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Yorodumi- PDB-2w21: Crystal structure of the aminoacid kinase domain of the glutamate... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2w21 | ||||||
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Title | Crystal structure of the aminoacid kinase domain of the glutamate 5 kinase of Escherichia coli. | ||||||
Components | GLUTAMATE 5-KINASE | ||||||
Keywords | TRANSFERASE / AMINO ACID KINASE FAMILY / PROLINE BIOSYNTHESIS / AMINO-ACID BIOSYNTHESIS / KINASE / CYTOPLASM / GLUTAMATE KINASEAMINO ACID KINASE FAMILY / GLUTAMATE KINASE | ||||||
Function / homology | Function and homology information proline binding / glutamate 5-kinase / glutamate 5-kinase activity / L-proline biosynthetic process / proline biosynthetic process / phosphorylation / magnesium ion binding / protein homodimerization activity / RNA binding / ATP binding ...proline binding / glutamate 5-kinase / glutamate 5-kinase activity / L-proline biosynthetic process / proline biosynthetic process / phosphorylation / magnesium ion binding / protein homodimerization activity / RNA binding / ATP binding / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | ESCHERICHIA COLI (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å | ||||||
Authors | Perez-Arellano, I. / Gil-Ortiz, F. / Marco-Marin, C. / Cervera, J. / Rubio, V. | ||||||
Citation | Journal: To be Published Title: The Structure of Glutamate 5 Kinase of Escherichia Coli without Substrates Authors: Perez-Arellano, I. / Gil-Ortiz, F. / Marco-Marin, C. / Cervera, J. / Rubio, V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2w21.cif.gz | 58.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2w21.ent.gz | 42.1 KB | Display | PDB format |
PDBx/mmJSON format | 2w21.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w2/2w21 ftp://data.pdbj.org/pub/pdb/validation_reports/w2/2w21 | HTTPS FTP |
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-Related structure data
Related structure data | 2j5tS 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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-Components
#1: Protein | Mass: 27280.154 Da / Num. of mol.: 1 / Fragment: AMINO ACID KINASE DOMAIN, RESIDUES 1-259 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Plasmid: PET22B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P0A7B5, glutamate 5-kinase | ||||
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#2: Chemical | ChemComp-SO4 / #3: Water | ChemComp-HOH / | Compound details | ENGINEERED | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.15 Å3/Da / Density % sol: 70.35 % / Description: NONE |
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Crystal grow | pH: 5.6 Details: LITHIUM SULFATE 1M, AMMONIUM SULFATE 0.5M, SODIUM SITRATE 0.1M PH 5.6 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.9796 |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 26, 2008 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9796 Å / Relative weight: 1 |
Reflection | Resolution: 2.95→122.17 Å / Num. obs: 10173 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 15.4 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 5.6 |
Reflection shell | Resolution: 2.95→3.11 Å / Redundancy: 15.7 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 1.7 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2J5T Resolution: 2.95→50 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.88 / SU B: 13.905 / SU ML: 0.257 / Cross valid method: THROUGHOUT / ESU R: 0.546 / ESU R Free: 0.337 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 52.6 Å2
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Refinement step | Cycle: LAST / Resolution: 2.95→50 Å
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Refine LS restraints |
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