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- PDB-8jdd: Crystal structure of H405A mLDHD in apo form -

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Basic information

Entry
Database: PDB / ID: 8jdd
TitleCrystal structure of H405A mLDHD in apo form
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 / D-lactate dehydrogenase activity / Mitochondrial protein import / ATP biosynthetic process / Mitochondrial protein degradation / FAD binding / flavin adenine dinucleotide 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 / Probable D-lactate dehydrogenase, mitochondrial
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 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 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)51,1712
Polymers50,3861
Non-polymers7861
Water6,792377
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)80.970, 103.400, 122.180
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-644-

HOH

21A-924-

HOH

31A-968-

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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 377 / 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: 51.53 %
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: 1.55→63.75 Å / Num. obs: 73286 / % possible obs: 98.5 % / Redundancy: 11 % / CC1/2: 0.999 / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.018 / Rrim(I) all: 0.064 / Χ2: 0.91 / Net I/σ(I): 21.4 / Num. measured all: 806063
Reflection shellResolution: 1.55→1.59 Å / % possible obs: 87.9 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.613 / Num. measured all: 21550 / Num. unique obs: 4764 / CC1/2: 0.721 / Rpim(I) all: 0.314 / Rrim(I) all: 0.695 / Χ2: 0.57 / Net I/σ(I) obs: 2.7

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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: 1.55→29.75 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 18.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1869 3664 5 %
Rwork0.1704 --
obs0.1712 73278 98.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.55→29.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3413 0 53 377 3843
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073554
X-RAY DIFFRACTIONf_angle_d1.0454845
X-RAY DIFFRACTIONf_dihedral_angle_d13.546492
X-RAY DIFFRACTIONf_chiral_restr0.062555
X-RAY DIFFRACTIONf_plane_restr0.007633
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.570.25951160.24772332X-RAY DIFFRACTION86
1.57-1.590.24871350.21972384X-RAY DIFFRACTION89
1.59-1.610.24961410.21442473X-RAY DIFFRACTION92
1.61-1.640.2281470.20032546X-RAY DIFFRACTION95
1.64-1.660.21011430.19452632X-RAY DIFFRACTION97
1.66-1.690.20541150.18792719X-RAY DIFFRACTION99
1.69-1.720.21081450.17662674X-RAY DIFFRACTION100
1.72-1.750.21311370.17572699X-RAY DIFFRACTION100
1.75-1.790.21141450.17732688X-RAY DIFFRACTION100
1.79-1.820.22061410.17892703X-RAY DIFFRACTION100
1.82-1.860.20281440.19212694X-RAY DIFFRACTION100
1.86-1.910.20141350.17722715X-RAY DIFFRACTION100
1.91-1.950.20071390.18022707X-RAY DIFFRACTION100
1.95-2.010.20941430.17832689X-RAY DIFFRACTION100
2.01-2.060.17561440.17232706X-RAY DIFFRACTION100
2.06-2.130.18331460.17122727X-RAY DIFFRACTION100
2.13-2.210.17731380.16762685X-RAY DIFFRACTION100
2.21-2.30.18161610.182738X-RAY DIFFRACTION100
2.3-2.40.22071450.17252697X-RAY DIFFRACTION100
2.4-2.530.20871320.17792749X-RAY DIFFRACTION100
2.53-2.680.20461510.18372707X-RAY DIFFRACTION100
2.68-2.890.1971490.18792756X-RAY DIFFRACTION100
2.89-3.180.18881320.17912743X-RAY DIFFRACTION100
3.18-3.640.19511400.15992770X-RAY DIFFRACTION100
3.64-4.590.15591350.14222792X-RAY DIFFRACTION100
4.59-29.750.15381650.1592889X-RAY DIFFRACTION100

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