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Yorodumi- PDB-2pur: Structure of dihydrodipicolinate synthase mutant Thr44Ser at 1.7 A. -
+Open data
-Basic information
Entry | Database: PDB / ID: 2pur | ||||||
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Title | Structure of dihydrodipicolinate synthase mutant Thr44Ser at 1.7 A. | ||||||
Components | Dihydrodipicolinate synthase | ||||||
Keywords | LYASE / TIM barrel | ||||||
Function / homology | Function and homology information 4-hydroxy-2-oxoglutarate aldolase activity / 4-hydroxy-tetrahydrodipicolinate synthase / 4-hydroxy-tetrahydrodipicolinate synthase activity / glyoxylate catabolic process / diaminopimelate biosynthetic process / lysine biosynthetic process via diaminopimelate / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Dobson, R.C.J. / Jameson, G.B. / Gerrard, J.A. | ||||||
Citation | Journal: Biochimie / Year: 2009 Title: Specificity versus catalytic potency: The role of threonine 44 in Escherichia coli dihydrodipicolinate synthase mediated catalysis. Authors: Dobson, R.C. / Perugini, M.A. / Jameson, G.B. / Gerrard, J.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2pur.cif.gz | 139.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2pur.ent.gz | 107 KB | Display | PDB format |
PDBx/mmJSON format | 2pur.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pu/2pur ftp://data.pdbj.org/pub/pdb/validation_reports/pu/2pur | HTTPS FTP |
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-Related structure data
Related structure data | 1xycS 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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Details | The biological unit is a tetramer generated from the dimer. -X,-X+Y,1/3-Z |
-Components
#1: Protein | Mass: 31417.979 Da / Num. of mol.: 2 / Mutation: T44S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: dapA / Production host: Escherichia coli (E. coli) / References: UniProt: P0A6L2, dihydrodipicolinate synthase #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-GOL / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.71 Å3/Da / Density % sol: 66.86 % |
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Crystal grow | Temperature: 280 K / Method: vapor diffusion, hanging drop / pH: 10 Details: Drops contained: protein solution (~5 mg mL-1 in Tris.HCl 20 mM, pH 8, 2.5 uL), precipitant (K2HPO4 1.8 M, pH 10, 1.2 uL), and N-octyl-beta-R-glucopyranoside (6% w/v, 0.6 uL). Crystals ...Details: Drops contained: protein solution (~5 mg mL-1 in Tris.HCl 20 mM, pH 8, 2.5 uL), precipitant (K2HPO4 1.8 M, pH 10, 1.2 uL), and N-octyl-beta-R-glucopyranoside (6% w/v, 0.6 uL). Crystals appeared after 3-5 days and grew to dimensions of up to 0.2 mm., VAPOR DIFFUSION, HANGING DROP, temperature 280K |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→33.31 Å / Num. obs: 101750 / % possible obs: 99.2 % / Observed criterion σ(I): 3 / Redundancy: 4.1 % / Rmerge(I) obs: 0.054 / Net I/σ(I): 12.6 |
Reflection shell | Resolution: 1.7→1.76 Å / Redundancy: 3.91 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 3 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1XYC, with residue 44 in each chain removed. Resolution: 1.7→33.31 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.953 / SU B: 1.989 / SU ML: 0.063 / Cross valid method: THROUGHOUT / ESU R: 0.08 / ESU R Free: 0.083 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.34 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→33.31 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.744 Å / Total num. of bins used: 20
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