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- PDB-1lvn: CRYSTAL STRUCTURE OF E. COLI AMINE OXIDASE COMPLEXED WITH TRANYLC... -

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Basic information

Entry
Database: PDB / ID: 1lvn
TitleCRYSTAL STRUCTURE OF E. COLI AMINE OXIDASE COMPLEXED WITH TRANYLCYPROMINE
ComponentsCopper amine oxidase
KeywordsOXIDOREDUCTASE / Inhibitor complex
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 / FOURIER SYNTHESIS / Resolution: 2.4 Å
AuthorsWilmot, C.M. / Phillips, S.E.
Citation
Journal: Febs Lett. / Year: 2004
Title: Medical implications from the crystal structure of a copper-containing amine oxidase complexed with the antidepressant drug tranylcypromine.
Authors: Wilmot, C.M. / Saysell, C.G. / Blessington, A. / Conn, D.A. / Kurtis, C.R. / McPherson, M.J. / Knowles, P.F. / Phillips, S.E.
#1: Journal: BIOCHEM.J. / Year: 2002
Title: Probing the catalytic mechanism of Escherichia coli amine oxidase using mutational variants and a reversible inhibitor as a substrate analogue.
Authors: Saysell, C.G. / Tambyrajah, W.S. / Murray, J.M. / Wilmot, C.M. / Phillips, S.E. / McPherson, M.J. / Knowles, P.F.
#2: Journal: Biochemistry / Year: 1997
Title: Catalytic Mechanism of the Quinoenzyme Amine Oxidase from Escherichia Coli: Exploring the Reductive Half-Reaction.
Authors: Wilmot, C.M. / Murray, J.M. / Alton, G. / Parsons, M.R. / Convery, M.A. / Blakeley, V. / Corner, A.S. / Palcic, M.M. / Knowles, P.F. / McPherson, M.J. / Phillips, S.E.V.
#3: Journal: Structure / Year: 1995
Title: Crystal Structure of a Quinoenzyme: Copper Amine Oxidase of Escherichia Coli at 2 Angstroms Resolution.
Authors: Parsons, M.R. / Convery, M.A. / Wilmot, C.M. / Yadav, K.D.S. / Blakeley, V. / Corner, A.S. / Phillips, S.E. / McPherson, M.J. / Knowles, P.F.
#4: Journal: Biochemistry / Year: 1999
Title: The active site base controls cofactor reactivity in Escherichia coli amine oxidase: X-ray crystallographic studies with mutational variants.
Authors: Murray, J.M. / Saysell, C.G. / Wilmot, C.M. / Tambyrajah, W.S. / Jaeger, J. / Knowles, P.F. / Phillips, S.E. / McPherson, M.J.
#5: Journal: Science / Year: 1999
Title: Visualization of dioxygen bound to copper during enzyme catalysis.
Authors: Wilmot, C.M. / Hajdu, J. / McPherson, M.J. / Knowles, P.F. / Phillips, S.E.
History
DepositionMay 28, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 5, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.1Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)163,2558
Polymers162,9682
Non-polymers2876
Water26,0681447
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16070 Å2
ΔGint-112 kcal/mol
Surface area49890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.236, 166.482, 79.628
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 Copper amine oxidase / Tyramine oxidase / 2-phenylenthylamine oxidase


Mass: 81483.922 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Cellular location: PERIPLASM / Plasmid: PKK233-3 / Cellular location (production host): PERIPLASM / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P46883, EC: 1.4.3.6
#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.: 1447 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.76 Å3/Da / Density % sol: 0.55 %
Crystal growTemperature: 291 K / Method: sitting drop / pH: 7.2
Details: 1.3M SODIUM CITRATE, 0.1M HEPES BUFFER, pH 7.2, INHIBITOR SOAKING SOLUTION 10:1 RATIO OF RACEMIC TRANYLCYPROMINE TO ENZYME MADE UP IN 1.4M SODIUM CITRATE, 0.1M HEPES BUFFER, PH 7.2. CRYSTAL ...Details: 1.3M SODIUM CITRATE, 0.1M HEPES BUFFER, pH 7.2, INHIBITOR SOAKING SOLUTION 10:1 RATIO OF RACEMIC TRANYLCYPROMINE TO ENZYME MADE UP IN 1.4M SODIUM CITRATE, 0.1M HEPES BUFFER, PH 7.2. CRYSTAL SOAKED FOR 20 DAYS.CRYOPROTECTANT 20% GLYCEROL, 1.4M SODIUM CITRATE BUFFER, PH 7.2, pH 7.20, Sitting drop, temperature 291.0K
Crystal grow
*PLUS
pH: 7 / Method: vapor diffusion / Details: Parsons, M.R., (1995) Structure, 3, 1171.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
12.3 Mammonium sulfate1reservoir
2100 mMHEPES1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87 / Wavelength: 0.87 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Oct 20, 1996
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 2.4→100 Å / Num. all: 64108 / Num. obs: 64108 / % possible obs: 90.1 % / Observed criterion σ(I): 0 / Redundancy: 2.56 % / Biso Wilson estimate: 36.6 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 7.5
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.251 / Mean I/σ(I) obs: 2.9 / % possible all: 80.6
Reflection
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 20 Å / Num. obs: 64108 / % possible obs: 90.1 % / Num. measured all: 163856 / Rmerge(I) obs: 0.075
Reflection shell
*PLUS
% possible obs: 80.6 % / Rmerge(I) obs: 0.251 / Mean I/σ(I) obs: 2.9

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
ROTAVATAdata reduction
CNSrefinement
CCP4(AGROVATAdata scaling
ROTAVATAdata scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 1SPU

1spu


Resolution: 2.4→20 Å / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
Details: CYCLES OF POSITIONAL POWELL MINIMIZATION AND INDIVIDUAL TEMPERATURE FACTOR REFINEMENT, WITH A MLF TARGET, AND AN OVERALL ANISOTROPIC TEMPERATURE FACTOR CORRECTION. COPPER ION RESTRAINTS WERE ...Details: CYCLES OF POSITIONAL POWELL MINIMIZATION AND INDIVIDUAL TEMPERATURE FACTOR REFINEMENT, WITH A MLF TARGET, AND AN OVERALL ANISOTROPIC TEMPERATURE FACTOR CORRECTION. COPPER ION RESTRAINTS WERE WEAKENED BY ADJUSTMENT OF THE NON-BONDED PARAMTERES, TO ENABLE THE COPPER ION/LIGAND DISTANCES TO REFLECT THE DATA MORE ACCURATELY.
RfactorNum. reflection% reflectionSelection details
Rfree0.229 2236 3.2 %BY COMPARISON TO A COMPLETE DUMMY REFLECTION SET TO 1.8 ANGSTROMS FOR THE CELL AND SPACE GROUP WITH THE REFLECTIONS RANDOMLY FLAGGED TO GIVE A MINIMUM OF 2000 REFLECTIONS IN THE TEST SET AT 2.6 ANGSTROMS. THIS GAVE A PERCENTAGE OF 3.6% OF REFLECTIONS, WHICH WAS THE OVERALL PERCENT VALUE IN THE TEST SET TO 1.8 ANGSTROMS.
Rwork0.185 ---
all0.185 70890 --
obs0.185 63358 89.4 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.921 Å20 Å20 Å2
2--8.229 Å20 Å2
3----9.15 Å2
Refinement stepCycle: LAST / Resolution: 2.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11319 0 52 1447 12818
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_mcbond_it1.2082.5
X-RAY DIFFRACTIONc_mcangle_it2.0254
X-RAY DIFFRACTIONc_scbond_it2.3264
X-RAY DIFFRACTIONc_scangle_it3.45.5
Refinement
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 20 Å / Rfactor Rfree: 0.226
Solvent computation
*PLUS
Displacement parameters
*PLUS

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