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- PDB-3amo: Time-resolved X-ray Crystal Structure Analysis of Enzymatic React... -

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Basic information

Entry
Database: PDB / ID: 3amo
TitleTime-resolved X-ray Crystal Structure Analysis of Enzymatic Reaction of Copper Amine Oxidase from Arthrobacter globiformis
Components(Phenylethylamine ...) x 2
KeywordsOXIDOREDUCTASE / Amine Oxidase / Topaquinone / TPQ / Reaction Intermediate / Substrate Schiff-base / Product Schiff-base / Phenylethylamine / TPQ Biogenesis
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 / molecular replacement / Resolution: 2.1 Å
AuthorsKataoka, M. / Oya, H. / Tominaga, A. / Otsu, M. / Okajima, T. / Tanizawa, K. / Yamaguchi, H.
CitationJournal: J.SYNCHROTRON RADIAT. / Year: 2011
Title: Detection of the reaction intermediates catalyzed by a copper amine oxidase.
Authors: Kataoka, M. / Oya, H. / Tominaga, A. / Otsu, M. / Okajima, T. / Tanizawa, K. / Yamaguchi, H.
History
DepositionAug 20, 2010Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 23, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phenylethylamine oxidase
B: Phenylethylamine oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,818103
Polymers141,7122
Non-polymers9,106101
Water13,403744
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13010 Å2
ΔGint-45 kcal/mol
Surface area41120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)190.868, 63.635, 157.558
Angle α, β, γ (deg.)90.000, 116.820, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-906-

HOH

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Components

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Phenylethylamine ... , 2 types, 2 molecules AB

#1: Protein Phenylethylamine oxidase / Primary amine oxidase


Mass: 70855.914 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arthrobacter globiformis (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P46881, primary-amine oxidase
#2: Protein Phenylethylamine oxidase / Primary amine oxidase


Mass: 70855.914 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arthrobacter globiformis (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P46881, primary-amine oxidase

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Non-polymers , 4 types, 845 molecules

#3: Chemical ChemComp-CU / COPPER (II) ION / Copper


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Chemical...
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 97 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 744 / 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: 3.01 Å3/Da / Density % sol: 59.17 %
Crystal growTemperature: 293 K / Method: microdialysis / pH: 6.8
Details: 20mM HEPES, 1.05M Sodium-potassium tartrate, pH 6.8, MICRODIALYSIS, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Jun 12, 2009
Diffraction measurementDetails: 0.80degrees, 5.0sec, detector distance 170.00mm
RadiationMonochromator: Fixed exit Si 111 double crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionAv R equivalents: 0.07
ReflectionResolution: 2.1→50 Å / Num. all: 633777 / Num. obs: 633777 / % possible obs: 94.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.8 % / Rmerge(I) obs: 0.07 / Rsym value: 0.07 / Net I/σ(I): 32.763
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.363 / Mean I/σ(I) obs: 6.482 / Rsym value: 0.363 / % possible all: 96.1
Cell measurementReflection used: 633777

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.33 Å25.49 Å
Translation2.33 Å25.49 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→50 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.925 / WRfactor Rfree: 0.2217 / WRfactor Rwork: 0.1762 / Occupancy max: 1 / Occupancy min: 0.19 / FOM work R set: 0.7994 / SU B: 4.649 / SU ML: 0.123 / SU R Cruickshank DPI: 0.2129 / SU Rfree: 0.1922 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.192 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.245 4577 5 %RANDOM
Rwork0.1893 ---
obs0.1921 91635 92.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 89.98 Å2 / Biso mean: 28.1203 Å2 / Biso min: 7.45 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å20 Å2-0.82 Å2
2--2.65 Å20 Å2
3----3.46 Å2
Refinement stepCycle: LAST / Resolution: 2.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9736 0 586 744 11066
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.02110573
X-RAY DIFFRACTIONr_angle_refined_deg1.9371.98614232
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.27251252
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.17423.056504
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.463151546
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.34315101
X-RAY DIFFRACTIONr_chiral_restr0.1320.21476
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0217992
X-RAY DIFFRACTIONr_mcbond_it1.0771.56209
X-RAY DIFFRACTIONr_mcangle_it1.783210038
X-RAY DIFFRACTIONr_scbond_it2.86134364
X-RAY DIFFRACTIONr_scangle_it4.2594.54194
LS refinement shellResolution: 2.101→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.296 321 -
Rwork0.247 6370 -
all-6691 -
obs--92.44 %

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