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Yorodumi- PDB-3i7s: Dihydrodipicolinate synthase mutant - K161A - with the substrate ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3i7s | |||||||||
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Title | Dihydrodipicolinate synthase mutant - K161A - with the substrate pyruvate bound in the active site. | |||||||||
Components | Dihydrodipicolinate synthase | |||||||||
Keywords | LYASE / dihydrodipicolinate synthyase / lysine biosynthesis / Amino-acid biosynthesis / Diaminopimelate biosynthesis / Schiff base | |||||||||
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 K-12 (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | |||||||||
Authors | Dobson, R.C.J. / Jameson, G.B. / Gerrard, J.A. / Soares da Costa, T.P. | |||||||||
Citation | Journal: Biochimie / Year: 2010 Title: How essential is the 'essential' active-site lysine in dihydrodipicolinate synthase? Authors: Soares da Costa, T.P. / Muscroft-Taylor, A.C. / Dobson, R.C. / Devenish, S.R. / 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 | 3i7s.cif.gz | 127.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3i7s.ent.gz | 98.6 KB | Display | PDB format |
PDBx/mmJSON format | 3i7s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i7/3i7s ftp://data.pdbj.org/pub/pdb/validation_reports/i7/3i7s | HTTPS FTP |
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-Related structure data
Related structure data | 3i7qC 3i7rC 1yxcS C: citing same article (ref.) 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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2 |
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Unit cell |
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Components on special symmetry positions |
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Details | The biological unit is a tetramer, generated from the dimer in the assymetric unit. |
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 31332.947 Da / Num. of mol.: 2 / Fragment: dihydrodipicolinate synthase / Mutation: K161A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: b2478, dapA, JW2463 / Plasmid: pJG001 / Production host: Escherichia coli (E. coli) / Strain (production host): E. coli BL21 (DE3) / References: UniProt: P0A6L2, dihydrodipicolinate synthase |
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-Non-polymers , 5 types, 189 molecules
#2: Chemical | ChemComp-GOL / #3: Chemical | ChemComp-K / #4: Chemical | #5: Chemical | #6: 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: 3.72 Å3/Da / Density % sol: 66.93 % |
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Crystal grow | Temperature: 276 K / Method: vapor diffusion, hanging drop / pH: 10 Details: 1.8M POTASSIUM PHOSPHATE, PH 10, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 276K |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Oct 10, 2007 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→32.17 Å / Num. all: 39830 / Num. obs: 39830 / % possible obs: 95 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.42 % / Rmerge(I) obs: 0.088 / Rsym value: 0.088 / Net I/σ(I): 7.4 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 3.27 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 2.8 / Rsym value: 0.35 / % possible all: 97.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1yxc Resolution: 2.3→32.17 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.921 / SU B: 12.332 / SU ML: 0.135 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.228 / ESU R Free: 0.196 / 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: 27.751 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→32.17 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.298→2.357 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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