+Open data
-Basic information
Entry | Database: PDB / ID: 1w6c | ||||||
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Title | AGAO holoenzyme in a small cell, at 2.2 angstroms | ||||||
Components | PHENYLETHYLAMINE OXIDASE | ||||||
Keywords | OXIDOREDUCTASE / AMINE OXIDASE / COPPER CONTAINING / METAL-BINDING / TPQ / QUINONE / HOLOENZYME | ||||||
Function / homology | Function and homology information : / : / : / primary-amine oxidase / amine metabolic process / quinone binding / copper ion binding Similarity search - Function | ||||||
Biological species | ARTHROBACTER GLOBIFORMIS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Duff, A.P. / Langley, D.B. / Juda, G.A. / Shepard, E.M. / Dooley, D.M. / Freeman, H.C. / Guss, J.M. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2006 Title: The Copper Containing Amine Oxidase from Arthrobacter Globiformis: Refinement at 1.55 And 2.20 A Resolution in Two Crystal Forms. Authors: Langley, D.B. / Duff, A.P. / Freeman, H.C. / Guss, J.M. #1: Journal: Protein Expr.Purif. / Year: 2001 Title: Construction, Overexpression, and Purification of Arthrobacter Globiformis Amine Oxidase-Strep- Tag II Fusion Protein Authors: Juda, G.A. / Bollinger, J.A. / Dooley, D.M. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1w6c.cif.gz | 233.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1w6c.ent.gz | 188.4 KB | Display | PDB format |
PDBx/mmJSON format | 1w6c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w6/1w6c ftp://data.pdbj.org/pub/pdb/validation_reports/w6/1w6c | HTTPS FTP |
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-Related structure data
Related structure data | 1w6gC 1av4S C: citing same article (ref.) 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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-Components
#1: Protein | Mass: 71763.766 Da / Num. of mol.: 1 / Fragment: AGAO HOLOENZYME, RESIDUES 3-638 Source method: isolated from a genetically manipulated source Details: RESIDUE A382 WAS AN ACTIVE SITE TYROSINE RESIDUE, WHICH WAS AUTOCATALYTICALLY MODIFIED TO BECOME TPQ Source: (gene. exp.) ARTHROBACTER GLOBIFORMIS (bacteria) / Plasmid: PAGAO2 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P46881, EC: 1.4.3.6 | ||||||||
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#2: Chemical | #3: Chemical | ChemComp-NA / | #4: Water | ChemComp-HOH / | Compound details | CATALYTIC ACTIVITY: RCH(2)NH(2) + H(2)O + O(2) = RCHO + NH(3) + H(2)O(2). | Sequence details | RESIDES 1-2, MT, ARE THOUGHT TO BE CLEAVED. THE WILD TYPE MATURE PROTEIN IS COMPOSED OF RESIDUES 3- ...RESIDES 1-2, MT, ARE THOUGHT TO BE CLEAVED. THE WILD TYPE MATURE PROTEIN IS COMPOSED OF RESIDUES 3-638. RESIDUES 639- 640, SN, IS A PRE-TAG SPACER. RESIDUES 641-648, WSHPQFEK, IS A STREP-TAG II. SEE JUDA ET AL. (2001) PROTEIN EXPRESSION | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.33 Å3/Da / Density % sol: 47.28 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: CRYSTALS WERE GROWN IN ABOUT 2 WEEKS BY HANGING-DROP VAPOR DIFFUSION AT 293K. THE RESERVOIR WAS 0.2M MG ACETATE, 20% PEG 8K, 0.1M NA CACODYLATE PH 6.5. THE DROPS WERE 1.5MICROL OF 11.7 MG/ML ...Details: CRYSTALS WERE GROWN IN ABOUT 2 WEEKS BY HANGING-DROP VAPOR DIFFUSION AT 293K. THE RESERVOIR WAS 0.2M MG ACETATE, 20% PEG 8K, 0.1M NA CACODYLATE PH 6.5. THE DROPS WERE 1.5MICROL OF 11.7 MG/ML PROTEIN, 0.05M HEPES, PH 7.0, PLUS 1.5MICROL OF RESERVOIR SOLUTION. A CRYSTAL WAS CRYOPROTECTED BY GRADUAL INCREMENTAL SOAKING IN RESERVOIR SOLUTION MIXED WITH GLYCEROL. THE CONCENTRATION OF GLYCEROL WAS INCREASED FROM 0 TO 30% IN 2-3% INCREMENTS DURING 2 HOURS. THE CRYSTAL WAS THEN FROZEN IN THE CRYOSTREAM. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08 |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Mar 20, 2002 Details: 58 CM LONG, PT-COATED, FUSED SILICA, VERTICAL FOCUSMIRROR |
Radiation | Monochromator: CYCLINDRICALLY BENT TRIANGULAR SI(111) ASYMMETRIC CUT, HORIZONTAL FOCUS MONOCHROMATOR Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.08 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→28.25 Å / Num. obs: 31420 / % possible obs: 94.4 % / Observed criterion σ(I): -3 / Redundancy: 2.2 % / Biso Wilson estimate: 29.49 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 13.68 |
Reflection shell | Resolution: 2.2→2.27 Å / Redundancy: 1.96 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 3.35 / % possible all: 84.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENRTY 1AV4 Resolution: 2.2→32.16 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.93 / SU B: 5.397 / SU ML: 0.136 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.279 / ESU R Free: 0.204 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. WATERS Z74, Z133 AND Z136 ARE ASSOCIATED WITH THE ACTIVE SITE COPPER ION AND ARE MODELLED DESPITE HAVING WEAK ELECTRON DENSITY.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.91 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→32.16 Å
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Refine LS restraints |
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