+Open data
-Basic information
Entry | Database: PDB / ID: 3i7q | ||||||
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Title | Dihydrodipicolinate synthase mutant - K161A | ||||||
Components | Dihydrodipicolinate synthase | ||||||
Keywords | LYASE / dihydrodipicolinate synthase / lysine biosynthesis | ||||||
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: 2 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 | 3i7q.cif.gz | 128.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3i7q.ent.gz | 99.7 KB | Display | PDB format |
PDBx/mmJSON format | 3i7q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i7/3i7q ftp://data.pdbj.org/pub/pdb/validation_reports/i7/3i7q | HTTPS FTP |
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-Related structure data
Related structure data | 3i7rC 3i7sC 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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2 |
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Unit cell |
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-Components
#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 (E. coli) / Gene: DapA / Plasmid: pJG001 / Production host: Escherichia coli (E. coli) / Strain (production host): E. coli BL21 (DE3) / References: UniProt: P0A6L2, dihydrodipicolinate synthase #2: Chemical | ChemComp-GOL / #3: Chemical | ChemComp-K / #4: Chemical | ChemComp-PO4 / | #5: 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: 3.73 Å3/Da / Density % sol: 67.02 % |
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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: 1.99→36.84 Å / Num. all: 63475 / Num. obs: 63475 / % possible obs: 99.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.23 % / Rmerge(I) obs: 0.91 / Net I/σ(I): 7.1 |
Reflection shell | Resolution: 1.99→2.07 Å / Redundancy: 4.02 % / Rmerge(I) obs: 0.453 / Mean I/σ(I) obs: 2.3 / % possible all: 96.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1yxc Resolution: 2→36.84 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.937 / SU B: 4.648 / SU ML: 0.103 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.141 / ESU R Free: 0.135 / 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: 29.134 Å2
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Refinement step | Cycle: LAST / Resolution: 2→36.84 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.996→2.047 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 28.0277 Å / Origin y: -16.6527 Å / Origin z: 6.6206 Å
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