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- PDB-5ts5: Crystal structure of L-amino acid oxidase from Bothrops atrox -

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Basic information

Entry
Database: PDB / ID: 5ts5
TitleCrystal structure of L-amino acid oxidase from Bothrops atrox
ComponentsAmine oxidase
KeywordsOXIDOREDUCTASE / snake venom
Function / homology
Function and homology information


envenomation resulting in positive regulation of platelet aggregation in another organism / L-amino-acid oxidase activity / L-phenylalaine oxidase activity / modulation of apoptotic process in another organism / L-amino-acid oxidase / hemolysis in another organism / regulation of platelet aggregation / toxin activity / defense response to Gram-negative bacterium / defense response to Gram-positive bacterium ...envenomation resulting in positive regulation of platelet aggregation in another organism / L-amino-acid oxidase activity / L-phenylalaine oxidase activity / modulation of apoptotic process in another organism / L-amino-acid oxidase / hemolysis in another organism / regulation of platelet aggregation / toxin activity / defense response to Gram-negative bacterium / defense response to Gram-positive bacterium / apoptotic process / extracellular region / metal ion binding
Similarity search - Function
Guanine Nucleotide Dissociation Inhibitor, domain 1 / Guanine Nucleotide Dissociation Inhibitor; domain 1 / Flavin amine oxidase / Polyamine Oxidase; Chain A, domain 2 - #10 / Polyamine Oxidase; Chain A, domain 2 / Amine oxidase / Flavin containing amine oxidoreductase / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich ...Guanine Nucleotide Dissociation Inhibitor, domain 1 / Guanine Nucleotide Dissociation Inhibitor; domain 1 / Flavin amine oxidase / Polyamine Oxidase; Chain A, domain 2 - #10 / Polyamine Oxidase; Chain A, domain 2 / Amine oxidase / Flavin containing amine oxidoreductase / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / Alpha-Beta Complex / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / L-amino-acid oxidase / L-amino-acid oxidase
Similarity search - Component
Biological speciesBothrops atrox (barba amarilla)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsFeliciano, P.R. / Nonato, M.C.
Funding support Brazil, 2items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)2009/10454-3 Brazil
Sao Paulo Research Foundation (FAPESP)2013/14988-8 Brazil
CitationJournal: Toxicon / Year: 2017
Title: Crystal structure and molecular dynamics studies of L-amino acid oxidase from Bothrops atrox.
Authors: Feliciano, P.R. / Rustiguel, J.K. / Soares, R.O. / Sampaio, S.V. / Cristina Nonato, M.
History
DepositionOct 27, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 26, 2017Provider: repository / Type: Initial release
Revision 1.1May 10, 2017Group: Database references
Revision 1.2Aug 29, 2018Group: Data collection / Database references / Structure summary
Category: entity / struct_ref_seq_dif / Item: _entity.pdbx_mutation / _struct_ref_seq_dif.details
Revision 1.3Apr 17, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jan 1, 2020Group: Author supporting evidence / Data collection / Category: chem_comp / pdbx_audit_support
Item: _chem_comp.type / _pdbx_audit_support.funding_organization
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / 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 / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_asym / struct_conn / struct_conn_type / 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_alt_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Feb 1, 2023Group: Advisory / Database references / Structure summary
Category: chem_comp / database_2 / pdbx_database_PDB_obs_spr
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Amine oxidase
B: Amine oxidase
C: Amine oxidase
D: Amine oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)225,42025
Polymers220,0674
Non-polymers5,35221
Water20,9691164
1
A: Amine oxidase
B: Amine oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,89914
Polymers110,0342
Non-polymers2,86512
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Amine oxidase
D: Amine oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,52011
Polymers110,0342
Non-polymers2,4879
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.640, 123.920, 105.080
Angle α, β, γ (deg.)90.00, 96.03, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Amine oxidase /


Mass: 55016.867 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Bothrops atrox (barba amarilla)
References: UniProt: A0A0S1LJ33, UniProt: P0CC17*PLUS, Oxidoreductases; Acting on the CH-NH2 group of donors; With oxygen as acceptor

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Sugars , 2 types, 5 molecules

#2: Polysaccharide alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 367.349 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-6DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2/a6-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#5: 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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3
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 , 4 types, 1180 molecules

#3: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Zn
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1164 / 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: 2.17 Å3/Da / Density % sol: 43.23 %
Crystal growTemperature: 295 K / Method: vapor diffusion / pH: 5
Details: zinc sulfate heptahydrate, sodium cacodylate pH 5, polyethylene glycol monomethyl ether 550

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: D03B-MX1 / Wavelength: 1.4586 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Apr 28, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.4586 Å / Relative weight: 1
ReflectionResolution: 2.3→34.84 Å / Num. obs: 80024 / % possible obs: 96.5 % / Redundancy: 2.1 % / Rmerge(I) obs: 0.146 / Net I/σ(I): 6.4
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.557 / Mean I/σ(I) obs: 1.7 / % possible all: 93.4

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1REO

1reo


Resolution: 2.3→34.572 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.21
RfactorNum. reflection% reflection
Rfree0.2303 3987 4.99 %
Rwork0.1801 --
obs0.1826 79964 96.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.3→34.572 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14993 0 319 1164 16476
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00315820
X-RAY DIFFRACTIONf_angle_d0.62921546
X-RAY DIFFRACTIONf_dihedral_angle_d16.4819380
X-RAY DIFFRACTIONf_chiral_restr0.0442364
X-RAY DIFFRACTIONf_plane_restr0.0042759
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.32810.30941200.23532610X-RAY DIFFRACTION93
2.3281-2.35750.27981370.23312620X-RAY DIFFRACTION93
2.3575-2.38850.31351300.24182626X-RAY DIFFRACTION93
2.3885-2.42130.29421520.23592593X-RAY DIFFRACTION94
2.4213-2.45580.3481290.22672642X-RAY DIFFRACTION93
2.4558-2.49250.27251330.21882656X-RAY DIFFRACTION94
2.4925-2.53140.28471440.2162652X-RAY DIFFRACTION94
2.5314-2.57290.2751200.22172649X-RAY DIFFRACTION95
2.5729-2.61730.2581200.22082684X-RAY DIFFRACTION95
2.6173-2.66480.26891490.21832653X-RAY DIFFRACTION95
2.6648-2.71610.28751380.20362710X-RAY DIFFRACTION95
2.7161-2.77150.27171640.20272660X-RAY DIFFRACTION96
2.7715-2.83170.28371370.20512738X-RAY DIFFRACTION96
2.8317-2.89760.24641290.19472693X-RAY DIFFRACTION96
2.8976-2.970.28131490.19582728X-RAY DIFFRACTION97
2.97-3.05020.25481650.20062733X-RAY DIFFRACTION97
3.0502-3.13990.26071340.192740X-RAY DIFFRACTION97
3.1399-3.24120.23991520.1812753X-RAY DIFFRACTION98
3.2412-3.3570.21081530.172802X-RAY DIFFRACTION98
3.357-3.49130.24981450.16742768X-RAY DIFFRACTION99
3.4913-3.650.19791620.16132778X-RAY DIFFRACTION99
3.65-3.84220.19141500.15072796X-RAY DIFFRACTION99
3.8422-4.08260.18061610.14412789X-RAY DIFFRACTION99
4.0826-4.39720.18171410.13622785X-RAY DIFFRACTION99
4.3972-4.83860.15351410.132795X-RAY DIFFRACTION98
4.8386-5.53630.20951450.152810X-RAY DIFFRACTION98
5.5363-6.96580.19081400.18632764X-RAY DIFFRACTION97
6.9658-34.57580.18241470.16582750X-RAY DIFFRACTION95

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