+Open data
-Basic information
Entry | Database: PDB / ID: 1w4n | ||||||
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Title | AGAO covalent complex with Tranylcypromine | ||||||
Components | PHENYLETHYLAMINE OXIDASE | ||||||
Keywords | OXIDOREDUCTASE / AMINE OXIDASE / ARTHROBACTER GLOBIFORMIS / COPPER CONTAINING / METAL-BINDING / TCQ / QUINONE / INHIBITED / TCP / TRANYLCYPROMINE | ||||||
Function / homology | Function and homology information primary-amine oxidase / aliphatic amine oxidase activity / primary amine 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: 1.65 Å | ||||||
Authors | Duff, A.P. / Trambaiolo, D.M. / 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: 2008 Title: Complexes of the Copper-Containing Amine Oxidase from Arthrobacter Globiformis with the Inhibitors Benzylhydrazine and Tranylcypromine. Authors: Langley, D.B. / Trambaiolo, D.M. / Duff, A.P. / Dooley, D.M. / Freeman, H.C. / Guss, J.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 | 1w4n.cif.gz | 468.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1w4n.ent.gz | 387.9 KB | Display | PDB format |
PDBx/mmJSON format | 1w4n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1w4n_validation.pdf.gz | 473.2 KB | Display | wwPDB validaton report |
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Full document | 1w4n_full_validation.pdf.gz | 485 KB | Display | |
Data in XML | 1w4n_validation.xml.gz | 55.3 KB | Display | |
Data in CIF | 1w4n_validation.cif.gz | 82.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w4/1w4n ftp://data.pdbj.org/pub/pdb/validation_reports/w4/1w4n | HTTPS FTP |
-Related structure data
Related structure data | 1w5zC 1av4S S: Starting model for refinement C: citing same article (ref.) |
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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: (-0.99875, 0.049895, 0.002583), Vector: |
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 71879.953 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: RESIDUES A382 AND B382 ARE ACTIVE SITE TYROSINE RESIDUES, WHICH WERE AUTOCATALYTICALLY MODIFIED TO BECOME TPQ, ARE COVALENTLY LINKED TO THE SUICIDE INHIBITOR TRANS-2-PHENYLCYCLOPROPYL-1- ...Details: RESIDUES A382 AND B382 ARE ACTIVE SITE TYROSINE RESIDUES, WHICH WERE AUTOCATALYTICALLY MODIFIED TO BECOME TPQ, ARE COVALENTLY LINKED TO THE SUICIDE INHIBITOR TRANS-2-PHENYLCYCLOPROPYL-1-AMINE. THIS MODIFIED TPQ IS NAMED TCQ 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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-Non-polymers , 5 types, 1049 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-GOL / #6: Water | ChemComp-HOH / | |
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-Details
Compound details | CATALYTIC ACTIVITY: RCH2NH2 + H2O + O2 = RCHO + NH3 + H2O2 |
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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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3 Å3/Da / Density % sol: 59 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: AGAO CRYSTALS WERE GROWN IN ABOUT 2 WEEKS BY HANGING-DROP VAPOR DIFFUSION AT 293K. THE RESERVOIR WAS 1.0-1.5M (NH4)2SO4, 2MM CUSO4, 0.15M NA CITRATE, PH 6.0-7.5. THE DROPS WERE 1.5MICROL OF ...Details: AGAO CRYSTALS WERE GROWN IN ABOUT 2 WEEKS BY HANGING-DROP VAPOR DIFFUSION AT 293K. THE RESERVOIR WAS 1.0-1.5M (NH4)2SO4, 2MM CUSO4, 0.15M NA CITRATE, PH 6.0-7.5. THE DROPS WERE 1.5MICROL OF 11.7 MG/ML PROTEIN, 0.05M HEPES, PH 7.0, PLUS 1.5MICROL OF RESERVOIR SOLUTION. A SINGLE CRYSTAL WAS SOAKED WITH TCP BY SLOWLY ADDING TCP TO THE DROP TO ACHIEVE A 100 FOLD EXCESS OF TCP OVER ENZYME ACTIVE SITES. THE CRYSTAL WAS CRYOPROTECTED BY GRADUAL INCREMENTAL SOAKING IN RESERVOIR SOLUTION MIXED WITH GLYCEROL, WITH THE CONCENTRAION OF TCP BEING MAINTAINED CONSTANT. THE CONCENTRATION OF GLYCEROL WAS INCREASED FROM 0 TO 30% IN 2-3% INCREMENTS DURING 2 HOURS. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jun 5, 2003 / 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: 1.65→28.25 Å / Num. obs: 200663 / % possible obs: 98.2 % / Observed criterion σ(I): -3 / Redundancy: 7.4 % / Biso Wilson estimate: 22.32 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 15.73 |
Reflection shell | Resolution: 1.65→1.67 Å / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 3 / % possible all: 80 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1AV4 Resolution: 1.65→28.28 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.958 / SU B: 1.782 / SU ML: 0.058 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.078 / ESU R Free: 0.08 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. TCQ WAS INITIALLY REFINED WITH MINIMAL RESTRAINTS. IT WAS DETERMINED THAT THE TCQ WAS IN THE SUBSTRATE SCHIFF BASE FORM. IN LATE ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. TCQ WAS INITIALLY REFINED WITH MINIMAL RESTRAINTS. IT WAS DETERMINED THAT THE TCQ WAS IN THE SUBSTRATE SCHIFF BASE FORM. IN LATE REFINEMENT, THE TCQ WAS RESTRAINED TO THE SUBSTRATE SCHIFF BASE FORM.
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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: 17.34 Å2
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Refinement step | Cycle: LAST / Resolution: 1.65→28.28 Å
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Refine LS restraints |
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