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- PDB-8w78: Structure of Drosophila melanogaster L-2-hydroxyglutarate dehydro... -

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Basic information

Entry
Database: PDB / ID: 8w78
TitleStructure of Drosophila melanogaster L-2-hydroxyglutarate dehydrogenase in complex with FAD and 2-oxoglutarate
ComponentsFI05204p
KeywordsOXIDOREDUCTASE / L-2-hydroxyglutarate dehydrogenase / L2HGDH / dehydrogenase / 2-oxoglutarate
Function / homology
Function and homology information


L-2-hydroxyglutarate dehydrogenase / 2-hydroxyglutarate dehydrogenase activity, forward reaction / Interconversion of 2-oxoglutarate and 2-hydroxyglutarate / 2-hydroxyglutarate dehydrogenase activity / (S)-2-hydroxy-acid oxidase activity / nucleotide binding / mitochondrion
Similarity search - Function
FAD dependent oxidoreductase / FAD dependent oxidoreductase / FAD/NAD(P)-binding domain superfamily
Similarity search - Domain/homology
2-OXOGLUTARIC ACID / FLAVIN-ADENINE DINUCLEOTIDE / L-2-hydroxyglutarate dehydrogenase, mitochondrial
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.81 Å
AuthorsYang, J. / Chen, X. / Jin, S. / Ding, J.
Funding support China, 2items
OrganizationGrant numberCountry
Chinese Academy of SciencesXDB37030305 China
National Natural Science Foundation of China (NSFC)32071190 China
CitationJournal: J.Biol.Chem. / Year: 2023
Title: Structure and biochemical characterization of l-2-hydroxyglutarate dehydrogenase and its role in the pathogenesis of l-2-hydroxyglutaric aciduria.
Authors: Yang, J. / Chen, X. / Jin, S. / Ding, J.
History
DepositionAug 30, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Nov 29, 2023Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2023Group: Database references / Category: citation
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Dec 20, 2023Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FI05204p
C: FI05204p
B: FI05204p
D: FI05204p
hetero molecules


Theoretical massNumber of molelcules
Total (without water)189,44416
Polymers183,6754
Non-polymers5,76912
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15570 Å2
ΔGint-66 kcal/mol
Surface area60430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.082, 102.330, 102.632
Angle α, β, γ (deg.)90.00, 108.33, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
FI05204p / L-2-hydroxyglutarate dehydrogenase / isoform A / isoform B / isoform C


Mass: 45918.824 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly)
Gene: L2HGDH, CG10639-RA, dL2HGDH, Dmel\CG10639, L-2-HGDH, CG10639, Dmel_CG10639
Production host: Escherichia coli (E. coli)
References: UniProt: Q9VJ28, (S)-2-hydroxy-acid oxidase, L-2-hydroxyglutarate dehydrogenase
#2: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#3: Chemical
ChemComp-AKG / 2-OXOGLUTARIC ACID


Mass: 146.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H6O5 / Feature type: SUBJECT OF INVESTIGATION
#4: Sugar
ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM
Has ligand of interestY
Has protein modificationY

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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: 2.64 Å3/Da / Density % sol: 53.35 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop
Details: 0.2 M magnesium formate and 18% (w/v) PEG 3350, 40 mM 2-OG

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 8, 2021
RadiationMonochromator: LN2-cooled DCM with Si(111) crystals / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.81→50 Å / Num. obs: 47660 / % possible obs: 99.4 % / Redundancy: 6.7 % / CC1/2: 0.994 / CC star: 0.998 / Rmerge(I) obs: 0.174 / Rpim(I) all: 0.072 / Rrim(I) all: 0.189 / Χ2: 0.972 / Net I/σ(I): 3.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.82-2.875.91.4323530.5330.8340.6261.5660.93198.6
2.87-2.926.21.33623490.5550.8450.5761.4590.89899.5
2.92-2.986.41.18323820.6510.8880.5021.2880.94199.4
2.98-3.046.60.9823550.7390.9220.4091.0640.93399.7
3.04-3.16.30.86723680.7790.9360.3710.9450.95198.7
3.1-3.186.10.69923190.8410.9560.3040.7650.97197.8
3.18-3.2670.57723810.9150.9780.2340.6230.95599.9
3.26-3.347.10.50224060.9180.9780.2020.5410.959100
3.34-3.4470.44923720.9140.9770.1810.4851.01399.7
3.44-3.5570.36223860.9540.9880.1470.3911.08199.8
3.55-3.6870.28624020.9720.9930.1160.3091.043100
3.68-3.836.90.23223820.9790.9950.0940.2511.01699.4
3.83-46.70.1823680.9820.9960.0750.1961.12499.6
4-4.216.20.12823570.990.9980.0550.141.02998.4
4.21-4.487.20.11124150.9940.9980.0440.1191.049100
4.48-4.827.10.09923800.9950.9990.040.1071.02799.9
4.82-5.3170.08924060.9960.9990.0360.0960.98899.8
5.31-6.076.40.08523970.9950.9990.0360.0930.93598.9
6.07-7.656.90.06824120.9970.9990.0280.0730.89499.7
7.65-506.60.03424700.99910.0140.0370.66799.2

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Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874: ???)refinement
HKL-2000data scaling
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.81→31.67 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2773 2005 4.84 %
Rwork0.2281 --
obs0.2305 41397 86.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.81→31.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12461 0 196 0 12657
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00212961
X-RAY DIFFRACTIONf_angle_d0.47117629
X-RAY DIFFRACTIONf_dihedral_angle_d20.8884577
X-RAY DIFFRACTIONf_chiral_restr0.0421978
X-RAY DIFFRACTIONf_plane_restr0.0032225
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.81-2.880.4318590.34621236X-RAY DIFFRACTION38
2.88-2.960.3498880.32181730X-RAY DIFFRACTION53
2.96-3.040.3402970.29172069X-RAY DIFFRACTION64
3.04-3.140.33781300.28862360X-RAY DIFFRACTION73
3.14-3.250.35881520.27762837X-RAY DIFFRACTION87
3.25-3.380.3221560.28143140X-RAY DIFFRACTION97
3.38-3.540.34431670.26653258X-RAY DIFFRACTION99
3.54-3.720.3281640.2493242X-RAY DIFFRACTION100
3.72-3.960.31571650.23163244X-RAY DIFFRACTION99
3.96-4.260.2581690.20963217X-RAY DIFFRACTION99
4.26-4.690.23671660.19223275X-RAY DIFFRACTION100
4.69-5.370.22881650.19273288X-RAY DIFFRACTION100
5.37-6.750.25721610.21563242X-RAY DIFFRACTION99
6.75-31.670.21131660.1913254X-RAY DIFFRACTION97

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