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Yorodumi- PDB-1ksi: CRYSTAL STRUCTURE OF A EUKARYOTIC (PEA SEEDLING) COPPER-CONTAININ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ksi | |||||||||
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Title | CRYSTAL STRUCTURE OF A EUKARYOTIC (PEA SEEDLING) COPPER-CONTAINING AMINE OXIDASE AT 2.2A RESOLUTION | |||||||||
Components | COPPER AMINE OXIDASE | |||||||||
Keywords | OXIDOREDUCTASE / OXIDASE / PEA SEEDLING | |||||||||
Function / homology | Function and homology information diamine oxidase activity / response to chemical / primary-amine oxidase / aliphatic amine oxidase activity / primary methylamine oxidase activity / amine metabolic process / quinone binding / copper ion binding Similarity search - Function | |||||||||
Biological species | Pisum sativum (garden pea) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SIROAS / Resolution: 2.2 Å | |||||||||
Authors | Wilce, M.C.J. / Kumar, V. / Freeman, H.C. / Guss, J.M. | |||||||||
Citation | Journal: Structure / Year: 1996 Title: Crystal structure of a eukaryotic (pea seedling) copper-containing amine oxidase at 2.2 A resolution. Authors: Kumar, V. / Dooley, D.M. / Freeman, H.C. / Guss, J.M. / Harvey, I. / McGuirl, M.A. / Wilce, M.C. / Zubak, V.M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ksi.cif.gz | 277.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ksi.ent.gz | 224.8 KB | Display | PDB format |
PDBx/mmJSON format | 1ksi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ksi_validation.pdf.gz | 558.9 KB | Display | wwPDB validaton report |
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Full document | 1ksi_full_validation.pdf.gz | 604.6 KB | Display | |
Data in XML | 1ksi_validation.xml.gz | 33.2 KB | Display | |
Data in CIF | 1ksi_validation.cif.gz | 51 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ks/1ksi ftp://data.pdbj.org/pub/pdb/validation_reports/ks/1ksi | 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 oper: (Code: given Matrix: (-1, -0.00135, -0.00049), Vector: |
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 73049.688 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: Q43077, EC: 1.4.3.6 |
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-Sugars , 2 types, 4 molecules
#2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Sugar | |
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-Non-polymers , 3 types, 575 molecules
#4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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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: 3.37 Å3/Da / Density % sol: 62 % |
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Crystal grow | pH: 4.8 Details: PROTEIN WAS CRYSTALLIZED FROM 1.44M LITHIUM SULFATE, PH 4.8. |
Crystal grow | *PLUS Temperature: 22 ℃ / Method: vapor diffusion, sitting drop / Details: macroseeding |
Components of the solutions | *PLUS Conc.: 1.44 M / Common name: lithium sulfate |
-Data collection
Diffraction | Mean temperature: 287 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1.07 |
Detector | Type: WEISSENBERG / Detector: DIFFRACTOMETER / Date: Jan 1, 1994 / Details: MIRRORS |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.07 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. obs: 86780 / % possible obs: 95.7 % / Observed criterion σ(I): -3 / Redundancy: 8 % / Rmerge(I) obs: 0.059 |
Reflection shell | Resolution: 2.2→2.3 Å / Redundancy: 1.1 % / % possible all: 55.1 |
Reflection | *PLUS Num. measured all: 683441 |
Reflection shell | *PLUS % possible obs: 55.1 % |
-Processing
Software |
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Refinement | Method to determine structure: SIROAS / Resolution: 2.2→7 Å / σ(F): 1
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Displacement parameters | Biso mean: 23 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→7 Å
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Refine LS restraints |
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Software | *PLUS Name: PROLSQ / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.181 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |