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- PDB-3kve: Structure of native L-amino acid oxidase from Vipera ammodytes am... -

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Basic information

Entry
Database: PDB / ID: 3kve
TitleStructure of native L-amino acid oxidase from Vipera ammodytes ammodytes: stabilization of the quaternary structure by divalent ions and structural changes in the dynamic active site
ComponentsL-amino acid oxidase
KeywordsOXIDOREDUCTASE / LAAO / snake venom / Vipera ammodytes ammodytes
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 / 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
Similarity search - Component
Biological speciesVipera ammodytes ammodytes (western sand viper)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.57 Å
AuthorsGergiova, D. / Murakami, M.T. / Perbandt, M. / Arni, R.K. / Betzel, C.
CitationJournal: To be Published
Title: Structure of native L-amino acid oxidase from Vipera ammodytes ammodytes: stabilization of the quaternary structure by divalent ions and structural changes in the dynamic active site
Authors: Gergiova, D. / Murakami, M.T. / Perbandt, M. / Arni, R.K. / Betzel, C.
History
DepositionNov 30, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 13, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Structure summary
Category: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / diffrn_source / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _diffrn_source.pdbx_synchrotron_site / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _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.value / _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 1.3Sep 6, 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)224,31216
Polymers220,0234
Non-polymers4,28912
Water9,980554
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18130 Å2
ΔGint-172 kcal/mol
Surface area67790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)196.978, 95.839, 108.442
Angle α, β, γ (deg.)90.00, 92.53, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-495-

HOH

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Components

#1: Protein
L-amino acid oxidase


Mass: 55005.801 Da / Num. of mol.: 4 / Source method: isolated from a natural source
Source: (natural) Vipera ammodytes ammodytes (western sand viper)
References: UniProt: P0DI84*PLUS
#2: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#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


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
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 554 / 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: 2.32 Å3/Da / Density % sol: 47.07 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.8 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jul 10, 2008 / Details: mirrors
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 2.57→27.4 Å / Num. all: 63563 / Num. obs: 62717 / % possible obs: 97.1 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 7.1 % / Biso Wilson estimate: 19.3 Å2 / Rmerge(I) obs: 0.172 / Net I/σ(I): 10.6
Reflection shellResolution: 2.57→2.66 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.448 / Num. unique all: 4853 / % possible all: 74.7

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
AMoREphasing
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1F8R

1f8r


Resolution: 2.57→27.4 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.851 / SU B: 22.231 / SU ML: 0.258 / Cross valid method: THROUGHOUT / ESU R Free: 0.377 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.27609 3212 5.1 %RANDOM
Rwork0.19105 ---
obs0.19537 60346 98.04 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.805 Å2
Baniso -1Baniso -2Baniso -3
1-1 Å20 Å20.11 Å2
2---0.74 Å20 Å2
3----0.25 Å2
Refinement stepCycle: LAST / Resolution: 2.57→27.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15456 0 272 554 16282
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.02216119
X-RAY DIFFRACTIONr_angle_refined_deg1.5231.9721831
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.47451934
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.4123.874777
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.38152730
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.40815108
X-RAY DIFFRACTIONr_chiral_restr0.1110.22309
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212300
X-RAY DIFFRACTIONr_nbd_refined0.2270.28897
X-RAY DIFFRACTIONr_nbtor_refined0.3190.210951
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.190.21029
X-RAY DIFFRACTIONr_metal_ion_refined0.1640.23
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1730.238
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1380.27
X-RAY DIFFRACTIONr_mcbond_it0.5731.59795
X-RAY DIFFRACTIONr_mcangle_it1.018215510
X-RAY DIFFRACTIONr_scbond_it1.46737293
X-RAY DIFFRACTIONr_scangle_it2.3954.56320
LS refinement shellResolution: 2.57→2.63 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.361 197 -
Rwork0.238 3624 -
obs--80.27 %
Refinement TLS params.Method: refined / Origin x: 46.5768 Å / Origin y: -16.0397 Å / Origin z: 27.1996 Å
111213212223313233
T0.002 Å20.0028 Å2-0.0006 Å2--0.0348 Å2-0.001 Å2---0.0218 Å2
L0.1216 °20.0055 °2-0.0027 °2-0.0676 °2-0.0091 °2--0.0855 °2
S-0.0038 Å °-0.0024 Å °-0.0042 Å °-0.0043 Å °0.0034 Å °-0.0037 Å °0.0013 Å °0.0023 Å °0.0004 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 486
2X-RAY DIFFRACTION1B3 - 486
3X-RAY DIFFRACTION1C3 - 486
4X-RAY DIFFRACTION1D3 - 486

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