+Open data
-Basic information
Entry | Database: PDB / ID: 2yxg | ||||||
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Title | Crystal structure of Dihyrodipicolinate Synthase (dapA) | ||||||
Components | Dihydrodipicolinate synthase | ||||||
Keywords | LYASE / MJ0244 / DIHYDRODIPICOLINATE SYNTHASE / TIM beta/alpha-barrel fold / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information 4-hydroxy-tetrahydrodipicolinate synthase / 4-hydroxy-tetrahydrodipicolinate synthase activity / diaminopimelate biosynthetic process / lysine biosynthetic process via diaminopimelate / cytoplasm Similarity search - Function | ||||||
Biological species | Methanocaldococcus jannaschii DSM 2661 (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Padmanabhan, B. / Bessho, Y. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2009 Title: Structure of dihydrodipicolinate synthase from Methanocaldococcus jannaschii. Authors: Padmanabhan, B. / Strange, R.W. / Antonyuk, S.V. / Ellis, M.J. / Hasnain, S.S. / Iino, H. / Agari, Y. / Bessho, Y. / Yokoyama, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2yxg.cif.gz | 236.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2yxg.ent.gz | 191.4 KB | Display | PDB format |
PDBx/mmJSON format | 2yxg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yx/2yxg ftp://data.pdbj.org/pub/pdb/validation_reports/yx/2yxg | HTTPS FTP |
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-Related structure data
Related structure data | 1o5kS S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | AUTHOR DETERMINED BIOLOGICAL UNIT: UNKNOWN |
-Components
#1: Protein | Mass: 31613.436 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanocaldococcus jannaschii DSM 2661 (archaea) Species: Methanocaldococcus jannaschii / Strain: DSM2661 / Gene: dapA / Plasmid: pET-21a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) / References: UniProt: Q57695, dihydrodipicolinate synthase #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: 2.37 Å3/Da / Density % sol: 48.15 % |
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Crystal grow | Temperature: 293 K / Method: oil-batch / pH: 6.5 Details: 18% PEG 8000, 0.1M Cacodylate, 0.2M Ca Acetate, pH 6.5, Oil-batch, temperature 293.0K |
-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX10.1 / Wavelength: 0.979 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD |
Radiation | Monochromator: double crystal monochromator with sagittal focussing Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. all: 59985 / Num. obs: 58517 / % possible obs: 97.6 % / Observed criterion σ(F): -3 / Redundancy: 3.9 % / Rmerge(I) obs: 0.067 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.211 / Num. unique all: 4918 / % possible all: 82.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1O5K Resolution: 2.2→20 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.925 / SU B: 5.776 / SU ML: 0.147 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.265 / ESU R Free: 0.211 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.881 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.203→2.26 Å / Total num. of bins used: 20
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