+Open data
-Basic information
Entry | Database: PDB / ID: 3og9 | ||||||
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Title | Structure of YahD with Malic acid | ||||||
Components | protein yahD a copper inducible hydrolase | ||||||
Keywords | HYDROLASE / alpha/beta hydrolase / copper homeostasis / malic acid | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Lactococcus lactis subsp. lactis (lactic acid bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å | ||||||
Authors | Martinez Font, J. / Mancini, S. / Tauberger, E. / Moniot, S. | ||||||
Citation | Journal: Fems Microbiol.Lett. / Year: 2011 Title: Regulation and structure of YahD, a copper inducible alpha/beta hydrolase of Lactococcus lactis IL1403 Authors: Martinez, J. / Mancini, S. / Tauberger, E. / Weise, C. / Saenger, W. / Solioz, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3og9.cif.gz | 107.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3og9.ent.gz | 82.9 KB | Display | PDB format |
PDBx/mmJSON format | 3og9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/og/3og9 ftp://data.pdbj.org/pub/pdb/validation_reports/og/3og9 | HTTPS FTP |
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-Related structure data
Related structure data | 2hliS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 23588.654 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lactococcus lactis subsp. lactis (lactic acid bacteria) Strain: IL1403 / Gene: yahD, LL0076, L795, L79507 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9CJC1 #2: Chemical | #3: Water | ChemComp-HOH / | Sequence details | THE AUTHORS STATE THAT THE UNP ENTRY Q9CJC1 SHOULD HAVE RESIDUES 191T AND 199K | |
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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: 2.21 Å3/Da / Density % sol: 44.45 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 37.5% PEG 3350, 150mM DL-Malic acid pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918 Å |
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Mar 9, 2009 |
Radiation | Monochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.918 Å / Relative weight: 1 |
Reflection | Resolution: 1.88→40 Å / Num. obs: 34965 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.139 / Net I/σ(I): 0.159 |
Reflection shell | Resolution: 1.88→1.93 Å / Rmerge(I) obs: 0.691 / Mean I/σ(I) obs: 3.9 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB CODE 2hli Resolution: 1.88→39.53 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.918 / SU B: 3.158 / SU ML: 0.095 / Cross valid method: THROUGHOUT / ESU R Free: 0.147 / 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: 13.441 Å2
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Refinement step | Cycle: LAST / Resolution: 1.88→39.53 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.88→1.929 Å / Total num. of bins used: 20
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