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- PDB-8jdu: Crystal structure of mLDHD in complex with 2-ketovaleric acid -

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Basic information

Entry
Database: PDB / ID: 8jdu
TitleCrystal structure of mLDHD in complex with 2-ketovaleric 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
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: 1.67 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)51,4094
Polymers50,4531
Non-polymers9573
Water5,549308
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)81.727, 102.960, 122.278
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-623-

HOH

21A-853-

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-69O / 2-oxopentanoic acid / 2-Ketopentanoic acid


Mass: 116.115 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H8O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 308 / 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: 2.55 Å3/Da / Density % sol: 51.75 %
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: BL02U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Apr 17, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.67→64.01 Å / Num. obs: 60435 / % possible obs: 99.9 % / Redundancy: 7.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.047 / Rpim(I) all: 0.018 / Rrim(I) all: 0.051 / Χ2: 0.87 / Net I/σ(I): 22 / Num. measured all: 467811
Reflection shellResolution: 1.67→1.76 Å / % possible obs: 99.4 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.611 / Num. measured all: 49737 / Num. unique obs: 8660 / CC1/2: 0.844 / Rpim(I) all: 0.269 / Rrim(I) all: 0.67 / Χ2: 0.66 / Net I/σ(I) obs: 2.9

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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: 1.67→30.57 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1988 2955 4.89 %
Rwork0.1803 --
obs0.1812 60419 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.67→30.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3410 0 62 308 3780
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073539
X-RAY DIFFRACTIONf_angle_d1.0814821
X-RAY DIFFRACTIONf_dihedral_angle_d10.89490
X-RAY DIFFRACTIONf_chiral_restr0.063552
X-RAY DIFFRACTIONf_plane_restr0.007629
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.67-1.690.27491260.24132650X-RAY DIFFRACTION98
1.69-1.720.25081520.22352678X-RAY DIFFRACTION100
1.72-1.750.23561340.22272699X-RAY DIFFRACTION100
1.75-1.790.24431370.21652714X-RAY DIFFRACTION100
1.79-1.820.22821440.21142718X-RAY DIFFRACTION100
1.82-1.860.27441340.22552714X-RAY DIFFRACTION100
1.86-1.910.22951430.19762727X-RAY DIFFRACTION100
1.91-1.950.23261340.1962725X-RAY DIFFRACTION100
1.95-2.010.21051340.19982714X-RAY DIFFRACTION100
2.01-2.070.20241190.18292730X-RAY DIFFRACTION100
2.07-2.130.20721460.18872747X-RAY DIFFRACTION100
2.13-2.210.21111460.18892684X-RAY DIFFRACTION100
2.21-2.30.2351350.19292766X-RAY DIFFRACTION100
2.3-2.40.22451340.19092732X-RAY DIFFRACTION100
2.4-2.530.22581440.19832742X-RAY DIFFRACTION100
2.53-2.690.20741450.19622743X-RAY DIFFRACTION100
2.69-2.890.19331460.19782764X-RAY DIFFRACTION100
2.89-3.180.21621510.18562749X-RAY DIFFRACTION100
3.18-3.640.19151320.17312784X-RAY DIFFRACTION100
3.64-4.590.16211490.14682803X-RAY DIFFRACTION100
4.59-30.570.17481700.16312881X-RAY DIFFRACTION99

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