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- PDB-1f8s: CRYSTAL STRUCTURE OF L-AMINO ACID OXIDASE FROM CALLOSELASMA RHODO... -

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Basic information

Entry
Database: PDB / ID: 1f8s
TitleCRYSTAL STRUCTURE OF L-AMINO ACID OXIDASE FROM CALLOSELASMA RHODOSTOMA, COMPLEXED WITH THREE MOLECULES OF O-AMINOBENZOATE.
ComponentsL-AMINO ACID OXIDASE
KeywordsOXIDOREDUCTASE / FLAVOENZYME / OXIDASE / ENANTIOMERIC SPECIFICITY / o-AMINOBENZOATE / ACTIVE SITE FUNNEL / HELICAL DOMAIN / FAD-BINDING DOMAIN
Function / homology
Function and homology information


L-phenylalaine oxidase activity / L-amino-acid oxidase / amino acid catabolic process / 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 ...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
2-AMINOBENZOIC ACID / FLAVIN-ADENINE DINUCLEOTIDE / L-amino-acid oxidase
Similarity search - Component
Biological speciesCalloselasma rhodostoma (Malayan pit viper)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å
AuthorsPawelek, P.D. / Cheah, J. / Coulombe, R. / Macheroux, P. / Ghisla, S. / Vrielink, A.
CitationJournal: EMBO J. / Year: 2000
Title: The structure of L-amino acid oxidase reveals the substrate trajectory into an enantiomerically conserved active site.
Authors: Pawelek, P.D. / Cheah, J. / Coulombe, R. / Macheroux, P. / Ghisla, S. / Vrielink, A.
History
DepositionJul 4, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 24, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Structure summary
Category: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / 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_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 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _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
E: L-AMINO ACID OXIDASE
F: L-AMINO ACID OXIDASE
G: L-AMINO ACID OXIDASE
H: L-AMINO ACID OXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)461,73948
Polymers450,3948
Non-polymers11,34540
Water42,8402378
1
A: L-AMINO ACID OXIDASE
B: L-AMINO ACID OXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,43512
Polymers112,5992
Non-polymers2,83610
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: L-AMINO ACID OXIDASE
D: L-AMINO ACID OXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,43512
Polymers112,5992
Non-polymers2,83610
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: L-AMINO ACID OXIDASE
F: L-AMINO ACID OXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,43512
Polymers112,5992
Non-polymers2,83610
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: L-AMINO ACID OXIDASE
H: L-AMINO ACID OXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,43512
Polymers112,5992
Non-polymers2,83610
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.553, 137.180, 212.634
Angle α, β, γ (deg.)90.00, 105.63, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
/ NCS ensembles :
ID
1
2
DetailsBiological unit is a dimer.

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Components

#1: Protein
L-AMINO ACID OXIDASE


Mass: 56299.258 Da / Num. of mol.: 8 / Source method: isolated from a natural source
Source: (natural) Calloselasma rhodostoma (Malayan pit viper)
Secretion: VENOM / References: UniProt: P81382, L-amino-acid oxidase
#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.: 8
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-BE2 / 2-AMINOBENZOIC ACID


Type: L-peptide linking / Mass: 137.136 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: C7H7NO2
#4: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2378 / 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: 2.42 Å3/Da / Density % sol: 49.12 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: PEG4000, ammonium sulfate, sodium citrate, glycerol, o-aminobenzoate., pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal grow
*PLUS
Details: Jancarik, J., (1991) J. Appl. Crystallogr., 24, 409.
Components of the solutions
*PLUS
Conc.: 10 mg/ml / Common name: protein

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Data collection

DiffractionMean temperature: 83 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 0.979
DetectorType: MARRESEARCH / Detector: AREA DETECTOR / Date: Aug 31, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.8→100 Å / Num. all: 395029 / Num. obs: 335974 / % possible obs: 85 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 11.6 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 11.7
Reflection shellResolution: 1.8→1.84 Å / Redundancy: 1.13 % / Rmerge(I) obs: 0.378 / Num. unique all: 12419 / % possible all: 47.4

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS0.9refinement
RefinementResolution: 2→500 Å / Rfactor Rfree error: 0.001 / Data cutoff high absF: 3864620.46 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER
Details: HIS223 IN CHAINS A-H WERE MODELLED AND REFINED WITH TWO ALTERNATE CONFORMATIONS EACH HAVING HALF OCCUPANCY F0-FC DENSITY OBSERVED EXTENDING FROM ALA149 SUGGESTING POSSIBLE SEQUENCING ERROR
RfactorNum. reflection% reflectionSelection details
Rfree0.225 28205 10 %RANDOM
Rwork0.205 ---
all-283071 --
obs-283071 98.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 35.32 Å2 / ksol: 0.376 e/Å3
Displacement parametersBiso mean: 19.3 Å2
Baniso -1Baniso -2Baniso -3
1-0.59 Å20 Å2-0.01 Å2
2--0.97 Å20 Å2
3----1.56 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.2 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 2→500 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms30784 0 776 2378 33938
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d4.06
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refine LS restraints NCS
Ens-IDDom-IDRefine-IDWeight Biso Weight position
11X-RAY DIFFRACTION250
22X-RAY DIFFRACTION2200
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.004 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.267 4255 9.8 %
Rwork0.241 39238 -
obs--90.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3FAD_COV.PARAMFAD_COV.TOP
X-RAY DIFFRACTION4CARBOHYDRATE.PARAMCARBOHYDRATE.TOP
X-RAY DIFFRACTION5BE2.PARAMBE2.TOP
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 50 Å / σ(F): 0 / % reflection Rfree: 10 % / Rfactor obs: 0.205
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 19.3 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg4.06
LS refinement shell
*PLUS
Rfactor Rfree: 0.267 / % reflection Rfree: 9.8 % / Rfactor Rwork: 0.241

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