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Yorodumi- PDB-4amx: CRYSTAL STRUCTURE OF THE GRACILARIOPSIS LEMANEIFORMIS ALPHA-1,4- ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4amx | ||||||
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Title | CRYSTAL STRUCTURE OF THE GRACILARIOPSIS LEMANEIFORMIS ALPHA-1,4- GLUCAN LYASE Covalent Intermediate Complex with 5-fluoro-glucosyl- fluoride | ||||||
Components | ALPHA-1,4-GLUCAN LYASE ISOZYME 1 | ||||||
Keywords | LYASE / ANHYDROFRUCTOSE PATHWAY / GLYCOSIDE HYDROLASE FAMILY 31 / SECONDARY CARBOHYDRATE BINDING SITE | ||||||
Function / homology | Function and homology information exo-(1,4)-alpha-D-glucan lyase activity / hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate binding / carbohydrate metabolic process Similarity search - Function | ||||||
Biological species | GRACILARIOPSIS LEMANEIFORMIS (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.1 Å | ||||||
Authors | Rozeboom, H.J. / Yu, S. / Madrid, S. / Kalk, K.H. / Dijkstra, B.W. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2013 Title: Crystal Structure of Alpha-1,4-Glucan Lyase, a Unique Glycoside Hydrolase Family Member with a Novel Catalytic Mechanism. Authors: Rozeboom, H.J. / Yu, S. / Madrid, S. / Kalk, K.H. / Zhang, R. / Dijkstra, B.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4amx.cif.gz | 1.6 MB | Display | PDBx/mmCIF format |
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PDB format | pdb4amx.ent.gz | 1.3 MB | Display | PDB format |
PDBx/mmJSON format | 4amx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/am/4amx ftp://data.pdbj.org/pub/pdb/validation_reports/am/4amx | HTTPS FTP |
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-Related structure data
Related structure data | 2x2hSC 2x2iC 2x2jC 4amwC C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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4 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: THR / End label comp-ID: THR / Refine code: 6 / Auth seq-ID: 14 - 1038 / Label seq-ID: 3 - 1027
NCS oper:
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-Components
#1: Protein | Mass: 116062.156 Da / Num. of mol.: 4 / Fragment: RESIDUES 62-1088 Source method: isolated from a genetically manipulated source Source: (gene. exp.) GRACILARIOPSIS LEMANEIFORMIS (eukaryote) Production host: OGATAEA POLYMORPHA RB11 (fungus) / References: UniProt: Q9STC1, EC: 4.2.2.13 #2: Sugar | #3: Chemical | ChemComp-GOL / #4: Sugar | ChemComp-AFR / | #5: Water | ChemComp-HOH / | Nonpolymer details | 5-FLUORO-ALPHA-D-GLUCOPYRANOSE (5GF): THE GLUCOSE FORM OF B9D 2-OXO-1,2,DIDEOXY-5F-D-GLUCOPYRANOSE ...5-FLUORO-ALPHA-D-GLUCOPYRAN | |
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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: 2.51 Å3/Da / Density % sol: 51 % / Description: NONE |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 18-21% PEG 8000, 0.1 M SODIUM ACETATE, PH 5.0-5.2, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.9748 |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 7, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9748 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→47.7 Å / Num. obs: 255868 / % possible obs: 96 % / Observed criterion σ(I): -3 / Redundancy: 1.9 % / Biso Wilson estimate: 24.8 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 5.1 |
Reflection shell | Resolution: 2.1→2.21 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 1.4 / % possible all: 92.3 |
-Processing
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB ENTRY 2X2H Resolution: 2.1→46.74 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.902 / SU B: 17.242 / SU ML: 0.196 / Cross valid method: THROUGHOUT / ESU R: 0.266 / ESU R Free: 0.216 / 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.721 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→46.74 Å
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Refine LS restraints |
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