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Yorodumi- PDB-3zqa: CRYSTALLOGRAPHIC STRUCTURE OF BETAINE ALDEHYDE DEHYDROGENASE MUTA... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3zqa | ||||||
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Title | CRYSTALLOGRAPHIC STRUCTURE OF BETAINE ALDEHYDE DEHYDROGENASE MUTANT C286A FROM PSEUDOMONAS AERUGINOSA IN COMPLEX WITH NADPH | ||||||
Components | BETAINE ALDEHYDE DEHYDROGENASE | ||||||
Keywords | OXIDOREDUCTASE / ALDEHYDE OXIDATION / NADPH COMPLEX | ||||||
Function / homology | Function and homology information 4-trimethylammoniobutyraldehyde dehydrogenase activity / aminobutyraldehyde dehydrogenase (NAD+) activity / betaine-aldehyde dehydrogenase / betaine-aldehyde dehydrogenase (NAD+) activity / glycine betaine biosynthetic process from choline / metal ion binding Similarity search - Function | ||||||
Biological species | PSEUDOMONAS AERUGINOSA (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å | ||||||
Authors | Diaz-Sanchez, A.G. / Gonzalez-Segura, L. / Rudino-Pinera, E. / Lira-Rocha, A. / Torres-Larios, A. / Munoz-Clares, R.A. | ||||||
Citation | Journal: Biochem.J. / Year: 2011 Title: Novel Nadph-Cysteine Covalent Adduct Found in the Active Site of an Aldehyde Dehydrogenase. Authors: Diaz-Sanchez, A.G. / Gonzalez-Segura, L. / Rudino-Pinera, E. / Lira-Rocha, A. / Torres-Larios, A. / Munoz-Clares, R.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3zqa.cif.gz | 857.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3zqa.ent.gz | 714.6 KB | Display | PDB format |
PDBx/mmJSON format | 3zqa.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3zqa_validation.pdf.gz | 3.5 MB | Display | wwPDB validaton report |
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Full document | 3zqa_full_validation.pdf.gz | 3.6 MB | Display | |
Data in XML | 3zqa_validation.xml.gz | 103.5 KB | Display | |
Data in CIF | 3zqa_validation.cif.gz | 145.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zq/3zqa ftp://data.pdbj.org/pub/pdb/validation_reports/zq/3zqa | HTTPS FTP |
-Related structure data
Related structure data | 2woxC 2wmeS S: Starting model for refinement C: citing same article (ref.) |
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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
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 53358.199 Da / Num. of mol.: 4 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Plasmid: PCALBETB / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS / References: UniProt: Q9HTJ1, betaine-aldehyde dehydrogenase |
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-Non-polymers , 7 types, 1930 molecules
#2: Chemical | ChemComp-GOL / #3: Chemical | ChemComp-PG4 / | #4: Chemical | #5: Chemical | ChemComp-NDP / #6: Chemical | ChemComp-K / #7: Chemical | ChemComp-TOE / | #8: Water | ChemComp-HOH / | |
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-Details
Compound details | ENGINEERED RESIDUE IN CHAIN A, CYS 286 TO ALA ENGINEERED RESIDUE IN CHAIN B, CYS 286 TO ALA ...ENGINEERED |
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Nonpolymer details | 1,2-ETHANEDIOL (EDO): FRAGMENT OF A PEG MOLECULE VISIBLE IN THE ELECTRON DENSITY. TETRAETHYLENE ...1,2-ETHANEDIOL |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.81 Å3/Da / Density % sol: 67.7 % / 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% (W:V)PEG 4000, 15% (V:V) GLYCEROL AND 2MM NADPH. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.9793 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Mar 20, 2010 / Details: DOUBLE CRYSTAL CHANNEL CUT, SI(III) 1M LONG |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 2.45→30 Å / Num. obs: 117977 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Biso Wilson estimate: 38.67 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 11.7 |
Reflection shell | Resolution: 2.45→2.5 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 2 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2WME Resolution: 2.45→38.515 Å / SU ML: 0.14 / σ(F): 1.34 / Phase error: 18.01 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 67.906 Å2 / ksol: 0.362 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.45→38.515 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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