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- PDB-3kn4: AGAO 6-phenyl-2,3-hexadienylamine complex -

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Basic information

Entry
Database: PDB / ID: 3kn4
TitleAGAO 6-phenyl-2,3-hexadienylamine complex
ComponentsPhenylethylamine oxidase
KeywordsOXIDOREDUCTASE / CuAO / amine oxidase / arthrobacter globiformis / copper containing / metal-binding / TPQ / quinone / inhibition / 6-phenyl-2 / 3-hexadienylamine / Disulfide bond
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
: / AGAO-like 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 ...: / AGAO-like 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 / 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: 2.05 Å
AuthorsNguyen, Y.H. / Ernberg, K.E. / Guss, J.M.
CitationJournal: To be Published
Title: AGAO 6-phenyl-2,3-hexadienylamine complex
Authors: Nguyen, Y.H. / Ernberg, K.E. / Guss, J.M.
History
DepositionNov 12, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 27, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Nov 1, 2023Group: 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 / 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_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_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.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 22, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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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)73,13315
Polymers71,9371
Non-polymers1,19614
Water5,873326
1
A: Phenylethylamine oxidase
hetero molecules

A: Phenylethylamine oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,26530
Polymers143,8742
Non-polymers2,39128
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area20060 Å2
ΔGint-123 kcal/mol
Surface area38890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)157.888, 63.335, 92.213
Angle α, β, γ (deg.)90.000, 112.090, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Phenylethylamine oxidase / Primary amine oxidase


Mass: 71937.023 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arthrobacter globiformis (bacteria) / Strain: ATCC8010,IFO12137
Description: THE CONSTRUCT THAT WAS CRYSTALLIZED ENCODES RESIDUES 3-628 OF PHENYLETHYLAMINE OXIDASE AND A PRE-TAG SPACER(RESIDUE 639-640) AND A STREP-TAG II (RESIDUE 641-648). SEE REFERENCE JUDA ET ...Description: THE CONSTRUCT THAT WAS CRYSTALLIZED ENCODES RESIDUES 3-628 OF PHENYLETHYLAMINE OXIDASE AND A PRE-TAG SPACER(RESIDUE 639-640) AND A STREP-TAG II (RESIDUE 641-648). SEE REFERENCE JUDA ET AL. (2001) PROTEIN EXPRESSION AND PURIFICATION, 22, 455-461
Gene: PAOX / Plasmid: PET-3C (Novagen), PAGAO2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P46881, primary-amine oxidase

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Non-polymers , 5 types, 340 molecules

#2: Chemical ChemComp-CU / COPPER (II) ION


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


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


Mass: 92.094 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 326 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsTHE C-TERMINAL OF SEQUENCE, SNWSHPQFEK, IS A PRE-TAG SPACER (RESIDUE 639-640) AND A STREP-TAG II ...THE C-TERMINAL OF SEQUENCE, SNWSHPQFEK, IS A PRE-TAG SPACER (RESIDUE 639-640) AND A STREP-TAG II (RESIDUE 641-648).

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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: 2.97 Å3/Da / Density % sol: 58.58 % / Mosaicity: 1.159 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 150mM Na Citrate pH 7.0, 800mM (NH4)2SO4), VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54178 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Aug 16, 2007 / Details: OSMIC MIRRORS
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. obs: 52557 / % possible obs: 99.2 % / Redundancy: 4.3 % / Biso Wilson estimate: 30.767 Å2 / Rmerge(I) obs: 0.091 / Χ2: 1.123 / Net I/σ(I): 10
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.05-2.123.90.45752291.15799.4
2.12-2.214.20.3952391.16799.9
2.21-2.314.30.32652611.19100
2.31-2.434.40.27953011.207100
2.43-2.584.50.22952541.209100
2.58-2.784.50.17452651.176100
2.78-3.064.40.12152921.1599.8
3.06-3.514.20.07952931.03599.5
3.51-4.4240.05252160.98797.9
4.42-504.20.03652070.92895.7

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.005data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1SIH

1sih


Resolution: 2.05→15.01 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.941 / WRfactor Rfree: 0.23 / WRfactor Rwork: 0.181 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.851 / SU B: 4.343 / SU ML: 0.114 / SU R Cruickshank DPI: 0.158 / SU Rfree: 0.151 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.158 / ESU R Free: 0.151 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.221 2660 5.1 %RANDOM
Rwork0.176 ---
obs0.178 49890 99.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 95.87 Å2 / Biso mean: 28.318 Å2 / Biso min: 12.92 Å2
Baniso -1Baniso -2Baniso -3
1--1.4 Å20 Å20.44 Å2
2--3.15 Å20 Å2
3----1.42 Å2
Refinement stepCycle: LAST / Resolution: 2.05→15.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4838 0 73 326 5237
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0225074
X-RAY DIFFRACTIONr_bond_other_d0.0010.023471
X-RAY DIFFRACTIONr_angle_refined_deg1.491.966904
X-RAY DIFFRACTIONr_angle_other_deg0.8863.0018367
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9315632
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.67523.171246
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.53715765
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3161547
X-RAY DIFFRACTIONr_chiral_restr0.0790.2741
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215722
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021093
X-RAY DIFFRACTIONr_mcbond_it2.02623092
X-RAY DIFFRACTIONr_mcbond_other0.62821261
X-RAY DIFFRACTIONr_mcangle_it3.1635000
X-RAY DIFFRACTIONr_scbond_it4.71841982
X-RAY DIFFRACTIONr_scangle_it6.52761896
LS refinement shellResolution: 2.051→2.104 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.343 169 -
Rwork0.305 3529 -
all-3698 -
obs--96.53 %

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