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- PDB-8jdf: Crystal structure of H405A mLDHD in complex with D-lactate -

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Basic information

Entry
Database: PDB / ID: 8jdf
TitleCrystal structure of H405A mLDHD in complex with D-lactate
ComponentsProbable D-lactate dehydrogenase, mitochondrial
KeywordsOXIDOREDUCTASE / D-lactate dehydrogenase / LDHD / 2-hydroxyacid
Function / homology
Function and homology information


D-lactate dehydrogenase (cytochrome) / D-lactate dehydrogenase (cytochrome) activity / lactate catabolic process / D-lactate dehydrogenase activity / Mitochondrial protein import / ATP biosynthetic process / Mitochondrial protein degradation / FAD binding / flavin adenine dinucleotide 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 / LACTIC ACID / Probable D-lactate dehydrogenase, mitochondrial
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.69 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 2.0Nov 15, 2023Group: Atomic model / Data collection / Category: atom_site / chem_comp_atom / chem_comp_bond
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2
Revision 2.1Feb 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)51,2613
Polymers50,3861
Non-polymers8762
Water6,467359
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)81.120, 103.420, 122.360
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-944-

HOH

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Components

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


Mass: 50385.789 Da / Num. of mol.: 1 / Mutation: H405A
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-LAC / LACTIC ACID


Mass: 90.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H6O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 359 / 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: 51.7 %
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: 1.69→63.83 Å / Num. obs: 56971 / % possible obs: 98.8 % / Redundancy: 12.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.028 / Rrim(I) all: 0.102 / Χ2: 0.95 / Net I/σ(I): 22.5 / Num. measured all: 716901
Reflection shellResolution: 1.69→1.73 Å / % possible obs: 97.1 % / Redundancy: 9.6 % / Rmerge(I) obs: 0.918 / Num. measured all: 38882 / Num. unique obs: 4065 / CC1/2: 0.84 / Rpim(I) all: 0.307 / Rrim(I) all: 0.97 / Χ2: 0.84 / Net I/σ(I) obs: 5.6

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Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.69→37.94 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1874 2808 4.93 %
Rwork0.1725 --
obs0.1732 56964 98.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.69→37.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3413 0 59 359 3831
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073559
X-RAY DIFFRACTIONf_angle_d1.0284851
X-RAY DIFFRACTIONf_dihedral_angle_d13.675492
X-RAY DIFFRACTIONf_chiral_restr0.059556
X-RAY DIFFRACTIONf_plane_restr0.007634
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.69-1.720.24611480.2012581X-RAY DIFFRACTION96
1.72-1.750.23841550.19522642X-RAY DIFFRACTION98
1.75-1.780.20381420.19362631X-RAY DIFFRACTION98
1.78-1.820.18761160.1852688X-RAY DIFFRACTION98
1.82-1.860.2231500.1892646X-RAY DIFFRACTION98
1.86-1.90.21121150.17622697X-RAY DIFFRACTION98
1.9-1.950.18031460.17442694X-RAY DIFFRACTION98
1.95-20.21141310.17882683X-RAY DIFFRACTION98
2-2.060.18761270.16472692X-RAY DIFFRACTION99
2.06-2.130.22161380.17052706X-RAY DIFFRACTION99
2.13-2.210.17991360.1672706X-RAY DIFFRACTION99
2.21-2.290.22051270.17652726X-RAY DIFFRACTION99
2.29-2.40.18181400.17872708X-RAY DIFFRACTION99
2.4-2.520.19081270.18342729X-RAY DIFFRACTION99
2.52-2.680.20281570.18162717X-RAY DIFFRACTION99
2.68-2.890.20981600.18472731X-RAY DIFFRACTION99
2.89-3.180.20991370.17932745X-RAY DIFFRACTION99
3.18-3.640.17761630.16842758X-RAY DIFFRACTION99
3.64-4.580.15811230.15012809X-RAY DIFFRACTION100
4.59-37.940.15761700.16762867X-RAY DIFFRACTION98

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