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- PDB-8qde: Crystal structure of a truncated human L-Lactate Dehydrogenase B ... -

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Basic information

Entry
Database: PDB / ID: 8qde
TitleCrystal structure of a truncated human L-Lactate Dehydrogenase B protein in complex with NADH and oxamate
ComponentsL-lactate dehydrogenase B chain
KeywordsOXIDOREDUCTASE / Complex / Truncated protein
Function / homology
Function and homology information


L-lactate dehydrogenase / oxidoreductase complex / pyruvate metabolic process / L-lactate dehydrogenase (NAD+) activity / NAD+ metabolic process / Pyruvate metabolism / lactate metabolic process / kinase binding / NAD binding / mitochondrial inner membrane ...L-lactate dehydrogenase / oxidoreductase complex / pyruvate metabolic process / L-lactate dehydrogenase (NAD+) activity / NAD+ metabolic process / Pyruvate metabolism / lactate metabolic process / kinase binding / NAD binding / mitochondrial inner membrane / membrane raft / mitochondrion / extracellular exosome / identical protein binding / membrane / cytoplasm / cytosol
Similarity search - Function
L-lactate dehydrogenase / L-lactate dehydrogenase active site. / L-lactate dehydrogenase, active site / L-lactate/malate dehydrogenase / Lactate/malate dehydrogenase, N-terminal / Lactate/malate dehydrogenase, C-terminal / lactate/malate dehydrogenase, NAD binding domain / lactate/malate dehydrogenase, alpha/beta C-terminal domain / Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / OXAMIC ACID / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / L-lactate dehydrogenase B chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.98 Å
AuthorsVan Gysel, M. / Wouters, J.
Funding support Belgium, 1items
OrganizationGrant numberCountry
Fonds National de la Recherche Scientifique (FNRS) Belgium
CitationJournal: To Be Published
Title: Crystal structure of a truncated human L-Lactate Dehydrogenase B protein in complex with NADH and oxamate
Authors: Van Gysel, M. / Wouters, J.
History
DepositionAug 29, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 11, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: L-lactate dehydrogenase B chain
B: L-lactate dehydrogenase B chain
C: L-lactate dehydrogenase B chain
D: L-lactate dehydrogenase B chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,68423
Polymers146,4374
Non-polymers4,24719
Water2,126118
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: assay for oligomerization
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22500 Å2
ΔGint-186 kcal/mol
Surface area44450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.530, 85.660, 207.100
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
L-lactate dehydrogenase B chain


Mass: 36609.156 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LDHB / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P07195

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Non-polymers , 6 types, 137 molecules

#2: Chemical
ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH


Mass: 665.441 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H29N7O14P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-OXM / OXAMIC ACID


Mass: 89.050 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3NO3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O4
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 118 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.17 Å3/Da / Density % sol: 43.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2M Lithium sulfate, 0.1M sodium acetate pH 4.5, 50% (v/v) PEG 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 2, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.98→44.31 Å / Num. obs: 26832 / % possible obs: 99.91 % / Redundancy: 13.5 % / Biso Wilson estimate: 63.72 Å2 / CC1/2: 0.995 / CC star: 0.999 / Rpim(I) all: 0.09164 / Rrim(I) all: 0.3387 / Net I/σ(I): 10.69
Reflection shellResolution: 2.98→3.087 Å / Redundancy: 13.8 % / Mean I/σ(I) obs: 1.76 / Num. unique obs: 2626 / CC1/2: 0.613 / CC star: 0.872 / Rpim(I) all: 0.4548 / Rrim(I) all: 1.697 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
MxCuBEdata collection
Coot0.9.4.1model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.98→44.31 Å / SU ML: 0.3836 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.685
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.31 1341 5 %
Rwork0.2308 25491 -
obs0.2346 26832 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 61.41 Å2
Refinement stepCycle: LAST / Resolution: 2.98→44.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9691 0 272 118 10081
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002410122
X-RAY DIFFRACTIONf_angle_d0.626413726
X-RAY DIFFRACTIONf_chiral_restr0.04251615
X-RAY DIFFRACTIONf_plane_restr0.00271689
X-RAY DIFFRACTIONf_dihedral_angle_d7.90341368
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.98-3.080.37211300.28712457X-RAY DIFFRACTION98.29
3.08-3.210.38931330.28692519X-RAY DIFFRACTION100
3.21-3.350.36121310.28062493X-RAY DIFFRACTION100
3.35-3.530.35711320.24962520X-RAY DIFFRACTION100
3.53-3.750.33441340.23572537X-RAY DIFFRACTION100
3.75-4.040.34221330.22482528X-RAY DIFFRACTION100
4.04-4.440.28711340.19752559X-RAY DIFFRACTION99.96
4.44-5.090.28421360.20542569X-RAY DIFFRACTION100
5.09-6.40.28761360.23832585X-RAY DIFFRACTION99.93
6.41-44.310.26331420.21942724X-RAY DIFFRACTION99.69

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