: Marina, A. / Alzari, P.M. / Bravo, J. / Uriarte, M. / Barcelona, B. / Fita, I. / Rubio, V. #2: 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 Thermostable Enzyme is a Carbamate Kinase, and Provides Insight 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 | 2we5.cif.gz | 205.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2we5.ent.gz | 164.7 KB | Display | PDB format |
PDBx/mmJSON format | 2we5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2we5_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 2we5_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 2we5_validation.xml.gz | 44.8 KB | Display | |
Data in CIF | 2we5_validation.cif.gz | 65 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/we/2we5 ftp://data.pdbj.org/pub/pdb/validation_reports/we/2we5 | HTTPS FTP |
-Related structure data
Related structure data | 2we4C 1b7bS 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: 32958.578 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ENTEROCOCCUS FAECALIS (bacteria) / Plasmid: PET15B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0A2X7, carbamate kinase #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-ACT / | #5: 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: 2.25 Å3/Da / Density % sol: 45 % / Description: NONE |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop Details: CRYSTALS WERE OBTAINED AT 4 DEGREES USING THE HANGING DROP VAPOUR DIFFUSION METHOD BY MIXING 1.5 MIRCROLITERS OF A 10 MG/ML PROTEIN SOLUTION IN 5 MM SODIUM CACODYLATE PH 6.5, 2 MM ADP, 5 MM ...Details: CRYSTALS WERE OBTAINED AT 4 DEGREES USING THE HANGING DROP VAPOUR DIFFUSION METHOD BY MIXING 1.5 MIRCROLITERS OF A 10 MG/ML PROTEIN SOLUTION IN 5 MM SODIUM CACODYLATE PH 6.5, 2 MM ADP, 5 MM MGCL2 AND 50 MM SODIUM PHOPHONOACETATE, AND 1.5 MICROLITERS OF THE RESERVOIR BUFFER CONTAINING 13-16% PEG 8000, 130-160 MM MAGNESIUM ACETATE AND 0.1 M SODIUM CACODYLATE PH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.9067 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 1, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9067 Å / Relative weight: 1 |
Reflection | Resolution: 1.39→50 Å / Num. obs: 172839 / % possible obs: 90.4 % / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Biso Wilson estimate: 20 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 7 |
Reflection shell | Resolution: 1.39→1.47 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 2.2 / % possible all: 87.1 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1B7B Resolution: 1.39→20 Å / Data cutoff high absF: 10000 / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Bsol: 46.1408 Å2 / ksol: 0.342447 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.7 Å2
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Refinement step | Cycle: LAST / Resolution: 1.39→20 Å
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Refine LS restraints |
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Xplor file |
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