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

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Basic information

Entry
Database: PDB / ID: 6lpt
TitleCrystal structure of human D-2-hydroxyglutarate dehydrogenase in complex with D-lactate (D-LAC)
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 / malate metabolic process / 2-oxoglutarate metabolic process / response to cobalt ion / protein 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 / malate metabolic process / 2-oxoglutarate metabolic process / response to cobalt ion / protein metabolic process / response to manganese ion / response to zinc ion / FAD binding / mitochondrial matrix / mitochondrion / zinc ion binding
Similarity search - Function
FAD-linked oxidase, C-terminal / FAD linked oxidases, C-terminal domain / Vanillyl-alcohol oxidase, C-terminal subdomain 2 / FAD-linked oxidase-like, C-terminal / 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
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / LACTIC ACID / D-2-hydroxyglutarate dehydrogenase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.621 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 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _struct_conn.ptnr2_label_atom_id
Revision 2.1Nov 29, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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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)106,5488
Polymers104,6662
Non-polymers1,8826
Water3,711206
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8850 Å2
ΔGint-127 kcal/mol
Surface area32460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.263, 94.411, 73.575
Angle α, β, γ (deg.)90.000, 111.770, 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, EC: 1.1.99.-
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / 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-LAC / LACTIC ACID / Lactic acid


Mass: 90.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H6O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 206 / Source method: isolated from a natural source / Formula: H2O
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: 2.23 Å3/Da / Density % sol: 44.77 %
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: 2.62→50 Å / Num. obs: 27511 / % possible obs: 99.5 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.154 / Rpim(I) all: 0.063 / Rrim(I) all: 0.166 / Χ2: 0.467 / Net I/σ(I): 3 / Num. measured all: 188447
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.62-2.7170.65627380.8410.2650.7080.41499.9
2.71-2.826.90.55927650.8680.2270.6040.41899.9
2.82-2.956.90.41827320.9280.170.4520.42799.9
2.95-3.116.90.34127310.9420.1390.3690.44299.6
3.11-3.36.20.24127270.9670.1040.2630.45298.8
3.3-3.567.20.17527600.9870.070.1890.47399.9
3.56-3.917.10.1327370.9920.0520.140.599.5
3.91-4.486.90.08527750.9950.0350.0920.5299.6
4.48-5.646.70.07327450.9960.030.0790.5198.8
5.64-506.70.0628010.9980.0250.0650.5199.1

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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: 2.621→36.387 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 22.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2313 1297 4.73 %
Rwork0.1912 26135 -
obs0.1931 27432 99.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 92.23 Å2 / Biso mean: 34.5101 Å2 / Biso min: 9.13 Å2
Refinement stepCycle: final / Resolution: 2.621→36.387 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7027 0 120 206 7353
Biso mean--28.28 31.17 -
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 (%)
2.621-2.72560.31281480.2409285998
2.7256-2.84960.26191550.21582898100
2.8496-2.99980.26351540.20822889100
2.9998-3.18760.25031220.21152925100
3.1876-3.43360.2581620.193288299
3.4336-3.77880.23371210.1752937100
3.7788-4.32480.18971210.16072948100
4.3248-5.44590.19591570.1677289699
5.4459-36.3870.22311570.2144290197

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