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- PDB-1chu: STRUCTURE OF L-ASPARTATE OXIDASE: IMPLICATIONS FOR THE SUCCINATE ... -

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Basic information

Entry
Database: PDB / ID: 1chu
TitleSTRUCTURE OF L-ASPARTATE OXIDASE: IMPLICATIONS FOR THE SUCCINATE DEHYDROGENASE/ FUMARATE REDUCATSE FAMILY
ComponentsPROTEIN (L-ASPARTATE OXIDASE)
KeywordsFLAVOENZYME / NAD BIOSYNTHESIS / FAD / OXIDOREDUCTASE
Function / homology
Function and homology information


Oxidoreductases; Acting on the CH-NH group of donors; With unknown physiological acceptors / L-aspartate oxidase / L-aspartate oxidase activity / : / 'de novo' NAD biosynthetic process from aspartate / flavin adenine dinucleotide binding / cytosol
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
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.2 Å
AuthorsMattevi, A.
CitationJournal: Structure Fold.Des. / Year: 1999
Title: Structure of L-aspartate oxidase: implications for the succinate dehydrogenase/fumarate reductase oxidoreductase family.
Authors: Mattevi, A. / Tedeschi, G. / Bacchella, L. / Coda, A. / Negri, A. / Ronchi, S.
History
DepositionMar 29, 1999Deposition site: PDBE / Processing site: RCSB
Revision 1.0Jun 23, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN (L-ASPARTATE OXIDASE)


Theoretical massNumber of molelcules
Total (without water)60,4301
Polymers60,4301
Non-polymers00
Water3,531196
1
A: PROTEIN (L-ASPARTATE OXIDASE)

A: PROTEIN (L-ASPARTATE OXIDASE)


Theoretical massNumber of molelcules
Total (without water)120,8612
Polymers120,8612
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Unit cell
Length a, b, c (Å)84.750, 84.750, 159.730
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 PROTEIN (L-ASPARTATE OXIDASE)


Mass: 60430.332 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: NADB / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P10902
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 196 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE CRYSTALLINE PROTEIN IS IN THE APO (FAD-FREE) FORM

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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: 2.74 Å3/Da / Density % sol: 47 %
Crystal growpH: 8.3 / Details: pH 8.3
Crystal grow
*PLUS
Temperature: 22 ℃ / pH: 8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
1100 mg/mlprotein1drop
220 mMHEPES1drop
312-14 %(w/v)PEG40001reservoir
4100 mMsodium acetate1reservoir
5100 mMTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 1
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 1, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. obs: 33258 / % possible obs: 96.9 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.049 / Net I/σ(I): 9.7
Reflection shellResolution: 2.2→2.3 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.14 / Mean I/σ(I) obs: 2.7 / % possible all: 87.4
Reflection shell
*PLUS
% possible obs: 87.4 %

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Processing

Software
NameVersionClassification
SHARPphasing
REFMACrefinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MIR / Resolution: 2.2→20 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.281 1705 5 %RANDOM
Rwork0.224 ---
obs0.225 33258 96.9 %-
Displacement parametersBiso mean: 41.7 Å2
Refinement stepCycle: LAST / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3761 0 0 196 3957
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0180.02
X-RAY DIFFRACTIONp_angle_d0.0450.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it23
X-RAY DIFFRACTIONp_mcangle_it3.15
X-RAY DIFFRACTIONp_scbond_it2.54
X-RAY DIFFRACTIONp_scangle_it3.56
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor

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