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- PDB-8jdy: Crystal structure of mLDHD in complex with 2-ketoisocaproic acid -

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Basic information

Entry
Database: PDB / ID: 8jdy
TitleCrystal structure of mLDHD in complex with 2-ketoisocaproic 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-OXO-4-METHYLPENTANOIC ACID / FLAVIN-ADENINE DINUCLEOTIDE / : / Probable D-lactate dehydrogenase, mitochondrial
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.59 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
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)81.650, 102.100, 123.080
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-603-

HOH

21A-879-

HOH

31A-883-

HOH

41A-887-

HOH

51A-891-

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-COI / 2-OXO-4-METHYLPENTANOIC ACID / alpha-ketoisocaproic 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.: 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: 2.54 Å3/Da / Density % sol: 51.61 %
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: 0.9792 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 19, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.59→34.02 Å / Num. obs: 69238 / % possible obs: 100 % / Redundancy: 12.8 % / CC1/2: 1 / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.017 / Rrim(I) all: 0.061 / Χ2: 0.98 / Net I/σ(I): 22 / Num. measured all: 886449
Reflection shellResolution: 1.59→1.63 Å / % possible obs: 100 % / Redundancy: 12 % / Rmerge(I) obs: 1.382 / Num. measured all: 61178 / Num. unique obs: 5108 / CC1/2: 0.671 / Rpim(I) all: 0.412 / Rrim(I) all: 1.444 / Χ2: 0.97 / Net I/σ(I) obs: 2.1

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Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874: ???)refinement
Aimlessdata scaling
xia2data reduction
PHASESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.59→34.02 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2036 3455 4.99 %
Rwork0.1747 --
obs0.1761 69237 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.59→34.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3401 0 63 308 3772
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063568
X-RAY DIFFRACTIONf_angle_d1.0964863
X-RAY DIFFRACTIONf_dihedral_angle_d16.021495
X-RAY DIFFRACTIONf_chiral_restr0.065555
X-RAY DIFFRACTIONf_plane_restr0.007636
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.59-1.610.32971430.27782595X-RAY DIFFRACTION100
1.61-1.630.27841210.25382636X-RAY DIFFRACTION100
1.63-1.660.2451290.2252616X-RAY DIFFRACTION100
1.66-1.690.23981360.21472582X-RAY DIFFRACTION100
1.69-1.710.20831400.21112596X-RAY DIFFRACTION100
1.71-1.740.25141440.19762601X-RAY DIFFRACTION100
1.74-1.770.2121420.1972615X-RAY DIFFRACTION100
1.77-1.810.20411350.1922593X-RAY DIFFRACTION100
1.81-1.850.22221330.1862609X-RAY DIFFRACTION100
1.85-1.890.21611360.18222616X-RAY DIFFRACTION100
1.89-1.930.22231320.18032618X-RAY DIFFRACTION100
1.93-1.980.21191520.19022616X-RAY DIFFRACTION100
1.98-2.030.22561140.18372640X-RAY DIFFRACTION100
2.03-2.090.23951320.17782625X-RAY DIFFRACTION100
2.09-2.160.18441480.17432610X-RAY DIFFRACTION100
2.16-2.230.18451510.17062606X-RAY DIFFRACTION100
2.24-2.320.20181370.17462629X-RAY DIFFRACTION100
2.32-2.430.18051370.17752646X-RAY DIFFRACTION100
2.43-2.560.27421200.18482655X-RAY DIFFRACTION100
2.56-2.720.23471690.18512605X-RAY DIFFRACTION100
2.72-2.930.21041460.18532624X-RAY DIFFRACTION100
2.93-3.220.20591550.17392645X-RAY DIFFRACTION100
3.22-3.690.19481180.16252689X-RAY DIFFRACTION100
3.69-4.650.18511530.1462694X-RAY DIFFRACTION100
4.65-34.020.17311320.17192821X-RAY DIFFRACTION100

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