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- PDB-2iid: Structure of L-amino acid oxidase from Calloselasma rhodostoma in... -

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Basic information

Entry
Database: PDB / ID: 2iid
TitleStructure of L-amino acid oxidase from Calloselasma rhodostoma in complex with L-phenylalanine
ComponentsL-amino-acid oxidase
KeywordsOXIDOREDUCTASE / flavoenzyme / FAD binding domain / reaction mechanism / sustrate binding
Function / homology
Function and homology information


L-phenylalaine oxidase activity / L-amino-acid oxidase / toxin activity / killing of cells of another organism / defense response to bacterium / apoptotic process / extracellular region
Similarity search - Function
Guanine Nucleotide Dissociation Inhibitor, domain 1 / Guanine Nucleotide Dissociation Inhibitor; domain 1 / 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 ...Guanine Nucleotide Dissociation Inhibitor, domain 1 / Guanine Nucleotide Dissociation Inhibitor; domain 1 / 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 / PHENYLALANINE / L-amino-acid oxidase
Similarity search - Component
Biological speciesCalloselasma rhodostoma (Malayan pit viper)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.8 Å
AuthorsMoustafa, I.M. / Foster, S. / Lyubimov, A.Y. / Vrielink, A.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: Crystal Structure of LAAO from Calloselasma rhodostoma with an L-Phenylalanine Substrate: Insights into Structure and Mechanism
Authors: Moustafa, I.M. / Foster, S. / Lyubimov, A.Y. / Vrielink, A.
History
DepositionSep 27, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 31, 2006Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...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 / 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 / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Aug 30, 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: L-amino-acid oxidase
B: L-amino-acid oxidase
C: L-amino-acid oxidase
D: L-amino-acid oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)231,20820
Polymers225,1974
Non-polymers6,01116
Water37,5612085
1
A: L-amino-acid oxidase
C: L-amino-acid oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,67710
Polymers112,5992
Non-polymers3,0798
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: L-amino-acid oxidase
D: L-amino-acid oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,53110
Polymers112,5992
Non-polymers2,9328
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.760, 154.003, 103.183
Angle α, β, γ (deg.)90.00, 109.52, 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
L-amino-acid oxidase / / LAO / LAAO / Apoxin I


Mass: 56299.258 Da / Num. of mol.: 4 / Source method: isolated from a natural source
Source: (natural) Calloselasma rhodostoma (Malayan pit viper)
Secretion: venom / References: UniProt: P81382, L-amino-acid oxidase

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Sugars , 2 types, 8 molecules

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


Type: oligosaccharide / Mass: 367.349 Da / Num. of mol.: 3
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
#3: 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.: 5
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 , 3 types, 2093 molecules

#4: Chemical
ChemComp-PHE / PHENYLALANINE / Phenylalanine


Type: L-peptide linking / Mass: 165.189 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H11NO2
#5: 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
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2085 / 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: 2.53 Å3/Da / Density % sol: 51.36 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 20-22% PEG 4000, 200mM Li2SO4, 10% glycerol, 100mM Tris-HCl, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.652549 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.652549 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 211556 / % possible obs: 99.5 % / Observed criterion σ(I): 0 / Redundancy: 4.06 % / Rmerge(I) obs: 0.101 / Net I/σ(I): 11.9
Reflection shellResolution: 1.8→1.86 Å / Rmerge(I) obs: 0.418 / Mean I/σ(I) obs: 3.1 / Num. unique all: 21240 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB entry 1F8R

1f8r


Resolution: 1.8→50 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.939 / SU B: 2.497 / SU ML: 0.078 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.118 / ESU R Free: 0.116 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21006 10609 5 %RANDOM
Rwork0.1716 ---
obs0.17354 200823 99.45 %-
all-200823 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.36 Å2
Baniso -1Baniso -2Baniso -3
1-0.68 Å20 Å2-0.8 Å2
2---0.72 Å20 Å2
3----0.5 Å2
Refinement stepCycle: LAST / Resolution: 1.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15436 0 402 2085 17923
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.02216393
X-RAY DIFFRACTIONr_angle_refined_deg1.4892.10122259
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.81651956
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.01524.021776
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.38152724
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3251596
X-RAY DIFFRACTIONr_chiral_restr0.1010.22387
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212460
X-RAY DIFFRACTIONr_nbd_refined0.2040.28275
X-RAY DIFFRACTIONr_nbtor_refined0.3110.211254
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1450.21871
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2310.237
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1330.232
X-RAY DIFFRACTIONr_mcbond_it0.8841.59957
X-RAY DIFFRACTIONr_mcangle_it1.431215684
X-RAY DIFFRACTIONr_scbond_it2.45137297
X-RAY DIFFRACTIONr_scangle_it3.6944.56575
LS refinement shellResolution: 1.8→1.85 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.301 801 -
Rwork0.221 14855 -
obs--99.97 %

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