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Yorodumi- PDB-5hxm: Cycloalternan-forming enzyme from Listeria monocytogenes in compl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5hxm | |||||||||
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Title | Cycloalternan-forming enzyme from Listeria monocytogenes in complex with panose | |||||||||
Components | Alpha-xylosidase | |||||||||
Keywords | HYDROLASE / Center for Structural Genomics of Infectious Diseases / CSGID / idp05250 / lmo2446 / Listeria monocytogenes EGD-e | |||||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | |||||||||
Authors | Halavaty, A.S. / Light, S.H. / Minasov, G. / Winsor, J. / Grimshaw, S. / Shuvalova, L. / Peterson, S. / 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 | 5hxm.cif.gz | 463.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5hxm.ent.gz | 372.7 KB | Display | PDB format |
PDBx/mmJSON format | 5hxm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hx/5hxm ftp://data.pdbj.org/pub/pdb/validation_reports/hx/5hxm | HTTPS FTP |
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-Related structure data
Related structure data | 5hopC 5hpoC 5i0dC 5i0eC 5i0fC 5i0gC 4kmqS S: Starting model for refinement 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 on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 122520.227 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Listeria monocytogenes (bacteria) / Gene: yicI_4, ABE87_12155, ARD00_02746 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Magic References: UniProt: A0A0R1CZZ2, UniProt: Q8Y4J2*PLUS, alpha-D-xyloside xylohydrolase |
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-Sugars , 2 types, 2 molecules
#2: Polysaccharide | Cyclic alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose-(1-3)-alpha-D-glucopyranose-(1-6)-alpha-D- ...Cyclic alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose-(1-3)-alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose Source method: isolated from a genetically manipulated source |
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#3: Polysaccharide | alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose Source method: isolated from a genetically manipulated source |
-Non-polymers , 4 types, 1033 molecules
#4: Chemical | ChemComp-MG / #5: Chemical | ChemComp-CA / | #6: Chemical | #7: 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: 2.56 Å3/Da / Density % sol: 52.07 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.3 Details: Protein: 0.5 NaCl, 10 mM Tris pH 8.3, 5 mM BME Crystallization: 200 mM magnesium formate and 25% PEG 3350 Soak for 1 minute in reservoir + 5 mM panose |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 14, 2014 / Details: Be-Lenses |
Radiation | Monochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97856 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→30 Å / Num. obs: 94486 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 30.8 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 20.6 |
Reflection shell | Resolution: 1.9→1.93 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 2.1 / % possible all: 99.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4kmq Resolution: 1.9→29.74 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.965 / SU B: 8.187 / SU ML: 0.116 / Cross valid method: THROUGHOUT / ESU R: 0.127 / ESU R Free: 0.123 / 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: 44.394 Å2
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Refinement step | Cycle: 1 / Resolution: 1.9→29.74 Å
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Refine LS restraints |
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