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Yorodumi- PDB-1l5v: Crystal Structure of the Maltodextrin Phosphorylase complexed wit... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1l5v | ||||||
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Title | Crystal Structure of the Maltodextrin Phosphorylase complexed with Glucose-1-phosphate | ||||||
Components | MALTODEXTRIN PHOSPHORYLASE | ||||||
Keywords | TRANSFERASE / phosphorylase / enzymatic catalysis / substrate complex | ||||||
Function / homology | Function and homology information maltodextrin phosphorylase activity / alpha-glucan catabolic process / glycogen phosphorylase / glycogen phosphorylase activity / linear malto-oligosaccharide phosphorylase activity / SHG alpha-glucan phosphorylase activity / glycogen catabolic process / pyridoxal phosphate binding / protein homodimerization activity / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2 Å | ||||||
Authors | Geremia, S. / Campagnolo, M. / Schinzel, R. / Johnson, L.N. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2002 Title: Enzymatic catalysis in crystals of Escherichia coli maltodextrin phosphorylase Authors: Geremia, S. / Campagnolo, M. / Schinzel, R. / Johnson, L.N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1l5v.cif.gz | 349.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1l5v.ent.gz | 281.8 KB | Display | PDB format |
PDBx/mmJSON format | 1l5v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1l5v_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 1l5v_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 1l5v_validation.xml.gz | 68.3 KB | Display | |
Data in CIF | 1l5v_validation.cif.gz | 101.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l5/1l5v ftp://data.pdbj.org/pub/pdb/validation_reports/l5/1l5v | HTTPS FTP |
-Related structure data
Related structure data | 1l5wC 1l6iC 1qm5S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 90547.062 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PMAP101 / Production host: Escherichia coli (E. coli) / Strain (production host): DELTA MALA518 / References: UniProt: P00490, glycogen phosphorylase #2: Sugar | #3: Chemical | #4: Chemical | #5: 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: 2.38 Å3/Da / Density % sol: 48 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: PEG 4000, TRIS, Lithium Chloride, Glucose-1-phosphate., pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 10, 1999 |
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→40 Å / Num. all: 110577 / Num. obs: 110577 / % possible obs: 94.7 % / Redundancy: 3.8 % / Biso Wilson estimate: 17.386 Å2 / Rmerge(I) obs: 0.15 / Net I/σ(I): 7.2 |
Reflection shell | Resolution: 2→2.1 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 1.8 / Num. unique all: 13882 / % possible all: 82.4 |
Reflection | *PLUS Lowest resolution: 40 Å / Num. measured all: 423852 |
Reflection shell | *PLUS % possible obs: 82.4 % |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 1QM5 Resolution: 2→20 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.923 / SU B: 7.69621 / SU ML: 0.20349 / Cross valid method: THROUGHOUT / ESU R: 0.2014 / ESU R Free: 0.16739 / Stereochemistry target values: Engh & Huber
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.975 Å2
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Refinement step | Cycle: LAST / Resolution: 2→20 Å
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Refine LS restraints |
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Refinement | *PLUS Rfactor obs: 0.182 / Rfactor Rfree: 0.22 / Rfactor Rwork: 0.18 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: p_angle_deg / Dev ideal: 1.8 |