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- PDB-6lpp: Crystal structure of human D-2-hydroxyglutarate dehydrogenase in ... -

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Basic information

Entry
Database: PDB / ID: 6lpp
TitleCrystal structure of human D-2-hydroxyglutarate dehydrogenase in complex with D-2-hydroxyglutarate (D-2-HG)
ComponentsD-2-hydroxyglutarate dehydrogenase, mitochondrial
KeywordsOXIDOREDUCTASE / dehydrogenase / FLAVOPROTEIN
Function / homology
Function and homology information


D-2-hydroxyglutarate dehydrogenase / (R)-2-hydroxyglutarate dehydrogenase activity / Interconversion of 2-oxoglutarate and 2-hydroxyglutarate / protein metabolic process / malate metabolic process / response to cobalt ion / 2-oxoglutarate metabolic process / response to manganese ion / response to zinc ion / FAD binding ...D-2-hydroxyglutarate dehydrogenase / (R)-2-hydroxyglutarate dehydrogenase activity / Interconversion of 2-oxoglutarate and 2-hydroxyglutarate / protein metabolic process / malate metabolic process / response to cobalt ion / 2-oxoglutarate metabolic process / response to manganese ion / response to zinc ion / FAD binding / mitochondrial matrix / mitochondrion / zinc ion binding
Similarity search - Function
Alpha-Beta Plaits - #2190 / Alpha-Beta Plaits - #2740 / : / FAD-linked oxidase, C-terminal / FAD linked oxidases, C-terminal domain / Vanillyl-alcohol oxidase, C-terminal subdomain 2 / FAD-linked oxidase-like, C-terminal / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase, domain 2 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 2 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3 - #10 ...Alpha-Beta Plaits - #2190 / Alpha-Beta Plaits - #2740 / : / FAD-linked oxidase, C-terminal / FAD linked oxidases, C-terminal domain / Vanillyl-alcohol oxidase, C-terminal subdomain 2 / FAD-linked oxidase-like, C-terminal / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase, domain 2 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 2 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3 - #10 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3 / FAD linked oxidase, N-terminal / FAD binding domain / FAD-binding, type PCMH, subdomain 1 / FAD-binding domain, PCMH-type / PCMH-type FAD-binding domain profile. / FAD-binding, type PCMH, subdomain 2 / FAD-binding, type PCMH-like superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
(2R)-2-hydroxypentanedioic acid / FLAVIN-ADENINE DINUCLEOTIDE / D-2-hydroxyglutarate dehydrogenase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsYang, J. / Zhu, H. / Ding, J.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31870723 China
National Natural Science Foundation of China (NSFC)31530013 China
CitationJournal: Cell Discov / Year: 2021
Title: Structure, substrate specificity, and catalytic mechanism of human D-2-HGDH and insights into pathogenicity of disease-associated mutations.
Authors: Yang, J. / Zhu, H. / Zhang, T. / Ding, J.
History
DepositionJan 12, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 13, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 28, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: D-2-hydroxyglutarate dehydrogenase, mitochondrial
B: D-2-hydroxyglutarate dehydrogenase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,30915
Polymers104,6662
Non-polymers2,64313
Water1,856103
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9080 Å2
ΔGint-127 kcal/mol
Surface area31370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.275, 94.593, 73.399
Angle α, β, γ (deg.)90.000, 111.900, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein D-2-hydroxyglutarate dehydrogenase, mitochondrial


Mass: 52332.875 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: D2HGDH, D2HGD / Production host: Escherichia coli (E. coli)
References: UniProt: Q8N465, Oxidoreductases; Acting on the CH-OH group of donors; With unknown physiological acceptors

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Non-polymers , 5 types, 116 molecules

#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


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


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-2HG / (2R)-2-hydroxypentanedioic acid


Mass: 148.114 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H8O5 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 103 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.22 Å3/Da / Density % sol: 44.7 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.1M BIS-TRIS, pH 6.5, 25% (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: 0.9789 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 31, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 2.639→50 Å / Num. obs: 26662 / % possible obs: 99 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.104 / Rpim(I) all: 0.065 / Rrim(I) all: 0.123 / Χ2: 0.487 / Net I/σ(I): 4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.65-2.743.20.37526220.8520.2470.4510.43698.1
2.74-2.853.10.32426180.8730.2180.3920.44997.7
2.85-2.983.50.27626620.9370.1710.3250.46299.9
2.98-3.143.50.22426830.950.1380.2640.46599.7
3.14-3.343.50.16626800.9690.1040.1970.47399.6
3.34-3.63.40.11926470.9830.0750.1420.49999
3.6-3.963.40.08826580.9890.0560.1050.51499.1
3.96-4.533.60.06526930.9940.040.0770.5499.6
4.53-5.713.30.05626820.9950.0360.0670.50399
5.71-503.40.0527170.9960.0320.0590.51898.7

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
HKL-3000data reduction
HKL-3000data scaling
PDB_EXTRACT3.25data extraction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6LPN

6lpn


Resolution: 2.65→40.781 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 26.08
RfactorNum. reflection% reflection
Rfree0.2459 1267 4.76 %
Rwork0.2035 --
obs0.2055 26610 98.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 81.45 Å2 / Biso mean: 34.6838 Å2 / Biso min: 0.26 Å2
Refinement stepCycle: final / Resolution: 2.65→40.781 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6886 0 170 103 7159
Biso mean--34.06 28.75 -
Num. residues----933
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.65-2.74460.29241300.2596261492
2.7446-2.86950.32821390.2452279098
2.8695-3.02070.32431610.23292845100
3.0207-3.20990.24691450.22862840100
3.2099-3.45760.2862990.2084287799
3.4576-3.80530.25561570.1914281499
3.8053-4.35540.19521330.16932854100
4.3554-5.48520.19421380.1725286399
5.4852-40.780.24361650.2142284698

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