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- PDB-1f8r: CRYSTAL STRUCTURE OF L-AMINO ACID OXIDASE FROM CALLOSELASMA RHODO... -

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Basic information

Entry
Database: PDB / ID: 1f8r
TitleCRYSTAL STRUCTURE OF L-AMINO ACID OXIDASE FROM CALLOSELASMA RHODOSTOMA COMPLEXED WITH CITRATE
ComponentsL-AMINO ACID OXIDASE
KeywordsOXIDOREDUCTASE / FLAVOENZYME / OXIDASE / ENANTIOMERIC SPECIFICITY / 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 / 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
CITRIC 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 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 / database_PDB_caveat / 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_validate_chiral / 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 / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_atom_id / _pdbx_validate_chiral.auth_comp_id / _pdbx_validate_chiral.auth_seq_id / _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

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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)232,27520
Polymers225,1974
Non-polymers7,07816
Water33,6701869
1
A: L-AMINO ACID OXIDASE
C: L-AMINO ACID OXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,13710
Polymers112,5992
Non-polymers3,5398
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)116,13710
Polymers112,5992
Non-polymers3,5398
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9870 Å2
ΔGint8 kcal/mol
Surface area36830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.496, 154.962, 102.947
Angle α, β, γ (deg.)90.00, 109.49, 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

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Protein , 1 types, 4 molecules ABCD

#1: Protein
L-AMINO ACID OXIDASE


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: GenBank: 6850960, UniProt: P81382*PLUS, L-amino-acid oxidase

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Sugars , 2 types, 8 molecules

#2: Polysaccharide
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][a-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-6-deoxy-Allp]{}}}LINUCSPDB-CARE
#3: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose


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

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Non-polymers , 3 types, 1877 molecules

#4: Chemical
ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H8O7
#5: Chemical
ChemComp-FAD / 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


Mass: 18.015 Da / Num. of mol.: 1869 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsF0-FC DENSITY OBSERVED EXTENDING FROM ALA149 SUGGESTING POSSIBLE SEQUENCING ERROR

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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: 2.65 Å3/Da / Density % sol: 53.64 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: PEG4000, ammonium sulfate, sodium citrate, glycerol, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 290.0K
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: 1.072
DetectorType: MARRESEARCH / Detector: AREA DETECTOR / Date: Aug 16, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.072 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 158011 / Num. obs: 139242 / % possible obs: 88.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.8 % / Biso Wilson estimate: 13.6 Å2 / Rmerge(I) obs: 0.046 / Net I/σ(I): 18.9
Reflection shellResolution: 2→2.07 Å / Redundancy: 2.01 % / Rmerge(I) obs: 0.159 / Num. unique all: 11263 / % possible all: 71.7
Reflection
*PLUS
Num. measured all: 391000

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
CNS0.5refinement
RefinementResolution: 2→500 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 2553955.22 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.21 13919 10 %RANDOM
Rwork0.185 ---
all-139206 --
obs-139206 88.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 57.6 Å2 / ksol: 0.388 e/Å3
Displacement parametersBiso mean: 24.5 Å2
Baniso -1Baniso -2Baniso -3
1-5.91 Å20 Å2-0.77 Å2
2---3.71 Å20 Å2
3----2.2 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.18 Å0.14 Å
Refinement stepCycle: LAST / Resolution: 2→500 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15291 0 472 1869 17632
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d24.3
X-RAY DIFFRACTIONc_improper_angle_d4.04
X-RAY DIFFRACTIONc_mcbond_it0.971.5
X-RAY DIFFRACTIONc_mcangle_it1.472
X-RAY DIFFRACTIONc_scbond_it1.592
X-RAY DIFFRACTIONc_scangle_it2.442.5
Refine LS restraints NCS
Ens-IDDom-IDRefine-IDWeight Biso Weight position
11X-RAY DIFFRACTION215
22X-RAY DIFFRACTION2150
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.006 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.248 2018 10 %
Rwork0.214 18086 -
obs--76.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3CIT.PARAMCIT.TOP
X-RAY DIFFRACTION4CARBOHYDRATE.PARAMCARBOHYDRATE.TOP
X-RAY DIFFRACTION5FAD_COV.PARAMFAD_COV.TOP
Software
*PLUS
Name: CNS / Version: 0.5 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 50 Å / σ(F): 0 / % reflection Rfree: 10 % / Rfactor obs: 0.185 / Rfactor Rfree: 0.21
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 24.5 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg4.04
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.248 / % reflection Rfree: 10 % / Rfactor Rwork: 0.214

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