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- PDB-8jdz: Crystal structure of mLDHD in complex with 2-keto-3-methylvaleric acid -

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Basic information

Entry
Database: PDB / ID: 8jdz
TitleCrystal structure of mLDHD in complex with 2-keto-3-methylvaleric acid
ComponentsProbable D-lactate dehydrogenase, mitochondrial
KeywordsOXIDOREDUCTASE / D-lactate dehydrogenase / LDHD / 2-hydroxyacid
Function / homology
Function and homology information


D-lactate dehydrogenase (cytochrome) / lactate catabolic process / D-lactate dehydrogenase (cytochrome) activity / Mitochondrial protein import / D-lactate dehydrogenase (NAD+) activity / ATP biosynthetic process / Mitochondrial protein degradation / FAD binding / mitochondrial inner membrane / mitochondrion
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
(3S)-3-methyl-2-oxopentanoic acid / FLAVIN-ADENINE DINUCLEOTIDE / : / Probable D-lactate dehydrogenase, mitochondrial
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.56 Å
AuthorsJin, S. / Chen, X. / Yang, J. / Ding, J.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31870723 China
Chinese Academy of SciencesXDB37030305 China
CitationJournal: Nat Commun / Year: 2023
Title: Lactate dehydrogenase D is a general dehydrogenase for D-2-hydroxyacids and is associated with D-lactic acidosis.
Authors: Jin, S. / Chen, X. / Yang, J. / Ding, J.
History
DepositionMay 15, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 18, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 21, 2024Group: 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 / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Probable D-lactate dehydrogenase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,4234
Polymers50,4531
Non-polymers9713
Water5,945330
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)82.070, 102.580, 122.940
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-665-

HOH

21A-894-

HOH

31A-911-

HOH

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Components

#1: Protein Probable D-lactate dehydrogenase, mitochondrial / DLD / Lactate dehydrogenase D


Mass: 50452.855 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ldhd / Production host: Escherichia coli (E. coli)
References: UniProt: Q7TNG8, D-lactate dehydrogenase (cytochrome)
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-1QQ / (3S)-3-methyl-2-oxopentanoic acid


Mass: 130.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H10O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 330 / 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: 2.56 Å3/Da / Density % sol: 52.03 %
Crystal growTemperature: 289 K / Method: vapor diffusion / Details: 4.0 M sodium formate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 23, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.56→41.03 Å / Num. obs: 73896 / % possible obs: 100 % / Redundancy: 13 % / CC1/2: 0.999 / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.022 / Rrim(I) all: 0.08 / Χ2: 0.98 / Net I/σ(I): 16.8 / Num. measured all: 962013
Reflection shellResolution: 1.56→1.6 Å / % possible obs: 99.9 % / Redundancy: 10.9 % / Rmerge(I) obs: 1.387 / Num. measured all: 58976 / Num. unique obs: 5430 / CC1/2: 0.686 / Rpim(I) all: 0.439 / Rrim(I) all: 1.456 / Χ2: 0.87 / Net I/σ(I) obs: 1.7

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Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874: ???)refinement
Aimlessdata scaling
xia2data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.56→34.13 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2052 3623 4.9 %
Rwork0.1804 --
obs0.1816 73885 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.56→34.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3401 0 63 330 3794
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063549
X-RAY DIFFRACTIONf_angle_d1.0214837
X-RAY DIFFRACTIONf_dihedral_angle_d13.564490
X-RAY DIFFRACTIONf_chiral_restr0.066554
X-RAY DIFFRACTIONf_plane_restr0.007632
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.56-1.580.28121340.26832717X-RAY DIFFRACTION100
1.58-1.60.30281520.26442641X-RAY DIFFRACTION100
1.6-1.630.30021500.25122631X-RAY DIFFRACTION100
1.63-1.650.29381530.25272673X-RAY DIFFRACTION100
1.65-1.680.31251400.25042673X-RAY DIFFRACTION100
1.68-1.70.26731370.23512688X-RAY DIFFRACTION100
1.7-1.730.2621230.2342693X-RAY DIFFRACTION100
1.73-1.760.26921470.20952695X-RAY DIFFRACTION100
1.76-1.80.2541390.21282660X-RAY DIFFRACTION100
1.8-1.830.20961510.20412671X-RAY DIFFRACTION100
1.83-1.870.24161470.212675X-RAY DIFFRACTION100
1.87-1.920.27251300.20242678X-RAY DIFFRACTION100
1.92-1.970.23521270.20542694X-RAY DIFFRACTION100
1.97-2.020.24261280.20652700X-RAY DIFFRACTION100
2.02-2.080.24281400.1932679X-RAY DIFFRACTION100
2.08-2.150.21421450.18472698X-RAY DIFFRACTION100
2.15-2.220.20991350.18742701X-RAY DIFFRACTION100
2.22-2.310.21351340.19262697X-RAY DIFFRACTION100
2.31-2.420.20821290.18912719X-RAY DIFFRACTION100
2.42-2.540.2371310.19342708X-RAY DIFFRACTION100
2.54-2.70.19261670.18892682X-RAY DIFFRACTION100
2.7-2.910.23621350.18752738X-RAY DIFFRACTION100
2.91-3.20.22871300.17742758X-RAY DIFFRACTION100
3.2-3.670.18191490.16352717X-RAY DIFFRACTION100
3.67-4.620.15491260.1412790X-RAY DIFFRACTION100
4.62-34.130.16191440.16292886X-RAY DIFFRACTION100

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