+Open data
-Basic information
Entry | Database: PDB / ID: 5g12 | ||||||
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Title | Pseudomonas aeruginosa HDAH (Y313F) unliganded. | ||||||
Components | HDAH | ||||||
Keywords | HYDROLASE / HDAH / HDAC / HDLP | ||||||
Function / homology | Function and homology information Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides / histone deacetylase activity / epigenetic regulation of gene expression / hydrolase activity / metal ion binding Similarity search - Function | ||||||
Biological species | PSEUDOMONAS AERUGINOSA (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.02 Å | ||||||
Authors | Kraemer, A. / Meyer-Almes, F.J. / Yildiz, O. | ||||||
Citation | Journal: Biochemistry / Year: 2016 Title: Crystal Structure of a Histone Deacetylase Homologue from Pseudomonas aeruginosa. Authors: Kramer, A. / Wagner, T. / Yildiz, O. / Meyer-Almes, F.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5g12.cif.gz | 160.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5g12.ent.gz | 125.9 KB | Display | PDB format |
PDBx/mmJSON format | 5g12.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5g12_validation.pdf.gz | 440.3 KB | Display | wwPDB validaton report |
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Full document | 5g12_full_validation.pdf.gz | 448.6 KB | Display | |
Data in XML | 5g12_validation.xml.gz | 31.2 KB | Display | |
Data in CIF | 5g12_validation.cif.gz | 45.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g1/5g12 ftp://data.pdbj.org/pub/pdb/validation_reports/g1/5g12 | HTTPS FTP |
-Related structure data
Related structure data | 5g0xSC 5g0yC 5g10C 5g11C 5g13C 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
#1: Protein | Mass: 40951.242 Da / Num. of mol.: 2 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Strain: PA01 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9HXM1 #2: Chemical | #3: Chemical | ChemComp-K / #4: 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: 2.08 Å3/Da / Density % sol: 40.94 % / Description: NONE |
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Crystal grow | pH: 7.5 / Details: pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.00002 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 4, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.00002 Å / Relative weight: 1 |
Reflection | Resolution: 2.02→75.79 Å / Num. obs: 46280 / % possible obs: 99.4 % / Observed criterion σ(I): 2.7 / Redundancy: 9.9 % / Rmerge(I) obs: 0.27 / Net I/σ(I): 6.2 |
Reflection shell | Resolution: 2.02→2.07 Å / Redundancy: 9.1 % / Rmerge(I) obs: 1.29 / Mean I/σ(I) obs: 2.7 / % possible all: 96.8 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 5G0X Resolution: 2.02→75.79 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.925 / SU B: 4.415 / SU ML: 0.122 / Cross valid method: THROUGHOUT / ESU R: 0.205 / ESU R Free: 0.171 / 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: 25.952 Å2
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Refinement step | Cycle: LAST / Resolution: 2.02→75.79 Å
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Refine LS restraints |
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