+Open data
-Basic information
Entry | Database: PDB / ID: 5l9k | ||||||
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Title | OCEANOBACILLUS IHEYENSIS MACRODOMAIN WITH ADPR | ||||||
Components | MACROD-TYPE MACRODOMAIN | ||||||
Keywords | HYDROLASE / macrodomain / ADP-ribosylation / deacetylase | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Oceanobacillus iheyensis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.77 Å | ||||||
Authors | Gil-Ortiz, F. / Zapata-Perez, R. / Martinez, A.B. / Juanhuix, J. / Sanchez-Ferrer, A. | ||||||
Funding support | Spain, 1items
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Citation | Journal: Open Biol / Year: 2017 Title: Structural and functional analysis of Oceanobacillus iheyensis macrodomain reveals a network of waters involved in substrate binding and catalysis. Authors: Zapata-Perez, R. / Gil-Ortiz, F. / Martinez-Monino, A.B. / Garcia-Saura, A.G. / Juanhuix, J. / Sanchez-Ferrer, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5l9k.cif.gz | 95.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5l9k.ent.gz | 71.1 KB | Display | PDB format |
PDBx/mmJSON format | 5l9k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5l9k_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 5l9k_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 5l9k_validation.xml.gz | 18.1 KB | Display | |
Data in CIF | 5l9k_validation.cif.gz | 26.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l9/5l9k ftp://data.pdbj.org/pub/pdb/validation_reports/l9/5l9k | HTTPS FTP |
-Related structure data
Related structure data | 5fudC 5l9qC 5lauC 5lbpC 5lccC 1spvS 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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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
NCS oper:
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-Components
#1: Protein | Mass: 22795.898 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Oceanobacillus iheyensis (strain DSM 14371 / CIP 107618 / JCM 11309 / KCTC 3954 / HTE831) (bacteria) Gene: OB2288 / Plasmid: pET28a-OiMacroD / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): ROSETTA 2 / References: UniProt: Q8EP31 #2: Chemical | #3: Chemical | #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: 2.58 Å3/Da / Density % sol: 52.34 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.2 M ammonium sulfate, 0.1 M MES pH 6.5, 30% (w/v) PEGMME 5K, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9794 Å | |||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 27, 2013 / Details: KB mirrors | |||||||||||||||
Radiation | Monochromator: Channel cut / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 | |||||||||||||||
Reflection twin |
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Reflection | Resolution: 1.77→48.95 Å / Num. obs: 41381 / % possible obs: 97.2 % / Redundancy: 3.6 % / Biso Wilson estimate: 17.263 Å2 / CC1/2: 0.997 / Rsym value: 0.066 / Net I/σ(I): 13.1 | |||||||||||||||
Reflection shell | Resolution: 1.77→1.87 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 2.2 / CC1/2: 0.743 / % possible all: 84.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1SPV Resolution: 1.77→48.35 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.961 / SU B: 1.339 / SU ML: 0.045 / Cross valid method: THROUGHOUT / ESU R: 0.021 / ESU R Free: 0.019 / 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: 24.014 Å2
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Refinement step | Cycle: 1 / Resolution: 1.77→48.35 Å
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Refine LS restraints |
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