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- PDB-2cfd: AGAO in complex with wc4l3 (Ru-wire inhibitor, 4-carbon linker, l... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2cfd | ||||||
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Title | AGAO in complex with wc4l3 (Ru-wire inhibitor, 4-carbon linker, lambda enantiomer, data set 3) | ||||||
![]() | PHENYLETHYLAMINE OXIDASE | ||||||
![]() | OXIDOREDUCTASE / AMINE OXIDASE / ARTHROBACTER GLOBIFORMIS / COPPER CONTAINING / TPQ / QUINONE / RUTHENIUM DIIMINE WIRES / COMPETITIVE INHIBITION / METAL-BINDING | ||||||
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. / Freeman, H.C. / Guss, J.M. / Juda, G.A. / Dooley, D.M. / Contakes, S.M. / Halpern-Manners, N.W. / Dunn, A.R. / Gray, H.B. | ||||||
![]() | ![]() Title: Enantiomer-Specific Binding of Ruthenium(II) Molecular Wires by the Amine Oxidase of Arthrobacter Globiformis. Authors: Langley, D.B. / Brown, D.E. / Cheruzel, L.E. / Contakes, S.M. / Duff, A.P. / Hilmer, K.M. / Dooley, D.M. / Gray, H.B. / Guss, J.M. / Freeman, H.C. | ||||||
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 | ![]() | 452.3 KB | Display | ![]() |
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PDB format | ![]() | 389.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 52.2 KB | Display | |
Data in CIF | ![]() | 75.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2cfgC ![]() 2cfkC ![]() 2cflC ![]() 2cfwC ![]() 2cg0C ![]() 2cg1C C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 71763.766 Da / Num. of mol.: 2 / 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 , 6 types, 667 molecules ![](data/chem/img/CU.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/R4A.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/R4A.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | #6: Chemical | ChemComp-GOL / #7: Water | ChemComp-HOH / | |
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-Details
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 |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.07 Å3/Da / Density % sol: 59.94 % |
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 7.5 Details: THE CRYSTAL WAS GROWN BY HANGING DROP OVER 150 MM CITRATE PH 7.5, 1000 MM NH4SO4. THE INHIBITOR WAS ADDED BY SOAKING, WITH ALL STEPS IN THE DARK. 3.4 MG OF THE INHIBITOR (WC4L) DISSOLVED IN ...Details: THE CRYSTAL WAS GROWN BY HANGING DROP OVER 150 MM CITRATE PH 7.5, 1000 MM NH4SO4. THE INHIBITOR WAS ADDED BY SOAKING, WITH ALL STEPS IN THE DARK. 3.4 MG OF THE INHIBITOR (WC4L) DISSOLVED IN 20 MICROLITRE ETHANOL. 1 MICROLITRE OF THIS WAS ADDED TO THE 200 MICROLITRE RESERVOIR. GLYCEROL WAS THEN ADDED IN 2-3% INCREMENTS TO THE RESERVOIR, WITH THE NEW RESERVOIR SOLUTION SUBSTITUTING FOR THE DROP SOLUTION. THE SOAK SAT FOR 24 HOURS IN 5% GLYCEROL. THE FINAL GLYCEROL CONCENTRATION WAS 30% |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 17, 2005 / Details: OSMIC MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→30 Å / Num. obs: 206776 / % possible obs: 94 % / Observed criterion σ(I): -3 / Redundancy: 5.027 % / Biso Wilson estimate: 21.49 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 9.5 |
Reflection shell | Resolution: 1.6→1.66 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 3.17 / % possible all: 90.6 |
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Processing
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Refinement | Method to determine structure: ![]()
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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: 21.44 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→29.99 Å
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Refine LS restraints |
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