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- PDB-1sih: AGAO in covalent complex with the inhibitor MOBA ("4-(4-methylphe... -

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Basic information

Entry
Database: PDB / ID: 1sih
TitleAGAO in covalent complex with the inhibitor MOBA ("4-(4-methylphenoxy)-2-butyn-1-amine")
ComponentsPhenylethylamine oxidase
KeywordsOXIDOREDUCTASE / CAO / CuAO / COPPER-CONTAINING / AMINE OXIDASE / TPQ / QUINONE / TRIHYDROXYPHENYLALANINE QUINONE / MOBA / 4-(4-methylphenoxyoxy)-2-butyn-1-amine / 4-(aryloxy)-2-butynamine / suicide inhibition
Function / homology
Function and homology information


primary-amine oxidase / aliphatic amine oxidase activity / primary methylamine oxidase activity / amine metabolic process / quinone binding / copper ion binding
Similarity search - Function
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 ...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 / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
COPPER (II) ION / Phenylethylamine oxidase
Similarity search - Component
Biological speciesArthrobacter globiformis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.73 Å
AuthorsGuss, J.M. / Langley, D.B. / Duff, A.P.
CitationJournal: Biochemistry / Year: 2004
Title: Differential Inhibition of Six Copper Amine Oxidases by a Family of 4-(Aryloxy)-2-butynamines: Evidence for a New Mode of Inactivation.
Authors: O'Connell, K.M. / Langley, D.B. / Shepard, E.M. / Duff, A.P. / Jeon, H.B. / Sun, G. / Freeman, H.C. / Guss, J.M. / Sayre, L.M. / Dooley, D.M.
History
DepositionFeb 29, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 7, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phenylethylamine oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,3066
Polymers71,9391
Non-polymers3675
Water8,179454
1
A: Phenylethylamine oxidase
hetero molecules

A: Phenylethylamine oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,61212
Polymers143,8782
Non-polymers73410
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area15550 Å2
ΔGint-136 kcal/mol
Surface area40640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)157.645, 62.787, 91.657
Angle α, β, γ (deg.)90.00, 112.18, 90.00
Int Tables number5
Space group name H-MC121
DetailsThe asymmetric unit contains half of one biological unit. Crystallographic symmetry is required to generate the other half of the dimer.

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Phenylethylamine oxidase / Amine oxidase


Mass: 71939.000 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: AGAO covalently inhibited / Source: (gene. exp.) Arthrobacter globiformis (bacteria) / Gene: ATCC8010,IFO12137 / Plasmid: PAGAO2 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P46881, EC: 1.4.3.6

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Non-polymers , 5 types, 459 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu
#4: Chemical ChemComp-NA / SODIUM ION


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


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 454 / 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: 3.05 Å3/Da / Density % sol: 59.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 2 microlitres of (AGAO 10 mg/ml, 50mM HEPES pH 7.0) plus 2 microlitres of the reservoir solution (1.1M (NH4)2SO4, 150mM Na-citrate pH 6.5) Crystals were cryoprotected and soaked with MOBA. ...Details: 2 microlitres of (AGAO 10 mg/ml, 50mM HEPES pH 7.0) plus 2 microlitres of the reservoir solution (1.1M (NH4)2SO4, 150mM Na-citrate pH 6.5) Crystals were cryoprotected and soaked with MOBA. Crystals were soaked in well solution plus 20% glycerol plus 10-fold excess of MOBA., for 48 hours. The glycerol concentration was then raised to 30% over 30 minutes, prior to flash freezing., VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Aug 1, 2003 / Details: Osmic mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.73→22.81 Å / Num. all: 80205 / Num. obs: 80205 / % possible obs: 92.3 % / Observed criterion σ(I): -3 / Redundancy: 5.5 % / Biso Wilson estimate: 21.196 Å2 / Rmerge(I) obs: 0.031 / Net I/σ(I): 29
Reflection shellResolution: 1.73→1.77 Å / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 7.4 / Num. unique all: 4943 / % possible all: 71.2

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MAR345data collection
MOSFLMdata reduction
CCP4(SCALAdata scaling
TRUNCATEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.73→22.81 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.967 / SU B: 1.482 / SU ML: 0.048 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / ESU R: 0.084 / ESU R Free: 0.081 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16837 4013 5 %RANDOM
Rwork0.14864 ---
all0.14963 80204 --
obs0.14963 80204 92.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 23.169 Å2
Baniso -1Baniso -2Baniso -3
1--0.77 Å20 Å20.33 Å2
2--1.61 Å20 Å2
3----0.59 Å2
Refinement stepCycle: LAST / Resolution: 1.73→22.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4881 0 19 454 5354
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0215037
X-RAY DIFFRACTIONr_bond_other_d0.0020.024503
X-RAY DIFFRACTIONr_angle_refined_deg1.3671.9446860
X-RAY DIFFRACTIONr_angle_other_deg0.785310417
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2125619
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0820.2741
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025715
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021095
X-RAY DIFFRACTIONr_nbd_refined0.1970.2857
X-RAY DIFFRACTIONr_nbd_other0.2530.25448
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0830.23201
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1230.2380
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0470.23
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1380.229
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3130.2199
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1490.243
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it2.96423085
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.25934987
X-RAY DIFFRACTIONr_scbond_it6.12741952
X-RAY DIFFRACTIONr_scangle_it8.16961870
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.73→1.774 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.195 243 -
Rwork0.172 4700 -
obs-4943 71.2 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.35140.77850.4751.39770.0202-0.35350.0939-0.2557-0.0076-0.0053-0.0483-0.1262-0.00410.1934-0.04560.052-0.0631-0.00040.1412-0.01630.061622.3124.60543.122
21.4057-0.12340.08950.4461-0.61661.67290.01020.27380.0359-0.0576-0.0022-0.0780.06160.2511-0.0080.11330.01020.02190.1232-0.00570.00478.98-2.73114.163
3-0.5001-0.5152-0.55951.1296-1.830.14580.12550.17590.2578-0.17030.07850.0111-0.33590.1544-0.2040.09160.0002-0.00010.091300.0915-15.54221.29528.883
40.88890.0076-0.31660.1982-0.07950.59620.0258-0.08220.08530.01180.0021-0.0213-0.01070.1149-0.02790.0572-0.0098-0.01230.0378-0.01230.0292-5.062-0.50245.164
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA9 - 997 - 97
2X-RAY DIFFRACTION2AA100 - 20398 - 201
3X-RAY DIFFRACTION3AA204 - 229202 - 227
4X-RAY DIFFRACTION4AA230 - 628228 - 626

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