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Open data
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Basic information
Entry | Database: PDB / ID: 3qze | ||||||
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Title | Crystal Structure of DapA (PA1010) at 1.6 A resolution | ||||||
![]() | Dihydrodipicolinate synthase | ||||||
![]() | LYASE / Alpha beta barrel / Dihydrodipicolinate synthase / cytoplasmic | ||||||
Function / homology | ![]() (R,S)-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 / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Schnell, R. / Sandalova, T. / Schneider, G. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 468.8 KB | Display | ![]() |
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PDB format | ![]() | 384.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 459.1 KB | Display | ![]() |
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Full document | ![]() | 467.2 KB | Display | |
Data in XML | ![]() | 50 KB | Display | |
Data in CIF | ![]() | 74.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3r5aC ![]() 3r5bC ![]() 3r5cC ![]() 3r5dC ![]() 2ojpS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 34044.047 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: N-terminal His6-tag and TEV protease site / Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-CL / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 41.41 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.6 Details: 0.1 M Tris-HCl pH 7.6, 0.2 M MgCl2, 18% PEG6000, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 19, 2010 Details: channel cut ESRF monochromator and a new torodial focusing mirror |
Radiation | Monochromator: channel cut ESRF monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.977 Å / Relative weight: 1 |
Reflection | Resolution: 1.59→41.25 Å / Num. all: 139082 / Num. obs: 139082 / % possible obs: 92.7 % / Observed criterion σ(F): 3.1 / Observed criterion σ(I): 3.1 / Redundancy: 2 % / Biso Wilson estimate: 15.7 Å2 / Rmerge(I) obs: 0.053 / Rsym value: 0.053 / Net I/σ(I): 9.5 |
Reflection shell | Resolution: 1.59→1.67 Å / Redundancy: 2 % / Rmerge(I) obs: 0.281 / Mean I/σ(I) obs: 3.1 / Num. unique all: 20245 / Rsym value: 0.281 / % possible all: 92.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 2OJP chain-A edited Resolution: 1.59→40 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.944 / SU B: 3.385 / SU ML: 0.054 / Isotropic thermal model: Overall / Cross valid method: THROUGHOUT / σ(I): 3.1 / ESU R Free: 0.09 / 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: 13.103 Å2
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Refinement step | Cycle: LAST / Resolution: 1.59→40 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.586→1.627 Å / Total num. of bins used: 20
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