+Open data
-Basic information
Entry | Database: PDB / ID: 3r5d | ||||||
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Title | Pseudomonas aeruginosa DapD (PA3666) apoprotein | ||||||
Components | Tetrahydrodipicolinate N-succinyletransferase | ||||||
Keywords | TRANSFERASE | ||||||
Function / homology | Function and homology information 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase / 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase activity / diaminopimelate biosynthetic process / lysine biosynthetic process via diaminopimelate / magnesium ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Pseudomonas aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Sandalova, T. / Schnell, R. / Schneider, G. | ||||||
Citation | Journal: Plos One / Year: 2012 Title: Tetrahydrodipicolinate N-succinyltransferase and dihydrodipicolinate synthase from Pseudomonas aeruginosa: structure analysis and gene deletion. Authors: Schnell, R. / Oehlmann, W. / Sandalova, T. / Braun, Y. / Huck, C. / Maringer, M. / Singh, M. / Schneider, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3r5d.cif.gz | 363.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3r5d.ent.gz | 295.7 KB | Display | PDB format |
PDBx/mmJSON format | 3r5d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3r5d_validation.pdf.gz | 498.4 KB | Display | wwPDB validaton report |
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Full document | 3r5d_full_validation.pdf.gz | 536.7 KB | Display | |
Data in XML | 3r5d_validation.xml.gz | 73.6 KB | Display | |
Data in CIF | 3r5d_validation.cif.gz | 103.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r5/3r5d ftp://data.pdbj.org/pub/pdb/validation_reports/r5/3r5d | HTTPS FTP |
-Related structure data
Related structure data | 3qzeC 3r5aC 3r5bC 3r5cSC 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
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-Components
#1: Protein | Mass: 36288.379 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PAO1 / Gene: dapD, PA3666 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q9Z9H2, UniProt: G3XD76*PLUS, 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.62 Å3/Da / Density % sol: 53.12 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.2 Details: 19-20% of PEG3350, 0.3-0.4M succinate, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 1 Å | |||||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 7, 2009 | |||||||||||||||
Radiation | Monochromator: Si (111) double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||
Reflection twin |
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Reflection | Resolution: 1.8→25.06 Å / Num. all: 190821 / Num. obs: 190821 / % possible obs: 91.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.6 % / Rmerge(I) obs: 0.057 / Rsym value: 0.057 / Net I/σ(I): 10.8 | |||||||||||||||
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 2.8 / Rsym value: 0.37 / % possible all: 62.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3R5C Resolution: 1.8→24.38 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.919 / SU B: 2.458 / SU ML: 0.073 / Cross valid method: THROUGHOUT / ESU R: 0.028 / ESU R Free: 0.027 / 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: 20.338 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→24.38 Å
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Refine LS restraints |
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Refine LS restraints NCS | Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 1.799→1.845 Å / Total num. of bins used: 20
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