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Yorodumi- PDB-1ekm: CRYSTAL STRUCTURE AT 2.5 A RESOLUTION OF ZINC-SUBSTITUTED COPPER ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ekm | ||||||
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Title | CRYSTAL STRUCTURE AT 2.5 A RESOLUTION OF ZINC-SUBSTITUTED COPPER AMINE OXIDASE OF HANSENULA POLYMORPHA EXPRESSED IN ESCHERICHIA COLI | ||||||
Components | COPPER AMINE OXIDASE | ||||||
Keywords | OXIDOREDUCTASE / amine oxidase / quinoprotein | ||||||
Function / homology | Function and homology information : / : / : / primary-amine oxidase / amine metabolic process / quinone binding / peroxisome / copper ion binding Similarity search - Function | ||||||
Biological species | Pichia angusta (fungus) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.5 Å | ||||||
Authors | Chen, Z. / Schwartz, B. / Williams, N.K. / Li, R. / Klinman, J.P. / Mathews, F.S. | ||||||
Citation | Journal: Biochemistry / Year: 2000 Title: Crystal structure at 2.5 A resolution of zinc-substituted copper amine oxidase of Hansenula polymorpha expressed in Escherichia coli. Authors: Chen, Z. / Schwartz, B. / Williams, N.K. / Li, R. / Klinman, J.P. / Mathews, F.S. #1: Journal: Structure / Year: 1998 Title: Copper Amine Oxidase from Hansenula polymorpha: the Crystal Structure Determined at 2.4 A Resolution Reveals the Active Conformation Authors: Li, R. / Klinman, J.P. / Mathews, F.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ekm.cif.gz | 414.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ekm.ent.gz | 347.4 KB | Display | PDB format |
PDBx/mmJSON format | 1ekm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ek/1ekm ftp://data.pdbj.org/pub/pdb/validation_reports/ek/1ekm | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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Details | Molecule is homodimer in solution. The biological unit is a dimer. Three dimers form a crystallographic hexamer which is non-biological. The asymmetric unit contains half of a hexamer, chains ABC. Chains B,C were not treated as independent during refinement but were generated by strict non-crystallographic symmetry. |
-Components
#1: Protein | Mass: 73731.141 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Details: ZINC-SUBSTITUTED / Source: (gene. exp.) Pichia angusta (fungus) / Plasmid: PET11A / Production host: Escherichia coli (E. coli) / References: UniProt: P12807, EC: 1.4.3.6 #2: Chemical | #3: 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: 2.7 Å3/Da / Density % sol: 54.39 % | ||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop Details: PEG 8000, potassium phosphate, VAPOR DIFFUSION, HANGING DROP, temperature 295.0K | ||||||||||||||||||||
Crystal | *PLUS Density % sol: 52 % | ||||||||||||||||||||
Crystal grow | *PLUS PH range low: 7.5 / PH range high: 6.2 | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Sep 25, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→500 Å / Num. all: 65122 / Num. obs: 64796 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 27.4 Å2 / Rmerge(I) obs: 0.087 / Net I/σ(I): 11.8 |
Reflection shell | Resolution: 2.5→2.6 Å / Redundancy: 2.46 % / Rmerge(I) obs: 0.185 / Num. unique all: 3689 / % possible all: 40.7 |
Reflection | *PLUS % possible obs: 77.4 % / Num. measured all: 226364 |
Reflection shell | *PLUS % possible obs: 40.7 % / Mean I/σ(I) obs: 3 |
-Processing
Software |
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Refinement | Resolution: 2.5→500 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER / Details: USED STRICT NCS CONSTRAINTS
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Refinement step | Cycle: LAST / Resolution: 2.5→500 Å
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Refine LS restraints |
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Software | *PLUS Name: CNS / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS % reflection Rfree: 10 % | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS |