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- PDB-8jdo: Crystal structure of H405A mLDHD in complex with D-2-hydroxyhexan... -

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Basic information

Entry
Database: PDB / ID: 8jdo
TitleCrystal structure of H405A mLDHD in complex with D-2-hydroxyhexanoic 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 / 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
(2R)-2-hydroxyhexanoic acid / FLAVIN-ADENINE DINUCLEOTIDE / Probable D-lactate dehydrogenase, mitochondrial
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.72 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
Water7,368409
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)81.378, 102.945, 122.357
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-931-

HOH

21A-969-

HOH

31A-984-

HOH

41A-1000-

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-7N6 / (2R)-2-hydroxyhexanoic acid


Mass: 132.158 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H12O3 / Feature type: SUBJECT OF INVESTIGATION
#3: 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 409 / 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: 51.63 %
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: 1.72→35 Å / Num. obs: 54480 / % possible obs: 99.7 % / Redundancy: 13.2 % / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.018 / Rrim(I) all: 0.065 / Χ2: 0.605 / Net I/σ(I): 6.1 / Num. measured all: 719432
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.72-1.7813.60.31253510.9780.9950.0870.3240.47799.2
1.78-1.8513.20.24553670.9840.9960.0690.2550.49699.4
1.85-1.9413.20.18253830.9910.9980.0520.1890.52899.4
1.94-2.0413.30.13754090.9950.9990.0390.1420.5699.6
2.04-2.1713.40.10653810.9960.9990.030.110.60699.7
2.17-2.3313.10.08854280.9970.9990.0250.0910.63999.9
2.33-2.5713.30.07554770.9980.9990.0210.0770.64599.9
2.57-2.9413.20.06254590.99810.0180.0650.674100
2.94-3.713.40.0555300.99910.0140.0520.729100
3.7-3512.50.04156950.99910.0120.0430.694100

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Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874: ???)refinement
HKL-2000data reduction
EVAL15data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.72→33.88 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 17.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1814 2000 3.67 %
Rwork0.1617 --
obs0.1625 54445 99.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.72→33.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3413 0 62 409 3884
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073562
X-RAY DIFFRACTIONf_angle_d1.0924854
X-RAY DIFFRACTIONf_dihedral_angle_d13.66494
X-RAY DIFFRACTIONf_chiral_restr0.069556
X-RAY DIFFRACTIONf_plane_restr0.007634
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.72-1.760.21711400.18323665X-RAY DIFFRACTION99
1.76-1.810.22931400.18033673X-RAY DIFFRACTION99
1.81-1.870.22321410.17463700X-RAY DIFFRACTION100
1.87-1.930.1891410.16123699X-RAY DIFFRACTION99
1.93-1.990.20781430.16543733X-RAY DIFFRACTION100
1.99-2.070.1771410.15683708X-RAY DIFFRACTION100
2.07-2.170.19941410.15643711X-RAY DIFFRACTION100
2.17-2.280.18931430.16123758X-RAY DIFFRACTION100
2.28-2.430.17871430.16553745X-RAY DIFFRACTION100
2.43-2.610.19531430.16923740X-RAY DIFFRACTION100
2.61-2.880.17991440.17453783X-RAY DIFFRACTION100
2.88-3.290.20321440.16823780X-RAY DIFFRACTION100
3.29-4.150.15651460.1473819X-RAY DIFFRACTION100
4.15-33.880.15611500.15553931X-RAY DIFFRACTION99

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