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

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Basic information

Entry
Database: PDB / ID: 8jde
TitleCrystal structure of 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) / 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 / LACTIC ACID / : / Probable D-lactate dehydrogenase, mitochondrial
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.729 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 / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / pdbx_struct_conn_angle / struct_conn
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 / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _struct_conn.ptnr2_label_atom_id
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)51,3834
Polymers50,4531
Non-polymers9313
Water4,756264
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)82.124, 102.403, 123.432
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-607-

HOH

21A-831-

HOH

31A-860-

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-LAC / LACTIC ACID


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


Mass: 18.015 Da / Num. of mol.: 264 / 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: 2.57 Å3/Da / Density % sol: 52.17 %
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: 1.729→68.37 Å / Num. obs: 51777 / % possible obs: 94.8 % / Redundancy: 6.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.04 / Rpim(I) all: 0.017 / Rrim(I) all: 0.043 / Χ2: 0.86 / Net I/σ(I): 22.5
Reflection shellResolution: 1.73→1.82 Å / % possible obs: 99.9 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.564 / Num. measured all: 46874 / Num. unique obs: 7889 / CC1/2: 0.866 / Rpim(I) all: 0.248 / Rrim(I) all: 0.617 / Χ2: 0.61 / Net I/σ(I) obs: 2.7

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Processing

Software
NameVersionClassification
PHENIX(1.17.1_3660: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.729→41.062 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1967 2568 4.96 %
Rwork0.1743 --
obs0.1754 51764 94.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.729→41.062 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3407 0 60 264 3731
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063565
X-RAY DIFFRACTIONf_angle_d0.9294859
X-RAY DIFFRACTIONf_dihedral_angle_d5.3842100
X-RAY DIFFRACTIONf_chiral_restr0.054556
X-RAY DIFFRACTIONf_plane_restr0.006635
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.729-1.7620.26891670.23892829X-RAY DIFFRACTION100
1.762-1.7980.27731650.23222836X-RAY DIFFRACTION100
1.798-1.8370.27691710.22222841X-RAY DIFFRACTION100
1.837-1.87980.28831340.22072828X-RAY DIFFRACTION100
1.8798-1.92680.2239940.2132189X-RAY DIFFRACTION75
1.9268-1.97890.22991490.20982844X-RAY DIFFRACTION100
1.9789-2.03710.23511490.19792862X-RAY DIFFRACTION100
2.0371-2.10290.238920.20071787X-RAY DIFFRACTION62
2.1029-2.1780.20171630.18082842X-RAY DIFFRACTION100
2.178-2.26520.20981000.19222063X-RAY DIFFRACTION72
2.2652-2.36830.21631440.18822917X-RAY DIFFRACTION100
2.3683-2.49310.20691300.18872872X-RAY DIFFRACTION100
2.4931-2.64930.22121500.19332885X-RAY DIFFRACTION100
2.6493-2.85380.20391430.19012871X-RAY DIFFRACTION100
2.8538-3.14090.19761500.18272903X-RAY DIFFRACTION100
3.1409-3.59520.18731490.16482902X-RAY DIFFRACTION100
3.5952-4.52870.16361560.14122906X-RAY DIFFRACTION99
4.5287-41.0620.17581620.15853019X-RAY DIFFRACTION99

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