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- PDB-2e2t: Substrate Schiff-base analogue of copper amine oxidase from Arthr... -

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Basic information

Entry
Database: PDB / ID: 2e2t
TitleSubstrate Schiff-base analogue of copper amine oxidase from Arthrobacter globiformis formed with phenylhydrazine
ComponentsPhenylethylamine oxidase
KeywordsOXIDOREDUCTASE / Amine oxidase / Topaquinone / TPQ / Substrate Schiff-base / phenylhydrazine
Function / homology
Function and homology information


: / : / : / primary-amine oxidase / amine metabolic process / quinone binding / copper ion binding
Similarity search - Function
Copper amine oxidase, catalytic domain / Copper amine oxidase copper-binding site signature. / Copper amine oxidase topaquinone signature. / Nuclear Transport Factor 2; Chain: A, - #40 / Copper amine oxidase / Copper amine oxidase, catalytic domain / Copper amine oxidase, N-terminal / Copper amine oxidase, catalytic domain superfamily / Copper amine oxidase, enzyme domain / Beta-galactosidase; Chain A, domain 5 ...Copper amine oxidase, catalytic domain / Copper amine oxidase copper-binding site signature. / Copper amine oxidase topaquinone signature. / Nuclear Transport Factor 2; Chain: A, - #40 / Copper amine oxidase / Copper amine oxidase, catalytic domain / Copper amine oxidase, N-terminal / Copper amine oxidase, catalytic domain superfamily / Copper amine oxidase, enzyme domain / Beta-galactosidase; Chain A, domain 5 / Nuclear Transport Factor 2; Chain: A, / Distorted Sandwich / Roll / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
COPPER (II) ION / Phenylethylamine oxidase
Similarity search - Component
Biological speciesArthrobacter globiformis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsMurakawa, T. / Okajima, T. / Taki, M. / Yamamoto, Y. / Kuroda, S. / Hayashi, H. / Tanizawa, K.
CitationJournal: To be Published
Title: Catalytic Regulation Conducted by the Substrate Schiff Base and Conserved Aspartic Acid Residue in Bacterial Copper Amine Oxidase Reaction
Authors: Murakawa, T. / Okajima, T. / Taki, M. / Yamamoto, Y. / Kuroda, S. / Hayashi, H. / Tanizawa, K.
History
DepositionNov 17, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 20, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.2Apr 24, 2013Group: Structure summary

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phenylethylamine oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,9062
Polymers70,8431
Non-polymers641
Water5,729318
1
A: Phenylethylamine oxidase
hetero molecules

A: Phenylethylamine oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,8134
Polymers141,6862
Non-polymers1272
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area13840 Å2
ΔGint-70 kcal/mol
Surface area41130 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)157.644, 63.081, 91.862
Angle α, β, γ (deg.)90.00, 112.16, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Phenylethylamine oxidase / Copper Amine Oxidase / Amine oxidase


Mass: 70842.875 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arthrobacter globiformis (bacteria) / Plasmid: pEPO-2 / Production host: Escherichia coli (E. coli) / Strain (production host): CD03 / References: UniProt: P46881, EC: 1.4.3.6
#2: Chemical ChemComp-CU / COPPER (II) ION / Copper


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 318 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.99 Å3/Da / Density % sol: 58.84 %
Crystal growTemperature: 289 K / Method: microdialysis / pH: 6.8
Details: 0.3mM phenylhydrazine for 12h and at 310K, 10mg/ml enzyme solution, 1.05M potassium tartrate, 25mM HEPES (pH6.8) at 289K, MICRODIALYSIS

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: Bruker DIP-6040 / Detector: CCD / Date: May 25, 2005
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.73→26.498 Å / Num. all: 87300 / Num. obs: 87299 / % possible obs: 100 % / Observed criterion σ(I): 5.1 / Rmerge(I) obs: 0.057
Reflection shellResolution: 1.73→1.82 Å / Rmerge(I) obs: 0.057 / % possible all: 100

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Processing

Software
NameClassification
CNSrefinement
MOSFLMdata reduction
SCALAdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.05→26.498 Å / σ(F): 1
RfactorNum. reflectionSelection details
Rfree0.243 2688 RANDOM
Rwork0.205 --
all-55339 -
obs-52651 -
Refinement stepCycle: LAST / Resolution: 2.05→26.498 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4875 0 1 318 5194
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.358

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