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- PDB-6ezz: Crystal structure of Escherichia coli amine oxidase mutant E573Q -

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Basic information

Entry
Database: PDB / ID: 6ezz
TitleCrystal structure of Escherichia coli amine oxidase mutant E573Q
ComponentsPrimary amine oxidase
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


phenylethylamine catabolic process / primary-amine oxidase / aliphatic amine oxidase activity / primary methylamine oxidase activity / amine metabolic process / L-phenylalanine catabolic process / quinone binding / periplasmic space / copper ion binding / calcium ion binding
Similarity search - Function
Copper amine oxidase-like, N-terminal domain / Copper amine oxidase-like, N-terminal / Copper amine oxidase-like, N-terminal domain superfamily / Copper amine oxidase N-terminal domain / Copper Amine Oxidase; Chain A, domain 1 / Copper amine oxidase, N3-terminal / Copper amine oxidase, N2-terminal / Copper amine oxidase, N2 domain / Copper amine oxidase, N3 domain / Copper amine oxidase, catalytic domain ...Copper amine oxidase-like, N-terminal domain / Copper amine oxidase-like, N-terminal / Copper amine oxidase-like, N-terminal domain superfamily / Copper amine oxidase N-terminal domain / Copper Amine Oxidase; Chain A, domain 1 / Copper amine oxidase, N3-terminal / Copper amine oxidase, N2-terminal / Copper amine oxidase, N2 domain / Copper amine oxidase, N3 domain / 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 / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
COPPER (II) ION / Primary amine oxidase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.8 Å
AuthorsGaule, T.G. / Smith, M.A. / Tych, K.M. / Pirrat, P. / Trinh, C.H. / Pearson, A.R. / Knowles, P.F. / McPherson, M.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/C00468X/1 United Kingdom
CitationJournal: Biochemistry / Year: 2018
Title: Oxygen Activation Switch in the Copper Amine Oxidase of Escherichia coli.
Authors: Gaule, T.G. / Smith, M.A. / Tych, K.M. / Pirrat, P. / Trinh, C.H. / Pearson, A.R. / Knowles, P.F. / McPherson, M.J.
History
DepositionNov 16, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 29, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 19, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Primary amine oxidase
B: Primary amine oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)163,70815
Polymers162,6722
Non-polymers1,03613
Water20,0511113
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry, Total buried surface area: 13851.5 Angstrom**2 Surface area of the complex: 51738.4 Angstrom**2 Change in solvent free energy: -60.6 Kcal/Mol
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16930 Å2
ΔGint-88 kcal/mol
Surface area50810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.521, 167.202, 79.939
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Primary amine oxidase / 2-phenylethylamine oxidase / Copper amine oxidase / Tyramine oxidase


Mass: 81335.750 Da / Num. of mol.: 2 / Mutation: E573Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: tynA, maoA, b1386, JW1381 / Plasmid: pKK233-3 / Production host: Escherichia coli (E. coli) / Strain (production host): XL1 blue / References: UniProt: P46883, primary-amine oxidase
#2: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1113 / 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: 2.78 Å3/Da / Density % sol: 55.82 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / Details: 1.6 M Sodium citrate, 100mM HEPES pH 6-7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 5, 2012
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.8→72.12 Å / Num. obs: 167221 / % possible obs: 99.31 % / Redundancy: 4.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.054 / Rpim(I) all: 0.027 / Rrim(I) all: 0.061 / Net I/σ(I): 14.7
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.666 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 7889 / CC1/2: 0.806 / % possible all: 95.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
Aimless0.5.31data scaling
REFMAC5.8.0158phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 1DYU

1dyu


Resolution: 1.8→72.12 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.966 / SU B: 3.115 / SU ML: 0.089 / Cross valid method: THROUGHOUT / ESU R: 0.102 / ESU R Free: 0.1 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1968 5691 3.4 %RANDOM
Rwork0.16567 ---
obs0.16674 161438 99.16 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 34.824 Å2
Baniso -1Baniso -2Baniso -3
1--1.57 Å20 Å20 Å2
2---2.45 Å20 Å2
3---4.03 Å2
Refinement stepCycle: 1 / Resolution: 1.8→72.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11343 0 58 1113 12514
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01911726
X-RAY DIFFRACTIONr_bond_other_d0.0020.0210706
X-RAY DIFFRACTIONr_angle_refined_deg1.5561.94815954
X-RAY DIFFRACTIONr_angle_other_deg0.942324933
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.56951448
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.02324.918549
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.614151933
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2611555
X-RAY DIFFRACTIONr_chiral_restr0.0930.21741
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02113061
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022286
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.3723.2825768
X-RAY DIFFRACTIONr_mcbond_other2.3723.2825767
X-RAY DIFFRACTIONr_mcangle_it3.3554.9117212
X-RAY DIFFRACTIONr_mcangle_other3.3554.9117213
X-RAY DIFFRACTIONr_scbond_it3.0833.6365958
X-RAY DIFFRACTIONr_scbond_other3.0823.6375958
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.8445.2978739
X-RAY DIFFRACTIONr_long_range_B_refined6.38438.8812785
X-RAY DIFFRACTIONr_long_range_B_other6.38438.88312786
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.799→1.846 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.328 417 -
Rwork0.312 11483 -
obs--96.48 %

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