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- PDB-8jdn: Crystal structure of H405A mLDHD in complex with D-2-hydroxyvaler... -

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Basic information

Entry
Database: PDB / ID: 8jdn
TitleCrystal structure of H405A mLDHD in complex with D-2-hydroxyvaleric 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
FLAVIN-ADENINE DINUCLEOTIDE / (2R)-2-oxidanylpentanoic acid / Probable D-lactate dehydrogenase, mitochondrial
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.56 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)51,2893
Polymers50,3861
Non-polymers9042
Water6,828379
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)81.464, 103.095, 122.608
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-605-

HOH

21A-914-

HOH

31A-967-

HOH

41A-975-

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-UE3 / (2R)-2-oxidanylpentanoic acid / (2R)-2-hydroxypentanoic acid


Mass: 118.131 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H10O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 379 / 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: 51.85 %
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: 1.56→67.85 Å / Num. obs: 72530 / % possible obs: 98.3 % / Redundancy: 7.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.061 / Rpim(I) all: 0.022 / Rrim(I) all: 0.065 / Χ2: 0.93 / Net I/σ(I): 19 / Num. measured all: 526815
Reflection shellResolution: 1.56→1.64 Å / % possible obs: 88.8 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.474 / Num. measured all: 33311 / Num. unique obs: 9484 / CC1/2: 0.789 / Rpim(I) all: 0.27 / Rrim(I) all: 0.55 / Χ2: 0.74 / Net I/σ(I) obs: 2.9

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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: 1.56→37.99 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1897 3609 4.98 %
Rwork0.1717 --
obs0.1726 72512 98.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.56→37.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3413 0 61 379 3853
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073542
X-RAY DIFFRACTIONf_angle_d1.0774827
X-RAY DIFFRACTIONf_dihedral_angle_d10.829490
X-RAY DIFFRACTIONf_chiral_restr0.062554
X-RAY DIFFRACTIONf_plane_restr0.007630
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.56-1.580.27031000.24142240X-RAY DIFFRACTION83
1.58-1.60.23311380.22842337X-RAY DIFFRACTION87
1.6-1.620.24371240.22222410X-RAY DIFFRACTION91
1.62-1.650.27691510.21632488X-RAY DIFFRACTION95
1.65-1.670.24641350.20952627X-RAY DIFFRACTION98
1.67-1.70.24161170.19092712X-RAY DIFFRACTION100
1.7-1.730.23061520.18922698X-RAY DIFFRACTION100
1.73-1.760.2281290.17812656X-RAY DIFFRACTION100
1.76-1.80.21761510.18112657X-RAY DIFFRACTION100
1.8-1.830.19441330.18262677X-RAY DIFFRACTION100
1.83-1.870.18171440.18292692X-RAY DIFFRACTION100
1.87-1.920.18621250.17842671X-RAY DIFFRACTION100
1.92-1.960.21460.18252673X-RAY DIFFRACTION100
1.96-2.020.22731380.18022689X-RAY DIFFRACTION100
2.02-2.080.16931500.17172681X-RAY DIFFRACTION100
2.08-2.140.18791350.1752711X-RAY DIFFRACTION100
2.14-2.220.17541430.172670X-RAY DIFFRACTION100
2.22-2.310.19521660.17632679X-RAY DIFFRACTION100
2.31-2.410.2061410.17132700X-RAY DIFFRACTION100
2.41-2.540.21151270.18372708X-RAY DIFFRACTION100
2.54-2.70.20771460.17482697X-RAY DIFFRACTION100
2.7-2.910.17431460.18052730X-RAY DIFFRACTION100
2.91-3.20.1751340.17182729X-RAY DIFFRACTION100
3.2-3.660.19631430.16222732X-RAY DIFFRACTION100
3.66-4.610.1661320.14292778X-RAY DIFFRACTION100
4.61-37.990.1661630.16532861X-RAY DIFFRACTION100

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