+Open data
-Basic information
Entry | Database: PDB / ID: 1spu | ||||||
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Title | STRUCTURE OF OXIDOREDUCTASE | ||||||
Components | COPPER AMINE OXIDASE | ||||||
Keywords | OXIDOREDUCTASE / COPPER / TPQ / PERIPLASMIC | ||||||
Function / homology | Function and homology information phenylethylamine catabolic process / primary-amine oxidase / aliphatic amine oxidase activity / primary methylamine oxidase activity / L-phenylalanine catabolic process / amine metabolic process / quinone binding / periplasmic space / copper ion binding / calcium ion binding Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / LEAST SQUARES REFINEMENT / Resolution: 2 Å | ||||||
Authors | Wilmot, C.M. / Phillips, S.E.V. | ||||||
Citation | Journal: Biochemistry / Year: 1997 Title: Catalytic mechanism of the quinoenzyme amine oxidase from Escherichia coli: exploring the reductive half-reaction. Authors: Wilmot, C.M. / Murray, J.M. / Alton, G. / Parsons, M.R. / Convery, M.A. / Blakeley, V. / Corner, A.S. / Palcic, M.M. / Knowles, P.F. / McPherson, M.J. / Phillips, S.E. #1: Journal: Structure / Year: 1995 Title: Crystal Structure of a Quinoenzyme: Copper Amine Oxidase of Escherichia Coli at 2 A Resolution Authors: Parsons, M.R. / Convery, M.A. / Wilmot, C.M. / Yadav, K.D. / Blakeley, V. / Corner, A.S. / Phillips, S.E. / McPherson, M.J. / Knowles, P.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1spu.cif.gz | 313.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1spu.ent.gz | 254.5 KB | Display | PDB format |
PDBx/mmJSON format | 1spu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1spu_validation.pdf.gz | 447.5 KB | Display | wwPDB validaton report |
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Full document | 1spu_full_validation.pdf.gz | 497.3 KB | Display | |
Data in XML | 1spu_validation.xml.gz | 68 KB | Display | |
Data in CIF | 1spu_validation.cif.gz | 98.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sp/1spu ftp://data.pdbj.org/pub/pdb/validation_reports/sp/1spu | HTTPS FTP |
-Related structure data
Related structure data | 1oacS S: Starting model for refinement |
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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: (0.35161, -0.936, -0.01658), Vector: |
-Components
#1: Protein | Mass: 81459.859 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Cellular location: PERIPLASM / References: UniProt: P46883, EC: 1.4.3.6 #2: Chemical | #3: Chemical | ChemComp-CA / #4: Water | ChemComp-HOH / | Compound details | IN THE NATIVE ENZYME, RESIDUE 466 IS 2,4,5-TRIHYDROXYPHENYLALANINE QUINONE (TPQ) FORMED BY POST- ...IN THE NATIVE ENZYME, RESIDUE 466 IS 2,4,5-TRIHYDROXY | Nonpolymer details | E. COLI AMINE OXIDASE IS A HOMODIMER. EACH SUBUNIT ACTIVE SITE CONTAINS ONE COPPER AND A REDOX ...E. COLI AMINE OXIDASE IS A HOMODIMER. EACH SUBUNIT ACTIVE SITE CONTAINS ONE COPPER AND A REDOX COFACTOR, TPQ, WHICH HAS BEEN CHEMICALLY | |
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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: 2.73 Å3/Da / Density % sol: 54.9 % | ||||||||||||||||||||
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Crystal grow | pH: 7.2 Details: 1.4M SODIUM CITRATE, 0.1M HEPES BUFFER, PH 7.2 PROTEIN SOLUTION CONCENTRATION 6.5 MG/ML INHIBITOR SOAKING SOLUTION 0.375MM 2-HYDRAZINOPYRIDINE MADE UP IN 1.4M SODIUM CITRATE, 0.1M HEPES ...Details: 1.4M SODIUM CITRATE, 0.1M HEPES BUFFER, PH 7.2 PROTEIN SOLUTION CONCENTRATION 6.5 MG/ML INHIBITOR SOAKING SOLUTION 0.375MM 2-HYDRAZINOPYRIDINE MADE UP IN 1.4M SODIUM CITRATE, 0.1M HEPES BUFFER, PH 7.2. CRYSTAL SOAKED FOR 30 DAYS. CRYOPROTECTANT 20% GLYCEROL, 1.44M SODIUM CITRATE BUFFER, PH 6.4 | ||||||||||||||||||||
Crystal grow | *PLUS pH: 7 / 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: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 15, 1996 / Details: MIRRORS |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.87 Å / Relative weight: 1 |
Reflection | Resolution: 2→20 Å / Num. obs: 100550 / % possible obs: 83.7 % / Observed criterion σ(I): 0 / Redundancy: 2.6 % / Biso Wilson estimate: 24.21 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 8.7 |
Reflection shell | Resolution: 2→2.05 Å / Redundancy: 2 % / Rmerge(I) obs: 0.22 / Mean I/σ(I) obs: 3.3 / % possible all: 72.9 |
Reflection | *PLUS Num. measured all: 264608 |
Reflection shell | *PLUS Num. measured obs: 12938 |
-Processing
Software |
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Refinement | Method to determine structure: LEAST SQUARES REFINEMENT Starting model: PDB ENTRY 1OAC Resolution: 2→20 Å / σ(F): 0
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Displacement parameters | Biso mean: 27.62 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati d res low obs: 8 Å / Luzzati sigma a obs: 0.31 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→20 Å
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Refine LS restraints |
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Software | *PLUS Name: PROLSQ / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 10 Å / Rfactor obs: 0.206 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |