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- PDB-8jdc: Crystal structure of mLDHD in apo form -

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Basic information

Entry
Database: PDB / ID: 8jdc
TitleCrystal structure of mLDHD in apo form
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
FLAVIN-ADENINE DINUCLEOTIDE / Probable D-lactate dehydrogenase, mitochondrial
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.696 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 13, 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)51,2382
Polymers50,4531
Non-polymers7861
Water5,314295
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)81.486, 103.162, 122.591
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-694-

HOH

21A-867-

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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 295 / 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: 51.83 %
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: Nov 28, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.696→78.93 Å / Num. obs: 51046 / % possible obs: 88.9 % / Redundancy: 7.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.054 / Rpim(I) all: 0.021 / Rrim(I) all: 0.058 / Χ2: 0.91 / Net I/σ(I): 18.8
Reflection shellResolution: 1.7→1.79 Å / % possible obs: 100 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.672 / Num. measured all: 52341 / Num. unique obs: 8242 / CC1/2: 0.844 / Rpim(I) all: 0.284 / Rrim(I) all: 0.731 / Χ2: 0.68 / Net I/σ(I) obs: 2.8

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Processing

Software
NameVersionClassification
PHENIX(1.17.1_3660: ???)refinement
XDSdata reduction
autoPROCdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.696→31.682 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1941 2533 4.96 %
Rwork0.1787 --
obs0.1795 51027 88.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.696→31.682 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3395 0 53 295 3743
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083526
X-RAY DIFFRACTIONf_angle_d0.9554805
X-RAY DIFFRACTIONf_dihedral_angle_d5.3182076
X-RAY DIFFRACTIONf_chiral_restr0.058551
X-RAY DIFFRACTIONf_plane_restr0.007626
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6962-1.72890.24741540.2342985X-RAY DIFFRACTION100
1.7289-1.76410.27351610.22142973X-RAY DIFFRACTION100
1.7641-1.80250.22881460.21163011X-RAY DIFFRACTION100
1.8025-1.84440.23871480.22232995X-RAY DIFFRACTION100
1.8444-1.89050.27391030.23131798X-RAY DIFFRACTION96
1.8905-1.94170.25461280.23762689X-RAY DIFFRACTION98
1.9417-1.99880.2467980.20581752X-RAY DIFFRACTION58
1.9988-2.06330.24341610.19312879X-RAY DIFFRACTION98
2.0633-2.1370.21071200.19332055X-RAY DIFFRACTION100
2.137-2.22250.20611360.18373029X-RAY DIFFRACTION100
2.2225-2.32370.20011160.19462233X-RAY DIFFRACTION74
2.3237-2.44610.21341540.19253026X-RAY DIFFRACTION100
2.4461-2.59930.22491630.19393023X-RAY DIFFRACTION100
2.5993-2.79990.241960.20072119X-RAY DIFFRACTION69
2.7999-3.08150.22731780.19253025X-RAY DIFFRACTION100
3.0815-3.52690.1831670.17453041X-RAY DIFFRACTION100
3.5269-4.44150.1411450.15092654X-RAY DIFFRACTION86
4.4415-31.6820.17021590.15673207X-RAY DIFFRACTION100

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