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

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Basic information

Entry
Database: PDB / ID: 6lpn
TitleCrystal structure of human D-2-hydroxyglutarate dehydrogenase in apo form
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-2-hydroxyglutarate dehydrogenase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.206 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)106,2374
Polymers104,6662
Non-polymers1,5712
Water9,206511
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8610 Å2
ΔGint-47 kcal/mol
Surface area32560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.258, 94.859, 72.740
Angle α, β, γ (deg.)90.000, 113.340, 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 511 / 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: 2.19 Å3/Da / Density % sol: 43.76 %
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: Oct 22, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 45047 / % possible obs: 99.7 % / Redundancy: 6.6 % / Biso Wilson estimate: 26.95 Å2 / Rmerge(I) obs: 0.269 / Rpim(I) all: 0.112 / Rrim(I) all: 0.292 / Χ2: 1.363 / Net I/σ(I): 2.8 / Num. measured all: 299485
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.2-2.285.60.89744680.6090.4070.9880.86599.9
2.28-2.376.20.69444710.7840.30.7580.68499.8
2.37-2.486.80.63745250.8250.2640.6910.70799.9
2.48-2.616.90.54244440.8780.2220.5860.80299.7
2.61-2.776.70.44945490.8880.1860.4870.89399.9
2.77-2.996.90.36744660.9230.150.3971.10199.6
2.99-3.297.10.29345180.9410.1190.3171.38199.8
3.29-3.766.60.23545030.9540.0990.2561.92399.5
3.76-4.7470.1945410.9690.0790.2062.56899.8
4.74-506.60.17245620.9720.0730.1882.53199.1

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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: 3PM9

3pm9


Resolution: 2.206→39.834 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 22.31
RfactorNum. reflection% reflection
Rfree0.2169 2356 5.24 %
Rwork0.1671 --
obs0.1697 45004 99.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 85.64 Å2 / Biso mean: 31.3427 Å2 / Biso min: 10.83 Å2
Refinement stepCycle: final / Resolution: 2.206→39.834 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7022 0 106 511 7639
Biso mean--24.39 38.37 -
Num. residues----933
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0067283
X-RAY DIFFRACTIONf_angle_d1.0629915
X-RAY DIFFRACTIONf_chiral_restr0.0641143
X-RAY DIFFRACTIONf_plane_restr0.0061264
X-RAY DIFFRACTIONf_dihedral_angle_d15.9314267
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.2063-2.25130.30851060.2312231592
2.2513-2.30030.27661390.20552491100
2.3003-2.35380.24771220.19622522100
2.3538-2.41260.25451550.18922531100
2.4126-2.47790.28051600.18992496100
2.4779-2.55080.24611410.18612484100
2.5508-2.63310.25451450.17832522100
2.6331-2.72720.24051320.1742502100
2.7272-2.83630.24881200.1719253899
2.8363-2.96540.2421440.16352520100
2.9654-3.12170.23851320.1662532100
3.1217-3.31720.23191430.16732549100
3.3172-3.57310.191400.15442501100
3.5731-3.93240.19321360.1485252599
3.9324-4.50080.16541520.13822540100
4.5008-5.66790.18961460.1587252099
5.6679-39.8340.19771430.172256099
Refinement TLS params.Method: refined / Origin x: -0.435 Å / Origin y: -18.869 Å / Origin z: 43.829 Å
111213212223313233
T0.1279 Å2-0.0007 Å2-0.0064 Å2-0.1443 Å2-0.0003 Å2--0.1378 Å2
L0.0485 °20.0062 °2-0.0335 °2-0.2465 °20.018 °2--0.1547 °2
S0.0084 Å °-0.0184 Å °0.0124 Å °-0.0393 Å °0.0102 Å °0.0093 Å °-0.0006 Å °0.0053 Å °-0 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA54 - 519
2X-RAY DIFFRACTION1allA601
3X-RAY DIFFRACTION1allA701 - 949
4X-RAY DIFFRACTION1allB701 - 962
5X-RAY DIFFRACTION1allB53 - 519
6X-RAY DIFFRACTION1allB601

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