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Yorodumi- PDB-3pud: Crystal structure of Dhydrodipicolinate synthase from Acinetobact... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3pud | ||||||
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Title | Crystal structure of Dhydrodipicolinate synthase from Acinetobacter baumannii at 2.8A resolution | ||||||
Components | Dihydrodipicolinate synthase | ||||||
Keywords | LYASE / TIM barrel / beta-alpha-barrel / Diaminopimelate biosynthesis / Lysine biosynthesis | ||||||
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 | Acinetobacter baumannii (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Jithesh, O. / Yamini, S. / Kaur, N. / Gautam, A. / Tewari, R. / Kushwaha, G.S. / Kaur, P. / Srinivasan, A. / Sharma, S. / Singh, T.P. | ||||||
Citation | Journal: To be Published Title: Crystal structure of Dhydrodipicolinate synthase from Acinetobacter baumannii at 2.8A resolution Authors: Jithesh, O. / Yamini, S. / Kaur, N. / Gautam, A. / Tewari, R. / Kushwaha, G.S. / Kaur, P. / Srinivasan, A. / Sharma, S. / Singh, T.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3pud.cif.gz | 121 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3pud.ent.gz | 94.7 KB | Display | PDB format |
PDBx/mmJSON format | 3pud.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pu/3pud ftp://data.pdbj.org/pub/pdb/validation_reports/pu/3pud | HTTPS FTP |
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-Related structure data
Related structure data | 3noeS 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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-Components
#1: Protein | Mass: 31279.842 Da / Num. of mol.: 2 / Fragment: DHDPS, residues in UNP 7-297 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Strain: ATCC 19606 / Gene: DHDPS, HMPREF0010_03414 / Plasmid: pRSETa / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: D0CFC3, dihydrodipicolinate synthase #2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-GOL / #4: 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: 2.74 Å3/Da / Density % sol: 55.1 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 5.6 Details: 1.8M ammonium sulphate, 0.1M bis-tris, pH 5.6, VAPOR DIFFUSION, temperature 298K |
-Data collection
Diffraction | Mean temperature: 77 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Oct 21, 2010 / Details: Mirror |
Radiation | Monochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→47.5 Å / Num. all: 16301 / Num. obs: 16301 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 45 Å2 / Rsym value: 0.109 / Net I/σ(I): 10.3 |
Reflection shell | Highest resolution: 2.8 Å / Rmerge(I) obs: 0.418 / Mean I/σ(I) obs: 2 / Rsym value: 0.418 / % possible all: 92.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3NOE Resolution: 2.8→47.47 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 7177473.49 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 30.2004 Å2 / ksol: 0.383388 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.8→47.47 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.98 Å / Rfactor Rfree error: 0.035 / Total num. of bins used: 6
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Xplor file |
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