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- PDB-8jdp: Crystal structure of H405A mLDHD in complex with D-2-hydroxyisova... -

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Basic information

Entry
Database: PDB / ID: 8jdp
TitleCrystal structure of H405A mLDHD in complex with D-2-hydroxyisovaleric 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 / DEAMINOHYDROXYVALINE / Probable D-lactate dehydrogenase, mitochondrial
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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
Water6,539363
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)81.820, 102.530, 122.930
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-935-

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-VAD / DEAMINOHYDROXYVALINE


Type: L-peptide linking / 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.: 363 / 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: 2.56 Å3/Da / Density % sol: 51.92 %
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: 1.6→39.37 Å / Num. obs: 67254 / % possible obs: 98.5 % / Redundancy: 11.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.018 / Rrim(I) all: 0.065 / Χ2: 0.95 / Net I/σ(I): 26.3 / Num. measured all: 788985
Reflection shellResolution: 1.6→1.64 Å / % possible obs: 86.8 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.436 / Num. measured all: 27145 / Num. unique obs: 4302 / CC1/2: 0.843 / Rpim(I) all: 0.187 / Rrim(I) all: 0.479 / Χ2: 0.66 / Net I/σ(I) obs: 6.1

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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: 1.6→29.81 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1854 3228 4.8 %
Rwork0.1716 --
obs0.1723 67249 98.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.6→29.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3409 0 61 363 3833
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053542
X-RAY DIFFRACTIONf_angle_d0.9584828
X-RAY DIFFRACTIONf_dihedral_angle_d10.789489
X-RAY DIFFRACTIONf_chiral_restr0.056554
X-RAY DIFFRACTIONf_plane_restr0.007630
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.620.20311020.19362381X-RAY DIFFRACTION85
1.62-1.650.21791320.18772467X-RAY DIFFRACTION89
1.65-1.680.2121290.18572617X-RAY DIFFRACTION94
1.68-1.710.19111500.18072759X-RAY DIFFRACTION98
1.71-1.740.20531490.17162766X-RAY DIFFRACTION100
1.74-1.770.20341480.17822793X-RAY DIFFRACTION100
1.77-1.810.21771360.1752803X-RAY DIFFRACTION100
1.81-1.840.21421370.18082812X-RAY DIFFRACTION100
1.84-1.890.19011460.18362774X-RAY DIFFRACTION100
1.89-1.940.24091310.18082843X-RAY DIFFRACTION100
1.94-1.990.19671490.18772797X-RAY DIFFRACTION100
1.99-2.050.21911340.17562826X-RAY DIFFRACTION100
2.05-2.110.19291540.17282789X-RAY DIFFRACTION100
2.11-2.190.16551410.16422846X-RAY DIFFRACTION100
2.19-2.270.17931620.17562782X-RAY DIFFRACTION100
2.27-2.380.1981310.17682831X-RAY DIFFRACTION100
2.38-2.50.21221460.17832839X-RAY DIFFRACTION100
2.5-2.660.20111260.18172835X-RAY DIFFRACTION100
2.66-2.870.18831370.17932855X-RAY DIFFRACTION100
2.87-3.150.18121490.17612842X-RAY DIFFRACTION100
3.15-3.610.16691310.16442884X-RAY DIFFRACTION100
3.61-4.550.15051600.14562875X-RAY DIFFRACTION100
4.55-29.810.18881480.17423005X-RAY DIFFRACTION100

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