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Basic information

Entry
Database: PDB / ID: 1dyu
TitleThe active site base controls cofactor reactivity in Escherichia coli amine oxidase: X-ray crystallographic studies with mutational variants.
ComponentsCOPPER AMINE OXIDASE
KeywordsOXIDOREDUCTASE / TPQ / COPPER AMINE OXIDASE / EC 1.4.3.4 / WILDTYPE / CATALYTIC BASE
Function / homology
Function and homology information


phenylethylamine catabolic process / primary-amine oxidase / 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 / MOLECULAR REPLACEMENT / Resolution: 2.04 Å
AuthorsMurray, J.M. / Wilmot, C.M. / Saysell, C.G. / Jaeger, J. / Knowles, P.F. / Phillips, S.E.V. / McPherson, M.J.
CitationJournal: Biochemistry / Year: 1999
Title: The Active Site Base Controls Cofactor Reactivity in Escherichia Coli Amine Oxidase : X-Ray Crystallographicstudies with Mutational Variants
Authors: Murray, J.M. / Wilmot, C.M. / Saysell, C.G. / Jaeger, J. / Knowles, P.F. / Phillips, S.E.V. / McPherson, M.J.
History
DepositionFeb 8, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 29, 2000Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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 / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET DETERMINATION METHOD: DSSP THERE ARE SEVERAL BIFURCATED SHEETS IN THIS STRUCTURE. EACH IS ... SHEET DETERMINATION METHOD: DSSP THERE ARE SEVERAL BIFURCATED SHEETS IN THIS STRUCTURE. EACH IS REPRESENTED BY TWO SHEETS WHICH HAVE ONE OR MORE IDENTICAL STRANDS. SHEETS C AND C1 REPRESENT ONE BIFURCATED SHEET. SHEETS K AND K1 REPRESENT ONE BIFURCATED SHEET.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: COPPER AMINE OXIDASE
B: COPPER AMINE OXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)163,0218
Polymers162,7332
Non-polymers2876
Water28,2481568
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15880 Å2
ΔGint-86.9 kcal/mol
Surface area62330 Å2
MethodPQS
Unit cell
Length a, b, c (Å)135.050, 167.170, 79.920
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsBIOLOGICAL_UNIT: DIMERIC

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Components

#1: Protein COPPER AMINE OXIDASE / TYRAMINE OXIDASE / 2-PHENYLENTHYLAMINE OXIDASE


Mass: 81366.727 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: EACH MONOMER CONTAINS ONE COPPER ATOM, TWO CALCIUM ATOMS, AND ONE 2,4,5, -TRIHYDROXYPHENYLALANINE QUINONE COFACTOR.
Source: (gene. exp.) ESCHERICHIA COLI (E. coli)
Description: CLONED AND OVER-EXPRESSED IN E. COLI USING PLASMID PKK233-3
Cellular location: PERIPLASM / Plasmid: PLASMID DERIVED FROM PKK233-3 / Cellular location (production host): PERIPLASM / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): JM109 / References: UniProt: P46883, monoamine 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.: 4 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1568 / 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: 2.73 Å3/Da / Density % sol: 55 %
Crystal growpH: 7.1 / Details: 1.2 M SODIUM CITRATE, 0.1 M HEPES PH 7.1
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11.3 Msodium citrate1reservoir
2100 mMHEPES1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID2 / Wavelength: 0.99
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99 Å / Relative weight: 1
ReflectionResolution: 2.04→20 Å / Num. obs: 105826 / % possible obs: 93.3 % / Redundancy: 3.2 % / Biso Wilson estimate: 36 Å2 / Rsym value: 0.06 / Net I/σ(I): 7.9
Reflection shellResolution: 2.04→2.38 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.07 / Mean I/σ(I) obs: 3.4 / Rsym value: 0.19 / % possible all: 91
Reflection
*PLUS
Rmerge(I) obs: 0.058
Reflection shell
*PLUS
% possible obs: 91 %

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Processing

Software
NameClassification
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1OAC

1oac


Resolution: 2.04→20 Å / Cross valid method: THROUGHOUT / σ(F): 0
Details: NEITHER THE N-TERMINAL OR C-TERMINAL AMINO ACIDS WERE WELL DEFINED BY THE ELECTRON DENSITY
RfactorNum. reflection% reflectionSelection details
Rfree0.237 3493 3.5 %RANDOM
Rwork0.185 ---
obs-105826 93.3 %-
Displacement parametersBiso mean: 31.9 Å2
Baniso -1Baniso -2Baniso -3
1-5.4 Å20 Å20 Å2
2--7.6 Å20 Å2
3----13 Å2
Refinement stepCycle: LAST / Resolution: 2.04→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11347 0 6 1568 12921
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.012
X-RAY DIFFRACTIONp_angle_d0.0250.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor

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