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Yorodumi- PDB-5ez4: 2.11 Angstrom resolution crystal structure of betaine aldehyde de... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ez4 | ||||||
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Title | 2.11 Angstrom resolution crystal structure of betaine aldehyde dehydrogenase (betB) P449M/Y450L double mutant from Staphylococcus aureus in complex with NAD+ and BME-modified Cys289 | ||||||
Components | Betaine aldehyde dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / BETAINE ALDEHYDE DEHYDROGENASE / ROSSMANN FOLD / STRUCTURAL GENOMICS / CENTER FOR STRUCTURAL GENOMICS OF INFECTIOUS DISEASES / CSGID | ||||||
Function / homology | Function and homology information betaine-aldehyde dehydrogenase / betaine-aldehyde dehydrogenase (NAD+) activity / glycine betaine biosynthetic process from choline / nucleotide binding / metal ion binding Similarity search - Function | ||||||
Biological species | Staphylococcus aureus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.11 Å | ||||||
Authors | Halavaty, A.S. / Minasov, G. / Chen, C. / Joo, J.C. / Yakunin, A.F. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
Citation | Journal: To Be Published Title: 2.11 Angstrom resolution crystal structure of betaine aldehyde dehydrogenase (betB) P449M/Y450L double mutant from Staphylococcus aureus in complex with NAD+ and BME-modified Cys289 Authors: Halavaty, A.S. / Minasov, G. / Chen, C. / Joo, J.C. / Yakunin, A.F. / Anderson, W.F. #1: Journal: Acta Crystallogr. D Biol. Crystallogr. / Year: 2015 Title: Structural and functional analysis of betaine aldehyde dehydrogenase from Staphylococcus aureus. Authors: Halavaty, A.S. / Rich, R.L. / Chen, C. / Joo, J.C. / Minasov, G. / Dubrovska, I. / Winsor, J.R. / Myszka, D.G. / Duban, M. / Shuvalova, L. / Yakunin, A.F. / Anderson, W.F. #2: Journal: Appl. Environ. Microbiol. / Year: 2014 Title: Structure-based mutational studies of substrate inhibition of betaine aldehyde dehydrogenase BetB from Staphylococcus aureus. Authors: Chen, C. / Joo, J.C. / Brown, G. / Stolnikova, E. / Halavaty, A.S. / Savchenko, A. / Anderson, W.F. / Yakunin, A.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ez4.cif.gz | 821.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ez4.ent.gz | 677.1 KB | Display | PDB format |
PDBx/mmJSON format | 5ez4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5ez4_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 5ez4_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 5ez4_validation.xml.gz | 94.4 KB | Display | |
Data in CIF | 5ez4_validation.cif.gz | 138.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ez/5ez4 ftp://data.pdbj.org/pub/pdb/validation_reports/ez/5ez4 | HTTPS FTP |
-Related structure data
Related structure data | 4mpbS S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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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: _ / End auth comp-ID: SER / End label comp-ID: SER / Refine code: _
NCS ensembles :
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-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 57176.312 Da / Num. of mol.: 4 / Mutation: P449M, Y450L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) / Plasmid: p15TV-LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)/PMAGIC / References: UniProt: Q9L4P8, betaine-aldehyde dehydrogenase |
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-Non-polymers , 5 types, 2019 molecules
#2: Chemical | ChemComp-NAD / #3: Chemical | ChemComp-NA / #4: Chemical | ChemComp-PGE / #5: Chemical | ChemComp-EPE / #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.95 Å3/Da / Density % sol: 58.26 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7 Details: Potein: 6 mg/ml, 10 mM Tris-HCl, pH 8.3, 500 mM NaCl, 5 mM BME, 5mM NAD+. Crystallization: Classics II D3: 100 mM HEPES, pH 7.0, 30%(v/v) Jeffamine ED-2001. Cryo: crystallization condition |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 29, 2015 |
Radiation | Monochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 |
Reflection | Resolution: 2.11→30 Å / Num. obs: 154078 / % possible obs: 99.9 % / Redundancy: 3.5 % / Biso Wilson estimate: 21.3 Å2 / Rmerge(I) obs: 0.136 / Net I/σ(I): 9.92 |
Reflection shell | Resolution: 2.11→2.15 Å / Redundancy: 3 % / Rmerge(I) obs: 0.496 / Mean I/σ(I) obs: 2.06 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 4MPB Resolution: 2.11→29.69 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.952 / SU B: 6.389 / SU ML: 0.089 / Cross valid method: THROUGHOUT / ESU R: 0.156 / ESU R Free: 0.135 / 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: 22.98 Å2
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Refinement step | Cycle: 1 / Resolution: 2.11→29.69 Å
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Refine LS restraints |
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