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Yorodumi- PDB-5ubu: 2.75 Angstrom Resolution Crystal Structure of Acetamidase from Ye... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ubu | ||||||
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Title | 2.75 Angstrom Resolution Crystal Structure of Acetamidase from Yersinia enterocolitica. | ||||||
Components | Putative acetamidase/formamidase | ||||||
Keywords | HYDROLASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / Acetamidase | ||||||
Function / homology | Acetamidase/Formamidase / Acetamidase/Formamidase family / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides / Putative acetamidase/formamidase Function and homology information | ||||||
Biological species | Yersinia enterocolitica subsp. palearctica serotype O:3 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.75 Å | ||||||
Authors | Minasov, G. / Shuvalova, L. / Flores, K. / Dubrovska, I. / Grimshaw, S. / Kwon, K. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
Citation | Journal: To Be Published Title: 2.75 Angstrom Resolution Crystal Structure of Acetamidase from Yersinia enterocolitica. Authors: Minasov, G. / Shuvalova, L. / Flores, K. / Dubrovska, I. / Grimshaw, S. / Kwon, K. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ubu.cif.gz | 525.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ubu.ent.gz | 452.8 KB | Display | PDB format |
PDBx/mmJSON format | 5ubu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5ubu_validation.pdf.gz | 452.4 KB | Display | wwPDB validaton report |
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Full document | 5ubu_full_validation.pdf.gz | 459.1 KB | Display | |
Data in XML | 5ubu_validation.xml.gz | 49.6 KB | Display | |
Data in CIF | 5ubu_validation.cif.gz | 70.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ub/5ubu ftp://data.pdbj.org/pub/pdb/validation_reports/ub/5ubu | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
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-Components
#1: Protein | Mass: 37376.402 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Yersinia enterocolitica subsp. palearctica serotype O:3 (bacteria) Strain: DSM 13030 / CIP 106945 / Y11 / Gene: Y11_22331 / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0H3NNJ4 #2: Chemical | ChemComp-NA / #3: 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: 3.27 Å3/Da / Density meas: 62.4 Mg/m3 / Density % sol: 62.12 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7 Details: Protein: 8.2 mg/ml, 0.5M Sodium chloride, 0.01M Tris HCl (pH 8.3); Screen: Classics II (B11), 2.1M DL-Malic acid (pH 7.0); Cryo: Screen : 50% Sucrose (1:1). |
-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: Oct 2, 2014 / Details: C(111) |
Radiation | Monochromator: beryllium lenses / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 |
Reflection | Resolution: 2.75→30 Å / Num. obs: 51774 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 7.9 % / Biso Wilson estimate: 53.7 Å2 / Rmerge(I) obs: 0.135 / Rsym value: 0.135 / Net I/σ(I): 17.8 |
Reflection shell | Resolution: 2.75→2.8 Å / Redundancy: 8 % / Rmerge(I) obs: 0.736 / Mean I/σ(I) obs: 3.1 / Num. unique all: 2554 / CC1/2: 0.849 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.75→29.81 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.93 / SU B: 20.527 / SU ML: 0.208 / Cross valid method: THROUGHOUT / ESU R: 0.67 / ESU R Free: 0.288 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 46.485 Å2
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Refinement step | Cycle: 1 / Resolution: 2.75→29.81 Å
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Refine LS restraints |
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