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Yorodumi- PDB-4kmq: 1.9 Angstrom resolution crystal structure of uncharacterized prot... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4kmq | ||||||
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Title | 1.9 Angstrom resolution crystal structure of uncharacterized protein lmo2446 from Listeria monocytogenes EGD-e | ||||||
Components | Lmo2446 protein | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / uncharacterized protein / Virulence / Pathogenesis / CSGID / NIAID / National Institute of Allergy and Infectious Diseases / Center for Structural Genomics of Infectious Diseases / TIM-barrel | ||||||
Function / homology | Function and homology information hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate binding / carbohydrate metabolic process / metal ion binding Similarity search - Function | ||||||
Biological species | Listeria monocytogenes (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å | ||||||
Authors | Halavaty, A.S. / Minasov, G. / Filippova, E.V. / Dubrovska, I. / Winsor, J. / Shuvalova, L. / Peterson, S. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
Citation | Journal: Nat Microbiol / Year: 2016 Title: Structure to function of an alpha-glucan metabolic pathway that promotes Listeria monocytogenes pathogenesis. Authors: Light, S.H. / Cahoon, L.A. / Halavaty, A.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 | 4kmq.cif.gz | 476.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4kmq.ent.gz | 401.5 KB | Display | PDB format |
PDBx/mmJSON format | 4kmq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/km/4kmq ftp://data.pdbj.org/pub/pdb/validation_reports/km/4kmq | HTTPS FTP |
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-Related structure data
Related structure data | 5do8C 5f7pC 5f7qC 5f7rC 5f7sC 5f7uC 5f7vC C: citing same article (ref.) |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 122520.227 Da / Num. of mol.: 1 / Fragment: UNP residues 31-1091 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Listeria monocytogenes (bacteria) / Strain: EGD-e / Gene: lmo2446 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Magic / References: UniProt: Q8Y4J2 | ||
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#2: Chemical | ChemComp-MG / #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.47 Å3/Da / Density % sol: 50.28 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.3 Details: crystallization conditions - The JCSG+ suite (A5: 200 mM Magnesium formate, 20 % w/v PEG3350), protein - 7.1 mg/mL in 10 mM Tris/HCl pH8.3, 500 mM NaCl, 5 mM BME, cryo - soaked in ...Details: crystallization conditions - The JCSG+ suite (A5: 200 mM Magnesium formate, 20 % w/v PEG3350), protein - 7.1 mg/mL in 10 mM Tris/HCl pH8.3, 500 mM NaCl, 5 mM BME, cryo - soaked in crystallization condition solution, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-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: Mar 15, 2013 / Details: BE-LENSES/DIAMOND LAUE MONO |
Radiation | Monochromator: DIAMOND[111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→30 Å / Num. obs: 185978 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 2.5 % / Biso Wilson estimate: 28.4 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 22.1 |
Reflection shell | Resolution: 1.9→1.93 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.502 / Mean I/σ(I) obs: 2 / Num. unique all: 9248 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.9→29.66 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.964 / SU B: 6.318 / SU ML: 0.083 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R: 0.126 / ESU R Free: 0.116 / 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: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.733 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→29.66 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.949 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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