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- PDB-2y73: THE NATIVE STRUCTURES OF SOLUBLE HUMAN PRIMARY AMINE OXIDASE AOC3 -

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Basic information

Entry
Database: PDB / ID: 2y73
TitleTHE NATIVE STRUCTURES OF SOLUBLE HUMAN PRIMARY AMINE OXIDASE AOC3
ComponentsMEMBRANE PRIMARY AMINE OXIDASE
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


aliphatic amine oxidase activity / primary-amine oxidase / primary methylamine oxidase activity / amine metabolic process / Phase I - Functionalization of compounds / microvillus / quinone binding / early endosome / cell adhesion / inflammatory response ...aliphatic amine oxidase activity / primary-amine oxidase / primary methylamine oxidase activity / amine metabolic process / Phase I - Functionalization of compounds / microvillus / quinone binding / early endosome / cell adhesion / inflammatory response / copper ion binding / protein heterodimerization activity / calcium ion binding / cell surface / endoplasmic reticulum / Golgi apparatus / identical protein binding / membrane / plasma membrane / cytoplasm
Similarity search - Function
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, 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 / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
COPPER (II) ION / FORMIC ACID / IMIDAZOLE / Amine oxidase [copper-containing] 3
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsElovaara, H. / Kidron, H. / Parkash, V. / Nymalm, Y. / Bligt, E. / Ollikka, P. / Smith, D.J. / Pihlavisto, M. / Salmi, M. / Jalkanen, S. / Salminen, T.A.
CitationJournal: Biochemistry / Year: 2011
Title: Identification of Two Imidazole Binding Sites and Key Residues for Substrate Specificity in Human Primary Amine Oxidase Aoc3.
Authors: Elovaara, H. / Kidron, H. / Parkash, V. / Nymalm, Y. / Bligt, E. / Ollikka, P. / Smith, D.J. / Pihlavisto, M. / Salmi, M. / Jalkanen, S. / Salminen, T.A.
History
DepositionJan 28, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 15, 2011Provider: repository / Type: Initial release
Revision 1.1Aug 10, 2011Group: Database references / Version format compliance
Revision 1.2Jul 12, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MEMBRANE PRIMARY AMINE OXIDASE
B: MEMBRANE PRIMARY AMINE OXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)173,30826
Polymers169,4692
Non-polymers3,83924
Water6,233346
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20250 Å2
ΔGint-126.3 kcal/mol
Surface area46190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)225.755, 225.755, 216.985
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein MEMBRANE PRIMARY AMINE OXIDASE / AMINE OXIDASE COPPER CONTAINING 3 / COPPER AMINE OXIDASE / HPAO / SEMICARBAZIDE-SENSITIVE AMINE ...AMINE OXIDASE COPPER CONTAINING 3 / COPPER AMINE OXIDASE / HPAO / SEMICARBAZIDE-SENSITIVE AMINE OXIDASE / SSAO / VASCULAR ADHESION PROTEIN 1 / VAP-1


Mass: 84734.562 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / References: UniProt: Q16853, primary-amine oxidase

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Sugars , 3 types, 8 molecules

#2: Polysaccharide alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#7: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 5 types, 362 molecules

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


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu
#5: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#6: Chemical
ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H5N2
#8: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH2O2
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 346 / 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: 2.2 Å3/Da / Density % sol: 45 % / Description: NONE
Crystal growpH: 7.4
Details: 0.7 M POTASSIUM/SODIUM TARTRATE, 100 MM IMIDAZOLE PH7.4, 200 MM NACL, 2M SODIUM FORMATE

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Data collection

DiffractionMean temperature: 183 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 0.9059
DetectorType: MARRESEARCH SX-165 / Detector: CCD / Date: Jun 9, 2006 / Details: VERTICALLY FOCUSING CYLINDRICAL MIRROR
RadiationMonochromator: SINGLE ASYMMETRICALLY CUT SI(111) CRYSTAL WITH HORIZONTAL DIFFRACTION PLANE
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9059 Å / Relative weight: 1
ReflectionResolution: 2.6→29.93 Å / Num. obs: 99745 / % possible obs: 99.9 % / Observed criterion σ(I): 3 / Redundancy: 11.8 % / Biso Wilson estimate: 36.03 Å2 / Rmerge(I) obs: 0.01 / Net I/σ(I): 17.5
Reflection shellResolution: 2.6→2.7 Å / Redundancy: 11.9 % / Rmerge(I) obs: 0.05 / Mean I/σ(I) obs: 5.1 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1US1

1us1


Resolution: 2.6→19.931 Å / SU ML: 0.32 / σ(F): 1.38 / Phase error: 20.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2126 4978 5 %
Rwork0.1748 --
obs0.1767 99551 99.99 %
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 20.63 Å2 / ksol: 0.327 e/Å3
Displacement parametersBiso mean: 37.3 Å2
Baniso -1Baniso -2Baniso -3
1--0.7569 Å20 Å20 Å2
2---0.7569 Å20 Å2
3---1.5137 Å2
Refinement stepCycle: LAST / Resolution: 2.6→19.931 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11087 0 242 346 11675
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01611695
X-RAY DIFFRACTIONf_angle_d1.77615949
X-RAY DIFFRACTIONf_dihedral_angle_d25.9514389
X-RAY DIFFRACTIONf_chiral_restr0.1031704
X-RAY DIFFRACTIONf_plane_restr0.0122082
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.69270.34264910.29969337X-RAY DIFFRACTION100
2.6927-2.80030.31014900.27149312X-RAY DIFFRACTION100
2.8003-2.92730.29684930.25729368X-RAY DIFFRACTION100
2.9273-3.08120.28844920.24399340X-RAY DIFFRACTION100
3.0812-3.27340.2574940.20549387X-RAY DIFFRACTION100
3.2734-3.52490.2274950.17739407X-RAY DIFFRACTION100
3.5249-3.87720.19884970.14939437X-RAY DIFFRACTION100
3.8772-4.43290.15684990.12149485X-RAY DIFFRACTION100
4.4329-5.56480.14135050.119586X-RAY DIFFRACTION100
5.5648-19.93120.17155220.15669914X-RAY DIFFRACTION100

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