+Open data
-Basic information
Entry | Database: PDB / ID: 2re1 | ||||||
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Title | Crystal structure of aspartokinase alpha and beta subunits | ||||||
Components | Aspartokinase, alpha and beta subunits | ||||||
Keywords | TRANSFERASE / Neisseria meningitidis / aspartokinase / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG | ||||||
Function / homology | Function and homology information aspartate kinase / aspartate kinase activity / homoserine biosynthetic process / threonine biosynthetic process / lysine biosynthetic process via diaminopimelate / ATP binding / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Neisseria meningitidis MC58 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.75 Å | ||||||
Authors | Chang, C. / Li, H. / Gu, M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published Title: Crystal structure of aspartokinase alpha and beta subunits. Authors: Chang, C. / Li, H. / Gu, M. / Joachimiak, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2re1.cif.gz | 65.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2re1.ent.gz | 52.7 KB | Display | PDB format |
PDBx/mmJSON format | 2re1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2re1_validation.pdf.gz | 435.6 KB | Display | wwPDB validaton report |
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Full document | 2re1_full_validation.pdf.gz | 440.7 KB | Display | |
Data in XML | 2re1_validation.xml.gz | 12.7 KB | Display | |
Data in CIF | 2re1_validation.cif.gz | 16.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/re/2re1 ftp://data.pdbj.org/pub/pdb/validation_reports/re/2re1 | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 18247.738 Da / Num. of mol.: 2 / Fragment: Residues 242-405 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Neisseria meningitidis MC58 (bacteria) / Species: Neisseria meningitidis / Strain: MC58 / Serogroup B / Gene: lysC, NMB1498 / Plasmid: pMCSG7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9JYN6, aspartate kinase #2: Chemical | |
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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: 2.51 Å3/Da / Density % sol: 51.01 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 20% PEG 1000, Imidazole, Ca(OAc)2, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97923 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 19, 2006 |
Radiation | Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97923 Å / Relative weight: 1 |
Reflection | Resolution: 2.75→50 Å / Num. all: 10415 / Num. obs: 10201 / % possible obs: 97.9 % / Observed criterion σ(I): -3 / Redundancy: 12.5 % / Biso Wilson estimate: 74.8 Å2 / Rmerge(I) obs: 0.115 / Net I/σ(I): 31.47 |
Reflection shell | Resolution: 2.75→2.77 Å / Redundancy: 8 % / Rmerge(I) obs: 0.115 / Mean I/σ(I) obs: 1.98 / Num. unique all: 187 / % possible all: 77 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.75→44.46 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.913 / SU B: 34.211 / SU ML: 0.307 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.093 / ESU R Free: 0.372 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 62.689 Å2
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Refinement step | Cycle: LAST / Resolution: 2.75→44.46 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.75→2.82 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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