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Yorodumi- PDB-1ahp: OLIGOSACCHARIDE SUBSTRATE BINDING IN ESCHERICHIA COLI MALTODEXTRI... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ahp | |||||||||
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Title | OLIGOSACCHARIDE SUBSTRATE BINDING IN ESCHERICHIA COLI MALTODEXTRIN PHSPHORYLASE | |||||||||
Components | E.COLI MALTODEXTRIN PHOSPHORYLASE | |||||||||
Keywords | ECOLI / PHOSPHORYLASE / OLIGOSACCHARIDE / INDUCED-FIT / SUBSTRATE / MALTODEXTRIN / STACKING | |||||||||
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 / MOLECULAR REPLACEMENT / Resolution: 3 Å | |||||||||
Authors | O'Reilly, M. / Watson, K.A. / Schinzel, R. / Palm, D. / Johnson, L.N. | |||||||||
Citation | Journal: Nat.Struct.Biol. / Year: 1997 Title: Oligosaccharide substrate binding in Escherichia coli maltodextrin phosphorylase. Authors: O'Reilly, M. / Watson, K.A. / Schinzel, R. / Palm, D. / 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 | 1ahp.cif.gz | 291.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ahp.ent.gz | 238.5 KB | Display | PDB format |
PDBx/mmJSON format | 1ahp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ahp_validation.pdf.gz | 1019 KB | Display | wwPDB validaton report |
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Full document | 1ahp_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 1ahp_validation.xml.gz | 41.9 KB | Display | |
Data in CIF | 1ahp_validation.cif.gz | 59.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ah/1ahp ftp://data.pdbj.org/pub/pdb/validation_reports/ah/1ahp | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS oper: (Code: given Matrix: (-0.726932, -0.000378, -0.686708), Vector: |
-Components
#1: Protein | Mass: 90365.008 Da / Num. of mol.: 2 / Mutation: N112A Source method: isolated from a genetically manipulated source Details: PYRIDOXAL PHOSPHATE COFACTOR ATTACHED TO LYS 645 / Source: (gene. exp.) Escherichia coli (E. coli) / Cellular location: CYTOPLASM / Cellular location (production host): CYTOPLASM / Production host: Escherichia coli (E. coli) / References: UniProt: P00490, glycogen phosphorylase #2: Polysaccharide | #3: Chemical | #4: Chemical | #5: Chemical | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 3.05 Å3/Da / Density % sol: 50 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 6.4 Details: 0.1M NATARTRATE, PH 6.4, 24% PEG 3350, 1MM SODIUM AZIDE, 16 DEG CELCIUS, 50MM MALTOHEXAOSE STOCK, 16.5MG/ML PROTEIN STOCK, HANGING DROPS 1MICRO LITRE WELL & 0.5 MICRO LITRE MALTOHEXAOSE 0.5 ...Details: 0.1M NATARTRATE, PH 6.4, 24% PEG 3350, 1MM SODIUM AZIDE, 16 DEG CELCIUS, 50MM MALTOHEXAOSE STOCK, 16.5MG/ML PROTEIN STOCK, HANGING DROPS 1MICRO LITRE WELL & 0.5 MICRO LITRE MALTOHEXAOSE 0.5 MICRO LITRE PROTEIN, vapor diffusion - hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 16 ℃ / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: SRS / Beamline: PX9.6 / Wavelength: 0.87 |
Detector | Type: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Feb 1, 1995 / Details: MIRRORS |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.87 Å / Relative weight: 1 |
Reflection | Resolution: 3→20 Å / Num. obs: 33108 / % possible obs: 81.7 % / Observed criterion σ(I): 1 / Redundancy: 1.6 % / Biso Wilson estimate: 57 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 5.4 |
Reflection shell | Resolution: 3→3.08 Å / Redundancy: 1 % / Rmerge(I) obs: 0.318 / Mean I/σ(I) obs: 1.9 / % possible all: 80.3 |
Reflection | *PLUS Num. measured all: 52324 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: MALP NATIVE STRUCTURE Resolution: 3→10 Å / Rfactor Rfree error: 0.017 / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: GROUPED B / Cross valid method: THROUGHOUT / σ(F): 1 Details: COORDINATES FOR MOLECULE A WERE PROVIDED BY THE DEPOSITOR. MOLECULE B WAS GENERATED BY THE PDB USING NCS SYMMETRY.
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Displacement parameters | Biso mean: 25.4 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3→10 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: STRICT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 3→3.13 Å / Rfactor Rfree error: 0.042 / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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