+Open data
-Basic information
Entry | Database: PDB / ID: 1h5q | ||||||
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Title | Mannitol dehydrogenase from Agaricus bisporus | ||||||
Components | NADP-DEPENDENT MANNITOL DEHYDROGENASE | ||||||
Keywords | OXIDOREDUCTASE / MANNITOL METABOLISM | ||||||
Function / homology | Function and homology information mannitol 2-dehydrogenase (NADP+) / mannitol 2-dehydrogenase (NADP+) activity / mannitol metabolic process / NADP binding / protein homotetramerization Similarity search - Function | ||||||
Biological species | AGARICUS BISPORUS (button mushroom) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Horer, S. / Stoop, J. / Mooibroek, H. / Baumann, U. / Sassoon, J. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2001 Title: The Crystallographic Structure of the Mannitol 2-Dehydrogenase Nadp+ Binary Complex from Agaricus Bisporus Authors: Horer, S. / Stoop, J. / Mooibroek, H. / Baumann, U. / Sassoon, J. #1: Journal: Acta Crystallogr.,Sect.D / Year: 2001 Title: Crystallization and Preliminary Crystallographic Analysis of Mannitol Dehydrogenase (Mtdh) from the Common Mushroom Agaricus Bisporus Authors: Sassoon, J. / Horer, S. / Stoop, J. / Mooibroek, H. / Baumann, U. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1h5q.cif.gz | 1.2 MB | Display | PDBx/mmCIF format |
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PDB format | pdb1h5q.ent.gz | 1 MB | Display | PDB format |
PDBx/mmJSON format | 1h5q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1h5q_validation.pdf.gz | 2.7 MB | Display | wwPDB validaton report |
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Full document | 1h5q_full_validation.pdf.gz | 2.8 MB | Display | |
Data in XML | 1h5q_validation.xml.gz | 109 KB | Display | |
Data in CIF | 1h5q_validation.cif.gz | 154.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h5/1h5q ftp://data.pdbj.org/pub/pdb/validation_reports/h5/1h5q | HTTPS FTP |
-Related structure data
Related structure data | 1cydS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 28237.947 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Source: (gene. exp.) AGARICUS BISPORUS (button mushroom) / Plasmid: PET28 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: O93868, mannitol 2-dehydrogenase (NADP+) #2: Chemical | ChemComp-NAP / #3: Chemical | ChemComp-NI / #4: 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: 2.4 Å3/Da / Density % sol: 47 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.5 / Details: 90 MM TRIS-HCL PH 7.5, 18% PEG4000, 9% ISOPROPANOL | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / Method: vapor diffusion, sitting drop / pH: 7.5 | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM1A / Wavelength: 0.8 |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jul 15, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→40 Å / Num. obs: 508943 / % possible obs: 98.4 % / Redundancy: 2.7 % / Rmerge(I) obs: 0.063 / Net I/σ(I): 11.8 |
Reflection shell | Resolution: 1.5→1.58 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.295 / Mean I/σ(I) obs: 3.1 / % possible all: 97 |
Reflection | *PLUS Lowest resolution: 40 Å |
Reflection shell | *PLUS % possible obs: 97 % / Num. unique obs: 173816 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1CYD Resolution: 1.5→20 Å / SU B: 1.45 / SU ML: 0.05 / Cross valid method: THROUGHOUT / ESU R Free: 0.07 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Refinement step | Cycle: LAST / Resolution: 1.5→20 Å
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Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||
Refine LS restraints | *PLUS
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