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

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Basic information

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


D-2-hydroxyglutarate dehydrogenase / (R)-2-hydroxyglutarate dehydrogenase activity / tartrate metabolic process / Interconversion of 2-oxoglutarate and 2-hydroxyglutarate / malate metabolic process / response to cobalt ion / 2-oxoglutarate metabolic process / response to manganese ion / lactate metabolic process / response to zinc ion ...D-2-hydroxyglutarate dehydrogenase / (R)-2-hydroxyglutarate dehydrogenase activity / tartrate metabolic process / Interconversion of 2-oxoglutarate and 2-hydroxyglutarate / malate metabolic process / response to cobalt ion / 2-oxoglutarate metabolic process / response to manganese ion / lactate metabolic process / 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
FLAVIN-ADENINE DINUCLEOTIDE / D-MALATE / D-2-hydroxyglutarate dehydrogenase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 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

Downloads & links

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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)106,6368
Polymers104,6662
Non-polymers1,9706
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9430 Å2
ΔGint-124 kcal/mol
Surface area32530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.615, 94.569, 73.673
Angle α, β, γ (deg.)90.000, 111.550, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#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
#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-MLT / D-MALATE / (2R)-2-HYDROXYBUTANEDIOIC ACID / 2-HYDROXY-SUCCINIC ACID


Mass: 134.087 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O5 / Feature type: SUBJECT OF INVESTIGATION
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: 2.25 Å3/Da / Density % sol: 45.28 %
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: 0.9788 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Apr 29, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9788 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 21823 / % possible obs: 95.7 % / Redundancy: 6.1 % / Biso Wilson estimate: 36.26 Å2 / Rmerge(I) obs: 0.297 / Rpim(I) all: 0.132 / Rrim(I) all: 0.326 / Χ2: 0.461 / Net I/σ(I): 2.2 / Num. measured all: 132903
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.8-2.95.10.80118780.6170.3830.8920.41381.8
2.9-3.025.60.82119340.5910.3790.9080.42986.2
3.02-3.155.60.721130.620.3220.7740.4392.9
3.15-3.325.90.63222370.7030.2890.6980.4498.9
3.32-3.5360.47722570.8050.2180.5270.44599.5
3.53-3.85.90.36722410.8690.1670.4050.47798.8
3.8-4.186.70.27322750.9520.1170.2980.484100
4.18-4.796.70.18622990.9750.080.2030.492100
4.79-6.036.40.19122600.9760.0810.2080.46798.7
6.03-506.70.11223290.9940.0460.1220.49399.7

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Processing

Software
NameVersionClassification
HKL-3000data reduction
HKL-3000data scaling
PHENIX1.15rc1_3420refinement
PDB_EXTRACT3.25data extraction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6LPN

6lpn


Resolution: 2.8→41.136 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.61
RfactorNum. reflection% reflection
Rfree0.2549 1079 4.98 %
Rwork0.2147 --
obs0.2167 21657 94.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 91.79 Å2 / Biso mean: 32.525 Å2 / Biso min: 12.65 Å2
Refinement stepCycle: final / Resolution: 2.8→41.136 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7027 0 126 0 7153
Biso mean--27.6 --
Num. residues----933
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0037305
X-RAY DIFFRACTIONf_angle_d0.8449944
X-RAY DIFFRACTIONf_chiral_restr0.0561145
X-RAY DIFFRACTIONf_plane_restr0.0041270
X-RAY DIFFRACTIONf_dihedral_angle_d17.7774270
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.8001-2.92750.30621040.262207677
2.9275-3.08180.29271390.2579232986
3.0818-3.27480.33911170.2582262996
3.2748-3.52750.30121420.22952691100
3.5275-3.88220.25481600.2123267899
3.8822-4.44340.1981350.17632722100
4.4434-5.5960.22791290.186272499
5.596-41.1360.23441530.2192272998

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