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- PDB-5z2g: Crystal Structure of L-amino acid oxidase from venom of Naja atra -

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Basic information

Entry
Database: PDB / ID: 5z2g
TitleCrystal Structure of L-amino acid oxidase from venom of Naja atra
ComponentsL-amino acid oxidase
KeywordsOXIDOREDUCTASE / L-amino acid oxidase / flavoenzyme / naja atra
Function / homology
Function and homology information


L-amino-acid oxidase / L-amino-acid oxidase activity / hemolysis in another organism / toxin activity / defense response to bacterium / apoptotic process / extracellular region
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
Similarity search - Component
Biological speciesNaja atra (Chinese cobra)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.676 Å
AuthorsKumar, J.V. / Chien, K.Y. / Wu, W.G. / Lin, C.C. / Chiang, L.C. / Lin, T.H.
CitationJournal: To Be Published
Title: Crystal Structure of L-amino acid oxidase from naja atra (Taiwan Cobra)
Authors: Kumar, J.V. / Chien, K.Y. / Lin, C.C. / Chiang, L.C. / Lin, T.H. / Wu, W.G.
History
DepositionJan 2, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 20, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_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 1.2Nov 22, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,5448
Polymers116,0882
Non-polymers2,4566
Water1,802100
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8040 Å2
ΔGint-4 kcal/mol
Surface area35590 Å2
2
A: L-amino acid oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,4935
Polymers58,0441
Non-polymers1,4494
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1930 Å2
ΔGint-5 kcal/mol
Surface area19900 Å2
MethodPISA
3
B: L-amino acid oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,0513
Polymers58,0441
Non-polymers1,0072
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1710 Å2
ΔGint-7 kcal/mol
Surface area19730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.836, 104.836, 214.270
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein L-amino acid oxidase


Mass: 58044.113 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Naja atra (Chinese cobra) / References: UniProt: A8QL58*PLUS
#2: 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
#3: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 100 / 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: 2.93 Å3/Da / Density % sol: 57.99 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7.2 / Details: 0.1mM Hepes, 10% PEG 6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 24, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.67→30 Å / Num. obs: 39179 / % possible obs: 99.47 % / Redundancy: 10.4 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 2.5
Reflection shellResolution: 2.68→2.73 Å / Rmerge(I) obs: 0.516 / Num. unique obs: 1911

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2IID

2iid


Resolution: 2.676→26.433 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2196 3430 5.07 %
Rwork0.1714 --
obs0.1738 39038 81.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.676→26.433 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7696 0 162 100 7958
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0118064
X-RAY DIFFRACTIONf_angle_d1.24710930
X-RAY DIFFRACTIONf_dihedral_angle_d13.4984754
X-RAY DIFFRACTIONf_chiral_restr0.0611172
X-RAY DIFFRACTIONf_plane_restr0.011378
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6759-2.71250.2847860.22671592X-RAY DIFFRACTION56
2.7125-2.75120.3007890.21931697X-RAY DIFFRACTION60
2.7512-2.79220.2428950.21571794X-RAY DIFFRACTION65
2.7922-2.83580.26821100.2022090X-RAY DIFFRACTION72
2.8358-2.88220.27671220.21252152X-RAY DIFFRACTION78
2.8822-2.93190.30681180.21372371X-RAY DIFFRACTION83
2.9319-2.98510.25961290.21752436X-RAY DIFFRACTION87
2.9851-3.04240.29271370.21132549X-RAY DIFFRACTION91
3.0424-3.10450.23861410.19822667X-RAY DIFFRACTION95
3.1045-3.17190.27211560.20462738X-RAY DIFFRACTION97
3.1719-3.24550.27611420.19472761X-RAY DIFFRACTION99
3.2455-3.32650.27581440.19772770X-RAY DIFFRACTION100
3.3265-3.41630.27471560.19462870X-RAY DIFFRACTION100
3.4163-3.51660.2251560.18922810X-RAY DIFFRACTION100
3.5166-3.62980.2491480.17172817X-RAY DIFFRACTION100
3.6298-3.75920.21341510.17052834X-RAY DIFFRACTION100
3.7592-3.90930.19711480.16362834X-RAY DIFFRACTION100
3.9093-4.08660.17991480.14312770X-RAY DIFFRACTION100
4.0866-4.30120.19361510.14382790X-RAY DIFFRACTION100
4.3012-4.56930.1591590.13392846X-RAY DIFFRACTION99
4.5693-4.92010.22461460.13572759X-RAY DIFFRACTION99
4.9201-5.41140.17781470.15282821X-RAY DIFFRACTION100
5.4114-6.18560.20031420.17142822X-RAY DIFFRACTION100
6.1856-7.76040.20781490.17412824X-RAY DIFFRACTION100
7.7604-26.43430.1751600.14872786X-RAY DIFFRACTION99

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