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- PDB-8w75: Structure of Drosophila melanogaster L-2-hydroxyglutarate dehydro... -

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Basic information

Entry
Database: PDB / ID: 8w75
TitleStructure of Drosophila melanogaster L-2-hydroxyglutarate dehydrogenase
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: 2.85 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
D: FI05204p
A: FI05204p
B: FI05204p
C: FI05204p
hetero molecules


Theoretical massNumber of molelcules
Total (without water)188,86012
Polymers183,6754
Non-polymers5,1858
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13400 Å2
ΔGint-67 kcal/mol
Surface area59360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.115, 103.178, 102.538
Angle α, β, γ (deg.)90.00, 108.61, 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: 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: 2.66 Å3/Da / Density % sol: 53.75 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / Details: 0.2 M magnesium formate, 18% (w/v) PEG 3350

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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: 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: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.847→50 Å / Num. obs: 45678 / % possible obs: 98.4 % / Redundancy: 6.7 % / CC1/2: 0.992 / CC star: 0.998 / Rmerge(I) obs: 0.128 / Rpim(I) all: 0.053 / Rrim(I) all: 0.139 / Χ2: 0.983 / Net I/σ(I): 4.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.85-2.95.71.23420750.6030.8670.531.3470.98389.9
2.9-2.9561.10321870.7350.920.4671.2010.97195.2
2.95-3.016.30.97222700.7930.9410.4051.0550.95198.4
3.01-3.076.70.82222900.8330.9530.3390.8910.9699.4
3.07-3.146.80.74123240.870.9650.3040.8020.95699.5
3.14-3.216.90.6122890.8960.9720.2490.660.96499.5
3.21-3.296.80.51422800.9390.9840.2110.5560.95799.1
3.29-3.386.70.42522640.940.9850.1750.460.97198.7
3.38-3.486.20.35522660.9510.9870.1520.3880.98897
3.48-3.5970.27123080.9820.9950.110.2931.01999.8
3.59-3.727.10.21923110.9830.9960.0880.2371.04599.7
3.72-3.877.10.18122920.9870.9970.0730.1951.07899.7
3.87-4.0470.13623120.9920.9980.0550.1471.07899.7
4.04-4.266.90.11123010.9930.9980.0450.121.10899.1
4.26-4.526.50.09422770.9940.9990.0390.1021.12897.9
4.52-4.876.90.08223060.9960.9990.0330.0891.04899
4.87-5.367.10.07723200.9960.9990.0310.0830.9999.8
5.36-6.1470.07123070.9970.9990.0290.0760.9199.4
6.14-7.736.60.05323290.99810.0220.0570.8398.6
7.73-506.60.03623700.99910.0150.0390.798.6

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Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.85→31.91 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 32.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2944 1991 4.97 %
Rwork0.2433 --
obs0.2458 40064 86.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.85→31.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11810 0 176 0 11986
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00512270
X-RAY DIFFRACTIONf_angle_d0.59616776
X-RAY DIFFRACTIONf_dihedral_angle_d18.6534089
X-RAY DIFFRACTIONf_chiral_restr0.0481929
X-RAY DIFFRACTIONf_plane_restr0.0042127
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.85-2.920.4435650.37161127X-RAY DIFFRACTION36
2.92-30.3798820.34011752X-RAY DIFFRACTION56
3-3.080.33911100.31262157X-RAY DIFFRACTION69
3.08-3.180.36161280.30692447X-RAY DIFFRACTION77
3.18-3.30.30891470.30142639X-RAY DIFFRACTION85
3.3-3.430.3681460.29142963X-RAY DIFFRACTION93
3.43-3.590.33161620.27293071X-RAY DIFFRACTION98
3.59-3.770.3281630.2583127X-RAY DIFFRACTION100
3.77-4.010.27351730.23073138X-RAY DIFFRACTION100
4.01-4.320.27271570.21363113X-RAY DIFFRACTION99
4.32-4.750.2731680.20913101X-RAY DIFFRACTION98
4.75-5.440.2551660.21493154X-RAY DIFFRACTION100
5.44-6.840.30351620.24073150X-RAY DIFFRACTION99
6.84-31.910.24241620.20883134X-RAY DIFFRACTION97
Refinement TLS params.Method: refined / Origin x: -16.6977 Å / Origin y: 10.2422 Å / Origin z: -24.1918 Å
111213212223313233
T0.2348 Å2-0.062 Å2-0.0437 Å2-0.2253 Å2-0.0513 Å2--0.084 Å2
L0.9567 °2-0.094 °2-0.2988 °2-0.6408 °2-0.0549 °2--0.4937 °2
S-0.0545 Å °-0.0225 Å °0.0479 Å °0.0013 Å °0.1583 Å °-0.0213 Å °-0.0087 Å °0.0212 Å °0.0044 Å °
Refinement TLS groupSelection details: all

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