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- PDB-8jdb: Crystal structure of H405A mLDHD in complex with D-2-hydroxyoctan... -

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Basic information

Entry
Database: PDB / ID: 8jdb
TitleCrystal structure of H405A mLDHD in complex with D-2-hydroxyoctanoic 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)-2-oxidanyloctanoic acid / Probable D-lactate dehydrogenase, mitochondrial
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 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)51,3323
Polymers50,3861
Non-polymers9462
Water7,548419
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)81.064, 103.112, 122.104
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-622-

HOH

21A-923-

HOH

31A-986-

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-UIT / (2R)-2-oxidanyloctanoic acid


Mass: 160.211 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H16O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 419 / 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: 2.53 Å3/Da / Density % sol: 51.42 %
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: 1.75→35 Å / Num. obs: 51748 / % possible obs: 100 % / Redundancy: 13.1 % / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.017 / Rrim(I) all: 0.062 / Χ2: 0.888 / Net I/σ(I): 7.4 / Num. measured all: 679102
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2
1.75-1.8113.30.2850880.9810.9950.0790.2910.618
1.81-1.8912.90.22551330.9870.9970.0650.2340.687
1.89-1.9713.10.18250950.990.9980.0520.1890.787
1.97-2.0713.50.14151700.9940.9980.040.1470.907
2.07-2.213.10.11451140.9950.9990.0330.1191.008
2.2-2.37130.09751550.9960.9990.0280.1011.061
2.37-2.6113.40.0851720.9980.9990.0230.0831.006
2.61-2.9913.20.06551980.99810.0190.0681.015
2.99-3.7713.30.0552100.99910.0140.0521.028
3.77-3512.40.03754130.99910.0110.0380.748

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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: 1.75→33.77 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 17.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1816 2000 3.87 %
Rwork0.159 --
obs0.1598 51719 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.75→33.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3413 0 64 419 3896
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073564
X-RAY DIFFRACTIONf_angle_d1.0164856
X-RAY DIFFRACTIONf_dihedral_angle_d13.669496
X-RAY DIFFRACTIONf_chiral_restr0.06556
X-RAY DIFFRACTIONf_plane_restr0.007634
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.790.19131400.16723467X-RAY DIFFRACTION99
1.79-1.840.20321400.1683513X-RAY DIFFRACTION100
1.84-1.90.21791410.16133497X-RAY DIFFRACTION100
1.9-1.960.22941420.16283525X-RAY DIFFRACTION100
1.96-2.030.20341420.15833535X-RAY DIFFRACTION100
2.03-2.110.18481430.15673536X-RAY DIFFRACTION100
2.11-2.210.19281410.15653506X-RAY DIFFRACTION100
2.21-2.320.21141420.1663543X-RAY DIFFRACTION100
2.32-2.470.1981430.16633539X-RAY DIFFRACTION100
2.47-2.660.18211430.17183564X-RAY DIFFRACTION100
2.66-2.920.17861430.17753566X-RAY DIFFRACTION100
2.92-3.350.20481450.16533586X-RAY DIFFRACTION100
3.35-4.220.1591460.14313620X-RAY DIFFRACTION100
4.22-33.770.15281490.14943722X-RAY DIFFRACTION99

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