+Open data
-Basic information
Entry | Database: PDB / ID: 2cfk | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | AGAO in complex with wc5 (Ru-wire inhibitor, 5-carbon linker) | |||||||||
Components | PHENYLETHYLAMINE OXIDASE | |||||||||
Keywords | OXIDOREDUCTASE / AMINE OXIDASE / ARTHROBACTER GLOBIFORMIS / COPPER / COPPER CONTAINING / TPQ / CUAO / QUINONE / RUTHENIUM DIIMINE WIRES / COMPETITIVE INHIBITION / METAL-BINDING | |||||||||
Function / homology | Function and homology information primary-amine oxidase / aliphatic amine oxidase activity / primary methylamine oxidase activity / amine metabolic process / quinone binding / copper ion binding Similarity search - Function | |||||||||
Biological species | ARTHROBACTER GLOBIFORMIS (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | |||||||||
Authors | 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. | |||||||||
Citation | Journal: J. Am. Chem. Soc. / Year: 2008 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 |
| |||||||||
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 |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2cfk.cif.gz | 252.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2cfk.ent.gz | 203 KB | Display | PDB format |
PDBx/mmJSON format | 2cfk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2cfk_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 2cfk_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 2cfk_validation.xml.gz | 29.4 KB | Display | |
Data in CIF | 2cfk_validation.cif.gz | 43.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cf/2cfk ftp://data.pdbj.org/pub/pdb/validation_reports/cf/2cfk | HTTPS FTP |
-Related structure data
Related structure data | 2cfdC 2cfgC 2cflC 2cfwC 2cg0C 2cg1C 1w6gS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-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 SELF-PROCESSED TO BECOME A 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 |
---|
-Non-polymers , 7 types, 439 molecules
#2: Chemical | ChemComp-CU / | ||||
---|---|---|---|---|---|
#3: Chemical | ChemComp-NA / | ||||
#4: Chemical | ChemComp-R5A / | ||||
#5: Chemical | ChemComp-R5B / | ||||
#6: Chemical | #7: Chemical | ChemComp-GOL / #8: Water | ChemComp-HOH / | |
-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 |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.06 Å3/Da / Density % sol: 59.86 % |
---|---|
Crystal grow | Method: vapor diffusion, hanging drop / pH: 6 Details: THE CRYSTAL WAS GROWN BY HANGING DROP OVER 150 MM CITRATE PH 6.0, 800 MM NH4SO4. THE INHIBITOR WAS ADDED BY SOAKING, WITH ALL STEPS IN THE DARK, OVER THREE DAYS. 25 MG OF THE INHIBITOR (WC5) ...Details: THE CRYSTAL WAS GROWN BY HANGING DROP OVER 150 MM CITRATE PH 6.0, 800 MM NH4SO4. THE INHIBITOR WAS ADDED BY SOAKING, WITH ALL STEPS IN THE DARK, OVER THREE DAYS. 25 MG OF THE INHIBITOR (WC5) DISSOLVED IN 250 MICROLITRE ETHANOL. 1MICROLITRE OF THIS WAS ADDED TO THE 200MICROLITRE RESERVOIR. GLYCEROL WAS THEN, ADDED IN 2-3% INCREMENTS, TO THE RESERVOIR, WITH THE NEW RESERVOIR SOLUTION SUBSTITUTING THE DROP SOLUTION. THE SOAK SAT FOR 24 HOURS AT 5% GLYCEROL. THE FINAL GLYCEROL CONCENTRATION WAS 30%. |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 21, 2004 / 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: 1.79→15 Å / Num. obs: 322625 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 4.2 % / Biso Wilson estimate: 21.59 Å2 / Rmerge(I) obs: 0.03 / Net I/σ(I): 24.4 |
Reflection shell | Resolution: 1.79→1.85 Å / Redundancy: 2.58 % / Rmerge(I) obs: 0.15 / Mean I/σ(I) obs: 4.33 / % possible all: 76.8 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1W6G Resolution: 1.8→15.02 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.967 / SU B: 1.82 / SU ML: 0.056 / Cross valid method: THROUGHOUT / ESU R: 0.087 / ESU R Free: 0.083 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 21.96 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→15.02 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|