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Yorodumi- PDB-2x2h: Crystal structure of the Gracilariopsis lemaneiformis alpha-1,4- ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2x2h | ||||||
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Title | Crystal structure of the Gracilariopsis lemaneiformis alpha-1,4- glucan lyase | ||||||
Components | ALPHA-1,4-GLUCAN LYASE ISOZYME 1 | ||||||
Keywords | LYASE / ANHYDROFRUCTOSE PATHWAY / GLYCOSIDE HYDROLASE FAMILY 31 / STARCH BINDING DOMAIN | ||||||
Function / homology | Function and homology information exo-(1,4)-alpha-D-glucan lyase activity / alpha-glucosidase activity / glucosidase II complex / N-glycan processing / carbohydrate binding / carbohydrate metabolic process Similarity search - Function | ||||||
Biological species | GRACILARIOPSIS LEMANEIFORMIS (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.06 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 | 2x2h.cif.gz | 1.7 MB | Display | PDBx/mmCIF format |
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PDB format | pdb2x2h.ent.gz | 1.4 MB | Display | PDB format |
PDBx/mmJSON format | 2x2h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2x2h_validation.pdf.gz | 490.6 KB | Display | wwPDB validaton report |
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Full document | 2x2h_full_validation.pdf.gz | 532.6 KB | Display | |
Data in XML | 2x2h_validation.xml.gz | 174.5 KB | Display | |
Data in CIF | 2x2h_validation.cif.gz | 261.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x2/2x2h ftp://data.pdbj.org/pub/pdb/validation_reports/x2/2x2h | HTTPS FTP |
-Related structure data
Related structure data | 2x2iC 2x2jC 4amwC 4amxC 2g3mS 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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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) Description: REPLICATING VECTOR WITH HARS SEQUENCE. COLLECTED AT TAPING BAY, TSINGTAO, CHINA Production host: PICHIA ANGUSTA (fungus) / Strain (production host): RB11 / References: UniProt: Q9STC1, EC: 4.2.2.13 #2: Chemical | ChemComp-GOL / #3: Chemical | ChemComp-ACT / #4: Chemical | #5: Water | ChemComp-HOH / | 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: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 0.9762 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Feb 23, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9762 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→50 Å / Num. obs: 258096 / % possible obs: 93.2 % / Observed criterion σ(I): 0 / Redundancy: 2 % / Biso Wilson estimate: 20.3 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 8.14 |
Reflection shell | Resolution: 2.05→2.12 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.22 / Mean I/σ(I) obs: 2.9 / % possible all: 76.4 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2G3M Resolution: 2.06→132.45 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.93 / SU B: 10.597 / SU ML: 0.126 / Cross valid method: THROUGHOUT / ESU R: 0.22 / ESU R Free: 0.178 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS.
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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: 32.244 Å2
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Refinement step | Cycle: LAST / Resolution: 2.06→132.45 Å
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Refine LS restraints |
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