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- PDB-9jlo: Crystal structure L-lactate dehydrogenase from Lactobacillus reut... -

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Basic information

Entry
Database: PDB / ID: 9jlo
TitleCrystal structure L-lactate dehydrogenase from Lactobacillus reuteri in its apoform
ComponentsL-lactate dehydrogenase
KeywordsOXIDOREDUCTASE / LDH / LreLLDH / L-lactate dehydrogenase / apoform
Function / homology
Function and homology information


L-lactate dehydrogenase / L-lactate dehydrogenase (NAD+) activity / lactate metabolic process / glycolytic process / cytoplasm
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
L-lactate dehydrogenase
Similarity search - Component
Biological speciesLimosilactobacillus reuteri (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsMatyuta, I.O. / Minyaev, M.E. / Shirokova, A.A. / Pometun, A.A. / Tishkov, V.I. / Popov, V.O. / Boyko, K.M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Novel extremely stable and active lactate dehydrogenase from l reuteri: structure-function studies and promising usage as an agent against pathogenic biofilms
Authors: Pometun, A.A. / Shirokova, A.A. / Boyko, K.M. / Matyuta, I.O. / Shaposhnikov, L.A. / Atroshenko, D.L. / Pometun, E.V. / Ageevets, V. / Kleimenov, S.Y. / Popov, V.O. / Tishkov, V.I.
History
DepositionSep 19, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 2, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: L-lactate dehydrogenase
B: L-lactate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,64010
Polymers68,1442
Non-polymers4978
Water1,67593
1
A: L-lactate dehydrogenase
B: L-lactate dehydrogenase
hetero molecules

A: L-lactate dehydrogenase
B: L-lactate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,28020
Polymers136,2874
Non-polymers99316
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565x,-y+1,-z1
Buried area18140 Å2
ΔGint-24 kcal/mol
Surface area41560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.521, 93.124, 101.517
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein L-lactate dehydrogenase / L-LDH


Mass: 34071.766 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Limosilactobacillus reuteri (bacteria) / Gene: ldh, B1A73_02515, lr1918 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A4L2V5, L-lactate dehydrogenase
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 93 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 2.65 Å3/Da / Density % sol: 53.57 %
Crystal growTemperature: 288 K / Method: vapor diffusion, sitting drop
Details: 1% w/v Tryptone, 0.001 M Sodium azide, 0.05 M HEPES sodium pH 7.0, 12% w/v Polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54184 Å
DetectorType: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Apr 21, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54184 Å / Relative weight: 1
ReflectionResolution: 2.15→22.26 Å / Num. obs: 40098 / % possible obs: 99.8 % / Redundancy: 7.7 % / CC1/2: 0.981 / Rmerge(I) obs: 0.273 / Rpim(I) all: 0.105 / Rrim(I) all: 0.293 / Χ2: 1.01 / Net I/σ(I): 5.4
Reflection shellResolution: 2.15→2.22 Å / % possible obs: 99.6 % / Redundancy: 6.1 % / Rmerge(I) obs: 0.814 / Num. measured all: 20819 / Num. unique obs: 3403 / CC1/2: 0.805 / Rpim(I) all: 0.351 / Rrim(I) all: 0.889 / Χ2: 0.92 / Net I/σ(I) obs: 1.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
Aimlessdata scaling
CrysalisProdata reduction
MOLREPphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6J9S

6j9s


Resolution: 2.15→22.26 Å / Cor.coef. Fo:Fc: 0.874 / Cor.coef. Fo:Fc free: 0.831 / SU B: 5.004 / SU ML: 0.136 / Cross valid method: THROUGHOUT / ESU R: 0.057 / ESU R Free: 0.046 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28259 1902 4.8 %RANDOM
Rwork0.24449 ---
obs0.2463 38022 78.09 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.039 Å2
Baniso -1Baniso -2Baniso -3
1--29.34 Å2-0 Å2-0 Å2
2--27.69 Å20 Å2
3---1.65 Å2
Refinement stepCycle: 1 / Resolution: 2.15→22.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4631 0 41 93 4765
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0134754
X-RAY DIFFRACTIONr_bond_other_d0.0030.0164646
X-RAY DIFFRACTIONr_angle_refined_deg2.1321.6366429
X-RAY DIFFRACTIONr_angle_other_deg1.3411.58610689
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.755634
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.43524.299214
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.41315810
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.151521
X-RAY DIFFRACTIONr_chiral_restr0.1050.2651
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.025437
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02961
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.862.3222521
X-RAY DIFFRACTIONr_mcbond_other2.862.3222520
X-RAY DIFFRACTIONr_mcangle_it3.9053.4783148
X-RAY DIFFRACTIONr_mcangle_other3.9043.4793149
X-RAY DIFFRACTIONr_scbond_it2.7292.4292233
X-RAY DIFFRACTIONr_scbond_other2.7282.4292234
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.8083.5883278
X-RAY DIFFRACTIONr_long_range_B_refined5.20227.8115035
X-RAY DIFFRACTIONr_long_range_B_other5.18927.8125028
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 9086 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.11 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.15→2.22 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0 0 -
Rwork0 0 -
obs--0 %

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