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Yorodumi- 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 | |||||||||
Components | (BETAINE ALDEHYDE ...) x 2 | |||||||||
Keywords | OXIDOREDUCTASE / ALDEHYDE OXIDATION / NAD / NADP COMPLEX | |||||||||
| Function / homology | Function and homology informationbetaine-aldehyde dehydrogenase (NAD+) activity / betaine-aldehyde dehydrogenase / glycine betaine biosynthetic process from choline / metal ion binding Similarity search - Function | |||||||||
| Biological species | ![]() | |||||||||
| Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | |||||||||
Authors | Gonzalez-Segura, L. / Rudino-Pinera, E. / Munoz-Clares, R.A. / Horjales, E. | |||||||||
Citation | Journal: J.Mol.Biol. / Year: 2009Title: 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: Molmil Jmol/JSmol |
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Downloads & links
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Download
| PDBx/mmCIF format | 2wme.cif.gz | 808 KB | Display | PDBx/mmCIF format |
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| PDB format | pdb2wme.ent.gz | 665.7 KB | Display | PDB format |
| PDBx/mmJSON format | 2wme.json.gz | Tree view | PDBx/mmJSON format | |
| Others | Other downloads |
-Validation report
| Summary document | 2wme_validation.pdf.gz | 3 MB | Display | wwPDB validaton report |
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| Full document | 2wme_full_validation.pdf.gz | 3.1 MB | Display | |
| Data in XML | 2wme_validation.xml.gz | 168.5 KB | Display | |
| Data in CIF | 2wme_validation.cif.gz | 241.4 KB | Display | |
| Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wm/2wme ftp://data.pdbj.org/pub/pdb/validation_reports/wm/2wme | HTTPS FTP |
-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 








| #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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.9795 |
| 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: 0.9795 Å / Relative weight: 1 |
| 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: MOLECULAR REPLACEMENTStarting 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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