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- PDB-3wsv: Crystal structure of minor L-lactate dehydrogenase from Enterococ... -

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Basic information

Entry
Database: PDB / ID: 3wsv
TitleCrystal structure of minor L-lactate dehydrogenase from Enterococcus mundtii in the ligands-unbound form
ComponentsL-lactate dehydrogenase
KeywordsOXIDOREDUCTASE / dehydrogenase
Function / homology
Function and homology information


L-lactate dehydrogenase / L-lactate dehydrogenase activity / glycolytic process / nucleotide binding / cytoplasm
Similarity search - Function
L-lactate dehydrogenase / L-lactate dehydrogenase active site. / L-lactate dehydrogenase, active site / L-2-Hydroxyisocaproate Dehydrogenase; Chain A, domain 2 / Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal / 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 ...L-lactate dehydrogenase / L-lactate dehydrogenase active site. / L-lactate dehydrogenase, active site / L-2-Hydroxyisocaproate Dehydrogenase; Chain A, domain 2 / Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal / 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 Rossmann-like Domain / NAD(P)-binding domain superfamily / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
L-lactate dehydrogenase
Similarity search - Component
Biological speciesEnterococcus mundtii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.38 Å
AuthorsMatoba, Y. / Sugiyama, M.
CitationJournal: Febs Open Bio / Year: 2014
Title: An alternative allosteric regulation mechanism of an acidophilic l-lactate dehydrogenase from Enterococcus mundtii 15-1A.
Authors: Matoba, Y. / Miyasako, M. / Matsuo, K. / Oda, K. / Noda, M. / Higashikawa, F. / Kumagai, T. / Sugiyama, M.
History
DepositionMar 27, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 10, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 1, 2014Group: Database references
Revision 1.2Jan 1, 2020Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
C: L-lactate dehydrogenase
D: L-lactate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,38912
Polymers141,6524
Non-polymers7378
Water7,350408
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15810 Å2
ΔGint-21 kcal/mol
Surface area45640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.430, 127.820, 133.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
L-lactate dehydrogenase


Mass: 35413.043 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus mundtii (bacteria) / Strain: 15-1A / Plasmid: pET-21a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: V5XPB8*PLUS, L-lactate dehydrogenase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 408 / Source method: isolated from a natural source / Formula: H2O

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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: 3.15 Å3/Da / Density % sol: 60.98 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.2
Details: 7% PEG 20000, 0.1M Mes-NaOH, pH 6.2, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Jun 26, 2009
RadiationMonochromator: Fixed exit Si double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.38→100 Å / Num. all: 71995 / Num. obs: 71995 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Biso Wilson estimate: 34.6 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 27.2
Reflection shellResolution: 2.38→2.47 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.409 / Mean I/σ(I) obs: 2.5 / Num. unique all: 6885 / % possible all: 96.3

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Processing

Software
NameVersionClassification
BSSdata collection
MOLREPphasing
CNS1.2refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1LDN

1ldn


Resolution: 2.38→29.96 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 2888756.6 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.271 3534 5.1 %RANDOM
Rwork0.232 ---
obs0.232 69778 96.4 %-
all-69778 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 48.6613 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 57.5 Å2
Baniso -1Baniso -2Baniso -3
1-6.26 Å20 Å20 Å2
2--16.04 Å20 Å2
3----22.3 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.4 Å0.38 Å
Refinement stepCycle: LAST / Resolution: 2.38→29.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9682 0 48 408 10138
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.72
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.551.5
X-RAY DIFFRACTIONc_mcangle_it2.652
X-RAY DIFFRACTIONc_scbond_it2.062
X-RAY DIFFRACTIONc_scangle_it3.132.5
LS refinement shellResolution: 2.38→2.53 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.362 515 4.7 %
Rwork0.337 10550 -
obs--92.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3gol.paramgol.top

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