+Open data
-Basic information
Entry | Database: PDB / ID: 1gpe | |||||||||
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Title | GLUCOSE OXIDASE FROM PENICILLIUM AMAGASAKIENSE | |||||||||
Components | PROTEIN (GLUCOSE OXIDASE) | |||||||||
Keywords | OXIDOREDUCTASE(FLAVOPROTEIN) | |||||||||
Function / homology | Function and homology information glucose oxidase / glucose oxidase activity / flavin adenine dinucleotide binding / extracellular region Similarity search - Function | |||||||||
Biological species | Penicillium amagasakiense (fungus) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | |||||||||
Authors | Hendle, J. / Kalisz, H.M. / Hecht, H.J. | |||||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 1999 Title: 1.8 and 1.9 A resolution structures of the Penicillium amagasakiense and Aspergillus niger glucose oxidases as a basis for modelling substrate complexes. Authors: Wohlfahrt, G. / Witt, S. / Hendle, J. / Schomburg, D. / Kalisz, H.M. / Hecht, H.J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1gpe.cif.gz | 255.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1gpe.ent.gz | 202.6 KB | Display | PDB format |
PDBx/mmJSON format | 1gpe.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gp/1gpe ftp://data.pdbj.org/pub/pdb/validation_reports/gp/1gpe | HTTPS FTP |
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-Related structure data
Related structure data | 1cf3C 1galS 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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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.99995, 0.00686, -0.00701), Vector: |
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 64016.750 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Penicillium amagasakiense (fungus) / References: UniProt: P81156, glucose oxidase |
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-Sugars , 3 types, 8 molecules
#2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Polysaccharide | Source method: isolated from a genetically manipulated source #4: Sugar | ChemComp-NAG / |
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-Non-polymers , 2 types, 711 molecules
#5: Chemical | #6: 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: 2.21 Å3/Da / Density % sol: 44 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.4 Details: 1.3 M AMMONIUM SULPHATE, 0.1 M CITRATE-PO4 BUFFER PH 7.4 | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop / Details: Kalisz, H.M., (1990) J.Mol.Biol., 213, 207. / PH range low: 5.6 / PH range high: 5.3 | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 290 K |
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Diffraction source | Source: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Details: MIRRORS |
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: 1.8→20 Å / Num. obs: 101999 / % possible obs: 94.7 % / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Biso Wilson estimate: 12.5 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 18.4 |
Reflection shell | Resolution: 1.8→1.88 Å / Redundancy: 2 % / Rmerge(I) obs: 0.132 / Mean I/σ(I) obs: 8.5 / % possible all: 90 |
Reflection shell | *PLUS Highest resolution: 1.8 Å / % possible obs: 90 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1GAL Resolution: 1.8→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.2
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Displacement parameters | Biso mean: 14.9 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→20 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 20 Å / % reflection Rfree: 5 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 1.8 Å / Lowest resolution: 1.88 Å / Rfactor Rfree: 0.237 / Rfactor obs: 0.179 |