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- PDB-7nay: Crystal structure of lactate dehydrogenase from Selenomonas rumin... -

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Basic information

Entry
Database: PDB / ID: 7nay
TitleCrystal structure of lactate dehydrogenase from Selenomonas ruminantium with NADH.
ComponentsL-lactate dehydrogenase
KeywordsOXIDOREDUCTASE / SELENOMONAS RUMINANTIUM / LACTATE DEHYDROGENASE / NADH
Function / homology
Function and homology information


L-lactate dehydrogenase / L-lactate dehydrogenase (NAD+) activity / lactate metabolic process / cytoplasm
Similarity search - Function
L-lactate dehydrogenase / 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
BORIC ACID / MALONIC ACID / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / L-lactate dehydrogenase
Similarity search - Component
Biological speciesSelenomonas ruminantium (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.84 Å
AuthorsBertrand, Q. / Robin, A. / Girard, E. / Madern, D.
Funding support France, 1items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR) France
CitationJournal: J.Struct.Biol. / Year: 2023
Title: Biochemical, structural and dynamical characterizations of the lactate dehydrogenase from Selenomonas ruminantium provide information about an intermediate evolutionary step prior to complete ...Title: Biochemical, structural and dynamical characterizations of the lactate dehydrogenase from Selenomonas ruminantium provide information about an intermediate evolutionary step prior to complete allosteric regulation acquisition in the super family of lactate and malate dehydrogenases.
Authors: Bertrand, Q. / Coquille, S. / Iorio, A. / Sterpone, F. / Madern, D.
History
DepositionJan 25, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 10, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Mar 20, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: L-lactate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,70813
Polymers35,9261
Non-polymers1,78212
Water5,188288
1
A: L-lactate dehydrogenase
hetero molecules

A: L-lactate dehydrogenase
hetero molecules

A: L-lactate dehydrogenase
hetero molecules

A: L-lactate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,83252
Polymers143,7034
Non-polymers7,12848
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_555x,-y,-z1
Buried area33960 Å2
ΔGint-36 kcal/mol
Surface area37010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.750, 104.260, 110.940
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-561-

HOH

21A-740-

HOH

31A-746-

HOH

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 35925.844 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Presence of 2 modified cysteines that are appearing during crystallisation process. Confirmed by Mass spectrometry on dissolved crystals.
Source: (gene. exp.) Selenomonas ruminantium (bacteria) / Gene: ldh, ldhL / Production host: Escherichia coli (E. coli) / References: UniProt: Q9EVR0, L-lactate dehydrogenase

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Non-polymers , 6 types, 300 molecules

#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical ChemComp-MLA / MALONIC ACID / DICARBOXYLIC ACID C3 / PROPANEDIOLIC ACID / METHANEDICARBOXYLIC ACID


Mass: 104.061 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H4O4
#4: Chemical ChemComp-BO3 / BORIC ACID


Mass: 61.833 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: BH3O3
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 288 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 51.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 21 % PEG 1500 150 mM Malonate-Imidazole-Boric Acid pH 5 (MIB-PACT) 10 mM Sodium Bicarbonate pH 8 10 mM Tb-XO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: Xenocs GeniX 3D Cu HF / Wavelength: 1.54179 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Dec 9, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54179 Å / Relative weight: 1
ReflectionResolution: 1.84→38.61 Å / Num. obs: 31954 / % possible obs: 99.9 % / Redundancy: 5.6 % / CC1/2: 0.99 / Net I/σ(I): 12.17
Reflection shellResolution: 1.84→1.95 Å / Redundancy: 5.3 % / Num. unique obs: 5035 / CC1/2: 0.83 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
XDS20200417data reduction
XDS20200417data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3D0O

3d0o


Resolution: 1.84→38.61 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.947 / SU B: 2.69 / SU ML: 0.079 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.117 / ESU R Free: 0.116 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.188 3196 10 %RANDOM
Rwork0.145 ---
obs0.149 28758 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 75.68 Å2 / Biso mean: 18.2 Å2 / Biso min: 8.58 Å2
Baniso -1Baniso -2Baniso -3
1--1.3 Å20 Å20 Å2
2--0.9 Å20 Å2
3---0.41 Å2
Refinement stepCycle: final / Resolution: 1.84→38.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2496 0 103 288 2887
Biso mean--23.84 31.99 -
Num. residues----322
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0132760
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172588
X-RAY DIFFRACTIONr_angle_refined_deg1.5961.6463741
X-RAY DIFFRACTIONr_angle_other_deg1.4511.5825980
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8755346
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.61422.955132
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.1615466
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.7761514
X-RAY DIFFRACTIONr_chiral_restr0.0840.2373
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023144
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02595
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_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.84→1.89 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.282 233 -
Rwork0.251 2095 -
all-2328 -
obs--99.83 %

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