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Yorodumi- PDB-5hop: 1.65 Angstrom resolution crystal structure of lmo0182 (residues 1... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5hop | ||||||
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Title | 1.65 Angstrom resolution crystal structure of lmo0182 (residues 1-245) from Listeria monocytogenes EGD-e | ||||||
Components | Lmo0182 protein | ||||||
Keywords | HYDROLASE / lmo0182 / Center for Structural Genomics of Infectious Diseases / CSGID / Listeria monocytogenes EGD-e | ||||||
Function / homology | Function and homology information hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate binding / carbohydrate metabolic process Similarity search - Function | ||||||
Biological species | Listeria monocytogenes serovar 1/2a (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.65 Å | ||||||
Authors | Halavaty, A.S. / Light, S.H. / Minasov, G. / Grimshaw, S. / Kwon, K. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
Citation | Journal: Structure / Year: 2017 Title: Transferase Versus Hydrolase: The Role of Conformational Flexibility in Reaction Specificity. Authors: Light, S.H. / Cahoon, L.A. / Mahasenan, K.V. / Lee, M. / Boggess, B. / Halavaty, A.S. / Mobashery, S. / Freitag, N.E. / Anderson, W.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5hop.cif.gz | 218.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5hop.ent.gz | 184.2 KB | Display | PDB format |
PDBx/mmJSON format | 5hop.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ho/5hop ftp://data.pdbj.org/pub/pdb/validation_reports/ho/5hop | HTTPS FTP |
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-Related structure data
Related structure data | 5hpoC 5hxmC 5i0dC 5i0eC 5i0fC 5i0gC C: citing same article (ref.) |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
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-Components
#1: Protein | Mass: 28503.094 Da / Num. of mol.: 2 / Mutation: UNP residues 2-245 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e) (bacteria) Strain: ATCC BAA-679 / EGD-e / Gene: lmo0182 / Plasmid: pMCSG53 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-Magic / References: UniProt: Q8YAE8 #2: Chemical | #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: 2.48 Å3/Da / Density % sol: 50.38 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5 Details: protein: 15.2 mg/ml in 10 mM Tris-HCl pH 8.3 0.5 mM TCEP crystallization: The PACT Suite C2(#26): 0.1 M PCB buffer pH 5.0 25% (w/v) PEG1500 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: Aug 13, 2015 |
Radiation | Monochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→30 Å / Num. obs: 65420 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 7.3 % / Biso Wilson estimate: 25 Å2 / Rmerge(I) obs: 0.087 / Net I/σ(I): 44.2 |
Reflection shell | Resolution: 1.65→1.68 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.641 / Mean I/σ(I) obs: 3.3 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.65→29.45 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.959 / SU B: 3.655 / SU ML: 0.063 / Cross valid method: THROUGHOUT / ESU R: 0.089 / ESU R Free: 0.089 / 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: 28.295 Å2
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Refinement step | Cycle: 1 / Resolution: 1.65→29.45 Å
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Refine LS restraints |
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