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Open data
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Basic information
Entry | Database: PDB / ID: 1w6g | ||||||
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Title | AGAO holoenzyme at 1.55 angstroms | ||||||
![]() | PHENYLETHYLAMINE OXIDASE | ||||||
![]() | OXIDOREDUCTASE / AMINE OXIDASE / ARTHROBACTER GLOBIFORMIS / COPPER CONTAINING / METAL-BINDING / TPQ / QUINONE / HOLOENZYME | ||||||
Function / homology | ![]() primary-amine oxidase / aliphatic amine oxidase activity / primary methylamine oxidase activity / amine metabolic process / quinone binding / copper ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Langley, D.B. / Duff, A.P. / Juda, G.A. / Shepard, E.M. / Dooley, D.M. / Freeman, H.C. / Guss, J.M. | ||||||
![]() | ![]() 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. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 247.6 KB | Display | ![]() |
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PDB format | ![]() | 199 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 413.1 KB | Display | ![]() |
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Full document | ![]() | 417.9 KB | Display | |
Data in XML | ![]() | 26.9 KB | Display | |
Data in CIF | ![]() | 42.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1w6cC ![]() 1av4S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 1 molecules A
#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.) ![]() ![]() ![]() |
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-Non-polymers , 5 types, 516 molecules ![](data/chem/img/CU.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-NA / | #4: Chemical | #5: Chemical | ChemComp-GOL / #6: Water | ChemComp-HOH / | |
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-Details
Compound details | CATALYTIC ACTIVITY: RCH(2)NH(2) + H(2)O + O(2) = RCHO + NH(3) + H(2)O(2). |
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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: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.03 Å3/Da / Density % sol: 59.41 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: THE CRYSTAL WAS GROWN BY HANGING DROP DIFFUSION AT 293K. THE RESERVOIR WAS 1.2M (NH4)2SO4, 12% DIOXANE, 0.1M MES PH6.5. THE DROP CONTAINED 1.5MICROLITER OF 11.7 MG/ML PROTEIN, 0.05M HEPES ...Details: THE CRYSTAL WAS GROWN BY HANGING DROP DIFFUSION AT 293K. THE RESERVOIR WAS 1.2M (NH4)2SO4, 12% DIOXANE, 0.1M MES PH6.5. THE DROP CONTAINED 1.5MICROLITER OF 11.7 MG/ML PROTEIN, 0.05M HEPES PH7.0, PLUS 1.5 MICROLITER 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., pH 7.00 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Mar 20, 2002 Details: 58 CM LONG, PT-COATED, FUSED SILICA, VERTICAL FOCUS MIRROR |
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: 1.55→25.85 Å / Num. obs: 117993 / % possible obs: 96 % / Observed criterion σ(I): -3 / Redundancy: 1.92 % / Biso Wilson estimate: 19.66 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 10.83 |
Reflection shell | Resolution: 1.55→1.61 Å / Redundancy: 1.83 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 1.74 / % possible all: 86.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1AV4 Resolution: 1.55→25.82 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.958 / SU B: 1.583 / SU ML: 0.052 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.066 / ESU R Free: 0.066 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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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: 13.98 Å2
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Refinement step | Cycle: LAST / Resolution: 1.55→25.82 Å
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Refine LS restraints |
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