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- PDB-2wme: Crystallographic structure of betaine aldehyde dehydrogenase from... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2wme | |||||||||
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Title | Crystallographic structure of betaine aldehyde dehydrogenase from Pseudomonas aeruginosa | |||||||||
![]() | (BETAINE ALDEHYDE ...) x 2 | |||||||||
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Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Gonzalez-Segura, L. / Rudino-Pinera, E. / Munoz-Clares, R.A. / Horjales, E. | |||||||||
![]() | ![]() Title: The Crystal Structure of a Ternary Complex of Betaine Aldehyde Dehydrogenase from Pseudomonas Aeruginosa Provides New Insight Into the Reaction Mechanism and Shows a Novel Binding Mode of the ...Title: The Crystal Structure of a Ternary Complex of Betaine Aldehyde Dehydrogenase from Pseudomonas Aeruginosa Provides New Insight Into the Reaction Mechanism and Shows a Novel Binding Mode of the 2'- Phosphate of Nadp(+) and a Novel Cation Binding Site. Authors: Gonzalez-Segura, L. / Rudino-Pinera, E. / Munoz-Clares, R.A. / Horjales, E. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 808 KB | Display | ![]() |
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PDB format | ![]() | 665.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1a4sS S: Starting model for refinement |
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Similar structure data |
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Links
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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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: PHE / End label comp-ID: PHE / Refine code: 6 / Auth seq-ID: 2 - 490 / Label seq-ID: 2 - 490
NCS ensembles :
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Components
-BETAINE ALDEHYDE ... , 2 types, 8 molecules ABDFGHCE
#1: Protein | Mass: 53390.262 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() ![]() #2: Protein | Mass: 53406.262 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() ![]() |
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-Non-polymers , 5 types, 2982 molecules ![](data/chem/img/NAP.gif)
![](data/chem/img/BME.gif)
![](data/chem/img/K.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/BME.gif)
![](data/chem/img/K.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-NAP / ![]() #4: Chemical | ChemComp-BME / ![]() #5: Chemical | ChemComp-K / #6: Chemical | ChemComp-GOL / ![]() #7: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.67 Å3/Da / Density % sol: 53.95 % / Description: NONE |
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Crystal grow![]() | pH: 7.5 Details: CRYSTALS WERE GROWN IN 85 MM HEPES, PH 7.5, 8.5 % (V:V) ISOPROPANOL, 17 % PEG 4000 AND 1 MM NADP |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Apr 11, 2005 Details: DOUBLE CRYSTAL CHANNEL CUT, SI(111), 1M LONG RH COATED TOROIDAL MIRROR FOR VERTICAL AND HORIZONTAL FOCUSING. |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2→47.3 Å / Num. obs: 277775 / % possible obs: 93 % / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Biso Wilson estimate: 22.83 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 8.2 |
Reflection shell | Resolution: 2→2.1 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 1.6 / % possible all: 79.3 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 1A4S Resolution: 2.1→42.68 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.92 / SU B: 7.919 / SU ML: 0.124 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.209 / ESU R Free: 0.182 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.707 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→42.68 Å
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Refine LS restraints |
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