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- PDB-8w7f: Structure of Drosophila melanogaster L-2-hydroxyglutarate dehydro... -

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Basic information

Entry
Database: PDB / ID: 8w7f
TitleStructure of Drosophila melanogaster L-2-hydroxyglutarate dehydrogenase bound with FAD and a sulfate ion
ComponentsFI05204p
KeywordsOXIDOREDUCTASE / L-2-hydroxyglutarate dehydrogenase / L2HGDH / dehydrogenase
Function / homology
Function and homology information


L-2-hydroxyglutarate dehydrogenase / : / Interconversion of 2-oxoglutarate and 2-hydroxyglutarate / (S)-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
FLAVIN-ADENINE DINUCLEOTIDE / L-2-hydroxyglutarate dehydrogenase, mitochondrial
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.299 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 20, 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
B: FI05204p
C: FI05204p
D: FI05204p
hetero molecules


Theoretical massNumber of molelcules
Total (without water)189,24416
Polymers183,6754
Non-polymers5,56912
Water10,323573
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15730 Å2
ΔGint-141 kcal/mol
Surface area59840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)174.518, 103.067, 122.876
Angle α, β, γ (deg.)90.00, 114.63, 90.00
Int Tables number5
Space group name H-MC121

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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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 573 / Source method: isolated from a natural source / Formula: H2O
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: 2.66 Å3/Da / Density % sol: 53.79 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 5.9
Details: 0.2 M lithium sulfate, 0.1 M Bis-Tris (pH 5.9), 23% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NFPSS / Beamline: BL18U / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 16, 2021
RadiationMonochromator: LN2-cooled DCM with Si(111) crystals / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.299→50 Å / Num. obs: 86886 / % possible obs: 99 % / Redundancy: 6.6 % / CC1/2: 0.992 / CC star: 0.998 / Rmerge(I) obs: 0.147 / Rpim(I) all: 0.061 / Rrim(I) all: 0.159 / Χ2: 0.471 / Net I/σ(I): 2.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.3-2.344.60.95942820.5180.8260.4771.0760.39798.4
2.34-2.385.40.87843140.6060.8690.4040.970.39898.9
2.38-2.436.10.83643410.6550.890.3640.9140.40599
2.43-2.486.40.7543180.7410.9230.3160.8150.41199.1
2.48-2.536.50.66143030.7980.9420.2790.7190.40998.7
2.53-2.596.40.58743200.8120.9470.2490.6390.40998.3
2.59-2.667.10.5443480.8820.9680.2160.5820.42399.6
2.66-2.737.10.46743930.9060.9750.1860.5030.42599.5
2.73-2.817.10.40343410.9280.9810.1620.4350.43199.5
2.81-2.970.34643280.9470.9860.140.3740.43999.3
2.9-36.90.28443300.9580.9890.1150.3070.45298.9
3-3.126.50.23542840.9690.9920.0990.2560.46698.2
3.12-3.266.90.19343660.9790.9950.0780.2080.48299
3.26-3.447.10.15443520.9870.9970.0620.1660.50599.7
3.44-3.657.10.12543890.9920.9980.0510.1350.5399.5
3.65-3.936.90.10143610.9930.9980.0410.1090.54499.2
3.93-4.336.70.08242960.9940.9990.0340.0890.57797.7
4.33-4.957.20.07643970.9960.9990.030.0820.57499.5
4.95-6.246.70.07743580.9950.9990.0320.0830.51898.3
6.24-506.80.06444650.9970.9990.0260.0690.54898.8

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
HKL-2000data scaling
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.299→33.26 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2376 1988 2.29 %
Rwork0.2041 --
obs0.2049 86751 98.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.299→33.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12403 0 372 573 13348
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00413076
X-RAY DIFFRACTIONf_angle_d0.54917782
X-RAY DIFFRACTIONf_dihedral_angle_d8.0047587
X-RAY DIFFRACTIONf_chiral_restr0.0421990
X-RAY DIFFRACTIONf_plane_restr0.0032239
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2994-2.35690.35231360.29185844X-RAY DIFFRACTION96
2.3569-2.42060.30821350.26556064X-RAY DIFFRACTION99
2.4206-2.49180.2861350.24586034X-RAY DIFFRACTION99
2.4918-2.57220.27811430.24056007X-RAY DIFFRACTION98
2.5722-2.66410.29091550.24056073X-RAY DIFFRACTION100
2.6641-2.77070.29351390.22866082X-RAY DIFFRACTION99
2.7707-2.89680.27321330.22856106X-RAY DIFFRACTION99
2.8968-3.04940.25511500.22146036X-RAY DIFFRACTION99
3.0494-3.24030.24291440.21866043X-RAY DIFFRACTION98
3.2403-3.49030.27071380.2076128X-RAY DIFFRACTION100
3.4903-3.8410.21151480.19086085X-RAY DIFFRACTION100
3.841-4.39570.21661420.16596046X-RAY DIFFRACTION98
4.3957-5.5340.18751460.17416146X-RAY DIFFRACTION99
5.534-33.260.20611440.19576069X-RAY DIFFRACTION97
Refinement TLS params.Method: refined / Origin x: -56.134 Å / Origin y: 36.487 Å / Origin z: 27.8642 Å
111213212223313233
T0.3136 Å20.0026 Å2-0.0064 Å2-0.2894 Å20.0082 Å2--0.2593 Å2
L0.3174 °20.0451 °20.0316 °2-0.1914 °20.0513 °2--0.1648 °2
S-0.0073 Å °0.0131 Å °-0.024 Å °-0.0111 Å °-0.0069 Å °-0.0087 Å °-0.0489 Å °0.0059 Å °-0 Å °
Refinement TLS groupSelection details: all

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