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- PDB-8jdr: Crystal structure of H405A mLDHD in complex with D-2-hydroxy-3-me... -

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Basic information

Entry
Database: PDB / ID: 8jdr
TitleCrystal structure of H405A mLDHD in complex with D-2-hydroxy-3-methyl-valeric acid
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 / 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 / (2R,3S)-3-methyl-2-oxidanyl-pentanoic acid / Probable D-lactate dehydrogenase, mitochondrial
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.64 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

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Assembly

Deposited unit
A: Probable D-lactate dehydrogenase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,3033
Polymers50,3861
Non-polymers9182
Water6,900383
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)82.471, 101.703, 123.546
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-936-

HOH

21A-958-

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-UEI / (2R,3S)-3-methyl-2-oxidanyl-pentanoic acid / (2R,3S)-2-hydroxy-3-methylpentanoic acid


Mass: 132.158 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H12O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 383 / 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: 52.15 %
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: 1.62→35 Å / Num. obs: 63606 / % possible obs: 96.5 % / Redundancy: 13 % / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.054 / Rpim(I) all: 0.016 / Rrim(I) all: 0.056 / Χ2: 0.637 / Net I/σ(I): 7.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.62-1.6810.80.27441970.9770.9940.0860.2870.49964.3
1.68-1.7512.90.2265130.9860.9970.0630.2290.546100
1.75-1.8213.30.17565380.9910.9980.050.1820.573100
1.82-1.92130.13565490.9940.9990.0390.140.619100
1.92-2.0413.20.10265540.9970.9990.0290.1060.659100
2.04-2.213.20.0865500.9970.9990.0230.0840.723100
2.2-2.42130.06766040.99810.0190.0690.724100
2.42-2.7713.50.05665830.99910.0160.0580.686100
2.77-3.4913.30.04366520.99910.0120.0450.682100
3.49-3512.60.03268660.99910.0090.0330.587100

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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: 1.64→34.3 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 16.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1802 2000 3.15 %
Rwork0.1632 --
obs0.1638 63578 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.64→34.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3413 0 62 383 3858
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073543
X-RAY DIFFRACTIONf_angle_d1.0584829
X-RAY DIFFRACTIONf_dihedral_angle_d10.887489
X-RAY DIFFRACTIONf_chiral_restr0.064555
X-RAY DIFFRACTIONf_plane_restr0.007630
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.64-1.680.22231390.16364263X-RAY DIFFRACTION98
1.68-1.730.18521410.15544386X-RAY DIFFRACTION100
1.73-1.780.19931420.1524328X-RAY DIFFRACTION100
1.78-1.840.20881410.15684379X-RAY DIFFRACTION100
1.84-1.90.1831420.1594344X-RAY DIFFRACTION100
1.9-1.980.19081410.15914373X-RAY DIFFRACTION100
1.98-2.070.18091430.14994397X-RAY DIFFRACTION100
2.07-2.180.18741420.154381X-RAY DIFFRACTION100
2.18-2.310.19721430.16074403X-RAY DIFFRACTION100
2.31-2.490.17021440.16524404X-RAY DIFFRACTION100
2.49-2.740.20421430.17144406X-RAY DIFFRACTION100
2.74-3.140.17521430.17044430X-RAY DIFFRACTION100
3.14-3.950.14631470.16014487X-RAY DIFFRACTION100
3.95-34.30.17871490.1734597X-RAY DIFFRACTION99

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