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Yorodumi- PDB-4amw: CRYSTAL STRUCTURE OF THE GRACILARIOPSIS LEMANEIFORMIS ALPHA-1,4- ... -
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Open data
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Basic information
| Entry | Database: PDB / ID: 4amw | |||||||||
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| Title | CRYSTAL STRUCTURE OF THE GRACILARIOPSIS LEMANEIFORMIS ALPHA-1,4- GLUCAN LYASE Covalent Intermediate Complex with 5-fluoro-idosyl- 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 informationexo-(1->4)-alpha-D-glucan lyase / 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 / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | |||||||||
Authors | Rozeboom, H.J. / Yu, S. / Madrid, S. / Kalk, K.H. / Dijkstra, B.W. | |||||||||
Citation | Journal: J.Biol.Chem. / Year: 2013Title: 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: Molmil Jmol/JSmol |
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Downloads & links
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Download
| PDBx/mmCIF format | 4amw.cif.gz | 1.7 MB | Display | PDBx/mmCIF format |
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| PDB format | pdb4amw.ent.gz | 1.4 MB | Display | PDB format |
| PDBx/mmJSON format | 4amw.json.gz | Tree view | PDBx/mmJSON format | |
| Others | Other downloads |
-Validation report
| Summary document | 4amw_validation.pdf.gz | 512.7 KB | Display | wwPDB validaton report |
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| Full document | 4amw_full_validation.pdf.gz | 557.7 KB | Display | |
| Data in XML | 4amw_validation.xml.gz | 166.6 KB | Display | |
| Data in CIF | 4amw_validation.cif.gz | 247.8 KB | Display | |
| Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/am/4amw ftp://data.pdbj.org/pub/pdb/validation_reports/am/4amw | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 2x2hSC ![]() 2x2iC ![]() 2x2jC ![]() 4amxC C: citing same article ( S: Starting model for refinement |
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| Similar structure data |
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Assembly
| Deposited unit | ![]()
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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: PICHIA ANGUSTA (fungus) / Strain (production host): RB11References: UniProt: Q9STC1, exo-(1->4)-alpha-D-glucan lyase #2: Sugar | #3: Chemical | ChemComp-GOL / #4: Sugar | ChemComp-5DI / | #5: Water | ChemComp-HOH / | Has protein modification | Y | Nonpolymer details | 2-OXO-1,2,DIDEOXY-5F-D-IDOPYRANOS | Sequence details | FIRST 50 AMINO ACIDS ARE A SIGNAL PEPTIDE. THE NEXT 11 AMINO ACIDS ARE NOT PRESENT IN THE ENZYME | |
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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: ID14-4 / Wavelength: 0.9395 |
| Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 22, 2010 |
| Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
| Radiation wavelength | Wavelength: 0.9395 Å / Relative weight: 1 |
| Reflection | Resolution: 1.9→45.6 Å / Num. obs: 340755 / % possible obs: 93.5 % / Observed criterion σ(I): -3 / Redundancy: 1.9 % / Biso Wilson estimate: 16.2 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 5.3 |
| Reflection shell | Resolution: 1.9→2 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 1.6 / % possible all: 94.1 |
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Processing
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| Refinement | Method to determine structure: MOLECULAR REPLACEMENTStarting model: PDB ENTRY 2X2H Resolution: 1.9→43.57 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.904 / SU B: 10.656 / SU ML: 0.133 / Cross valid method: THROUGHOUT / ESU R: 0.181 / ESU R Free: 0.167 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED.
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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: 24.752 Å2
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| Refinement step | Cycle: LAST / Resolution: 1.9→43.57 Å
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| Refine LS restraints |
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GRACILARIOPSIS LEMANEIFORMIS (eukaryote)
X-RAY DIFFRACTION
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PDBj







PICHIA ANGUSTA (fungus)



