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- PDB-8jdv: Crystal structure of mLDHD in complex with 2-ketohexanoic acid -

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Basic information

Entry
Database: PDB / ID: 8jdv
TitleCrystal structure of mLDHD in complex with 2-ketohexanoic 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-Ketohexanoic acid / FLAVIN-ADENINE DINUCLEOTIDE / : / Probable D-lactate dehydrogenase, mitochondrial
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 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

Downloads & links

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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
Water4,522251
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)82.782, 101.403, 124.580
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-834-

HOH

21A-846-

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-7N5 / 2-Ketohexanoic 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.: 251 / 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: 2.59 Å3/Da / Density % sol: 52.53 %
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: BL18U1 / Wavelength: 1.0385 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 9, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0385 Å / Relative weight: 1
ReflectionResolution: 1.95→35 Å / Num. obs: 37866 / % possible obs: 100 % / Redundancy: 13.1 % / CC1/2: 0.992 / CC star: 0.998 / Rmerge(I) obs: 0.138 / Rpim(I) all: 0.04 / Rrim(I) all: 0.144 / Χ2: 0.614 / Net I/σ(I): 3.8 / Num. measured all: 496275
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2
1.95-2.0213.10.79737160.9330.9830.2260.8290.448
2.02-2.113.40.54737290.9620.990.1540.5680.476
2.1-2.2130.42237650.9750.9940.1210.4390.504
2.2-2.3113.20.34637320.980.9950.0980.360.589
2.31-2.46130.26137610.9860.9960.0750.2720.543
2.46-2.6513.60.20737700.990.9970.0580.2150.593
2.65-2.9113.10.14937770.9940.9980.0430.1560.65
2.91-3.3313.30.10438130.9960.9990.030.1080.747
3.33-4.213.10.07238270.9980.9990.0210.0750.848
4.2-3512.40.05939760.9970.9990.0180.0620.735

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Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.96→34.47 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2051 2000 5.28 %
Rwork0.1684 --
obs0.1704 37844 99.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.96→34.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3399 0 63 251 3713
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083528
X-RAY DIFFRACTIONf_angle_d1.0834806
X-RAY DIFFRACTIONf_dihedral_angle_d13.645491
X-RAY DIFFRACTIONf_chiral_restr0.064551
X-RAY DIFFRACTIONf_plane_restr0.006629
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.96-20.24761240.19082217X-RAY DIFFRACTION87
2-2.060.22481430.16432564X-RAY DIFFRACTION100
2.06-2.120.19841420.15422539X-RAY DIFFRACTION100
2.12-2.190.19721420.15592556X-RAY DIFFRACTION100
2.19-2.270.21351430.16012576X-RAY DIFFRACTION100
2.27-2.360.22151440.16842556X-RAY DIFFRACTION100
2.36-2.460.22741420.17042553X-RAY DIFFRACTION100
2.46-2.590.23851440.17422582X-RAY DIFFRACTION100
2.59-2.760.22771420.17312560X-RAY DIFFRACTION100
2.76-2.970.18611450.17382586X-RAY DIFFRACTION100
2.97-3.270.21141450.16732591X-RAY DIFFRACTION100
3.27-3.740.19161450.16812618X-RAY DIFFRACTION100
3.74-4.710.17141480.15122634X-RAY DIFFRACTION100
4.71-34.470.21661510.18832712X-RAY DIFFRACTION99

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