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- PDB-6grr: Crystal structure of Escherichia coli amine oxidase mutant I342F/E573Q -

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Basic information

Entry
Database: PDB / ID: 6grr
TitleCrystal structure of Escherichia coli amine oxidase mutant I342F/E573Q
Components(Amine oxidase) x 2
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


Oxidoreductases; Acting on the CH-NH2 group of donors; With oxygen as acceptor / aliphatic amine oxidase activity / phenylethylamine catabolic process / primary amine oxidase activity / : / : / : / primary-amine oxidase / L-phenylalanine catabolic process / amine metabolic process ...Oxidoreductases; Acting on the CH-NH2 group of donors; With oxygen as acceptor / aliphatic amine oxidase activity / phenylethylamine catabolic process / primary amine oxidase activity / : / : / : / primary-amine oxidase / L-phenylalanine catabolic process / amine metabolic 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 / Amine oxidase / Primary amine oxidase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.7 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
DepositionJun 12, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 5, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 19, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
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: Amine oxidase
B: Amine oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)162,29917
Polymers161,0792
Non-polymers1,22015
Water21,7081205
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17380 Å2
ΔGint-76 kcal/mol
Surface area50520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.152, 166.836, 79.734
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Amine oxidase /


Mass: 80405.719 Da / Num. of mol.: 1 / Mutation: I342F, E573Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: RK56_010715 / Plasmid: pKK233-2 / Production host: Escherichia coli (E. coli) / Variant (production host): XL-1
References: UniProt: A0A2K0PX72, UniProt: P46883*PLUS, Oxidoreductases; Acting on the CH-NH2 group of donors; With oxygen as acceptor
#2: Protein Amine oxidase /


Mass: 80673.055 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: RK56_010715 / Plasmid: pKK233-2 / Production host: Escherichia coli (E. coli) / Variant (production host): XL-1 blue
References: UniProt: A0A2K0PX72, UniProt: P46883*PLUS, Oxidoreductases; Acting on the CH-NH2 group of donors; With oxygen as acceptor

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Non-polymers , 4 types, 1220 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-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1205 / 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: 2.79 Å3/Da / Density % sol: 55.92 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: 100 mM HEPES, 1.2 M sodium citrate / PH range: 6.9 - 7.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 10, 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: 1.7→105.05 Å / Num. obs: 196242 / % possible obs: 99.2 % / Redundancy: 5.1 % / CC1/2: 1 / Rmerge(I) obs: 0.036 / Rpim(I) all: 0.018 / Rrim(I) all: 0.04 / Net I/σ(I): 21.4
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.785 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 9515 / CC1/2: 0.873 / Rpim(I) all: 0.379 / Rrim(I) all: 0.875 / % possible all: 97.06

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 1DYU

1dyu


Resolution: 1.7→105.05 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.969 / SU B: 2.588 / SU ML: 0.078 / Cross valid method: THROUGHOUT / ESU R: 0.087 / ESU R Free: 0.086 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19326 6714 3.4 %RANDOM
Rwork0.16638 ---
obs0.1673 189466 99.15 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 33.255 Å2
Baniso -1Baniso -2Baniso -3
1--1.5 Å20 Å20 Å2
2---2.57 Å20 Å2
3---4.07 Å2
Refinement stepCycle: 1 / Resolution: 1.7→105.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11349 0 70 1205 12624
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01911737
X-RAY DIFFRACTIONr_bond_other_d0.0020.0210708
X-RAY DIFFRACTIONr_angle_refined_deg1.4461.94915962
X-RAY DIFFRACTIONr_angle_other_deg0.908324931
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.47351444
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.87124.882549
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.283151928
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4881555
X-RAY DIFFRACTIONr_chiral_restr0.0840.21739
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02113068
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022295
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_it1.9533.155770
X-RAY DIFFRACTIONr_mcbond_other1.9533.1495769
X-RAY DIFFRACTIONr_mcangle_it2.8644.7157216
X-RAY DIFFRACTIONr_mcangle_other2.8654.7157217
X-RAY DIFFRACTIONr_scbond_it2.5053.4525967
X-RAY DIFFRACTIONr_scbond_other2.53.4535967
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.9825.0458747
X-RAY DIFFRACTIONr_long_range_B_refined5.59937.39312937
X-RAY DIFFRACTIONr_long_range_B_other5.59637.39212937
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.308 485 -
Rwork0.293 13704 -
obs--97.79 %

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