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- PDB-2e5v: Crystal structure of L-Aspartate Oxidase from hyperthermophilic a... -

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Basic information

Entry
Database: PDB / ID: 2e5v
TitleCrystal structure of L-Aspartate Oxidase from hyperthermophilic archaeon Sulfolobus tokodaii
ComponentsL-aspartate oxidase
KeywordsOXIDOREDUCTASE / L-Aspartate Oxidase / Archaea
Function / homology
Function and homology information


L-aspartate oxidase / L-aspartate oxidase activity / : / NAD biosynthetic process / nucleotide binding / cytoplasm
Similarity search - Function
L-aspartate oxidase / Fumarate reductase/succinate dehydrogenase flavoprotein-like, C-terminal domain / Flavocytochrome C3; Chain A, domain 1 / Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain / Fumarate reductase/succinate dehydrogenase flavoprotein-like, C-terminal / Fumarate reductase flavoprotein C-term / Fumarate reductase/succinate dehydrogenase flavoprotein-like, C-terminal domain superfamily / Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain superfamily / FAD-dependent oxidoreductase 2, FAD binding domain / FAD binding domain ...L-aspartate oxidase / Fumarate reductase/succinate dehydrogenase flavoprotein-like, C-terminal domain / Flavocytochrome C3; Chain A, domain 1 / Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain / Fumarate reductase/succinate dehydrogenase flavoprotein-like, C-terminal / Fumarate reductase flavoprotein C-term / Fumarate reductase/succinate dehydrogenase flavoprotein-like, C-terminal domain superfamily / Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain superfamily / FAD-dependent oxidoreductase 2, FAD binding domain / FAD binding domain / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / Alpha-Beta Complex / Up-down Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / L-aspartate oxidase
Similarity search - Component
Biological speciesSulfolobus tokodaii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.09 Å
AuthorsYoneda, K. / Sakuraba, H. / Asai, I. / Tsuge, H. / Katunuma, N. / Ohshima, T.
CitationJournal: Biochim.Biophys.Acta / Year: 2008
Title: Structure of l-aspartate oxidase from the hyperthermophilic archaeon Sulfolobus tokodaii
Authors: Sakuraba, H. / Yoneda, K. / Asai, I. / Tsuge, H. / Katunuma, N. / Ohshima, T.
History
DepositionDec 25, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 1, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: L-aspartate oxidase
B: L-aspartate oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,9496
Polymers105,3072
Non-polymers1,6424
Water13,565753
1
A: L-aspartate oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,4753
Polymers52,6541
Non-polymers8212
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: L-aspartate oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,4753
Polymers52,6541
Non-polymers8212
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)54.970, 103.256, 163.817
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein L-aspartate oxidase / LASPO / Quinolinate synthetase B


Mass: 52653.637 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus tokodaii (archaea) / Plasmid: PET11a / Production host: Escherichia coli (E. coli) / References: UniProt: Q972D2, L-aspartate oxidase
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#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.: 753 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 43.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.6
Details: 23% PEG 8000, 0.1M Tris/HCl, 0.2M MgCl2, pH 8.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 2, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.09→87.37 Å / Num. obs: 56198 / Biso Wilson estimate: 20.4 Å2

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Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SIRAS / Resolution: 2.09→20 Å / Cross valid method: THROUGHOUT
RfactorNum. reflectionSelection details
Rfree0.209 -RANDOM
Rwork0.194 --
obs-48610 -
Refinement stepCycle: LAST / Resolution: 2.09→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7428 0 108 753 8289
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
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_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d2.08
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it0.521.5
X-RAY DIFFRACTIONc_mcangle_it0.852
X-RAY DIFFRACTIONc_scbond_it1.382
X-RAY DIFFRACTIONc_scangle_it1.92.5

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