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- PDB-3vpg: L-lactate dehydrogenase from Thermus caldophilus GK24 -

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Basic information

Entry
Database: PDB / ID: 3vpg
TitleL-lactate dehydrogenase from Thermus caldophilus GK24
ComponentsL-lactate dehydrogenase
KeywordsOXIDOREDUCTASE / Rossmann fold / Dehydrogenase
Function / homology
Function and homology information


L-lactate dehydrogenase / L-lactate dehydrogenase activity / glycolytic process / 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 speciesThermus caldophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsArai, K. / Ohno, T. / Miyanaga, A. / Fushinobu, S. / Taguchi, H.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: The core of allosteric motion in Thermus caldophilus L-lactate dehydrogenase.
Authors: Ikehara, Y. / Arai, K. / Furukawa, N. / Ohno, T. / Miyake, T. / Fushinobu, S. / Nakajima, M. / Miyanaga, A. / Taguchi, H.
History
DepositionMar 1, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 6, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 8, 2014Group: Database references
Revision 1.2Nov 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)131,4636
Polymers131,2784
Non-polymers1842
Water14,322795
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10730 Å2
ΔGint-65 kcal/mol
Surface area46560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.240, 135.073, 85.877
Angle α, β, γ (deg.)90.00, 94.44, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 32819.578 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus caldophilus (bacteria) / Gene: ldh / Production host: Escherichia coli (E. coli) / References: UniProt: P06150, L-lactate dehydrogenase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 795 / 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: 2.39 Å3/Da / Density % sol: 48.52 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 2-(N-monorpholino)ethanesulfonic acid, polyethyleneglycol 6000, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 0.978 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 5, 2001
RadiationMonochromator: Triangular Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.8→29.2 Å / Num. obs: 111821 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 18.7 Å2
Reflection shellResolution: 1.8→1.9 Å / % possible all: 96.9

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
CNSrefinement
MOSFLMdata reduction
SCALAdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2LDB

2ldb


Resolution: 1.8→29.19 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 2346171.61 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.227 5621 5 %RANDOM
Rwork0.191 ---
obs0.191 111821 98.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 47.9062 Å2 / ksol: 0.350139 e/Å3
Displacement parametersBiso mean: 25.1 Å2
Baniso -1Baniso -2Baniso -3
1--0.94 Å20 Å22.17 Å2
2--0.76 Å20 Å2
3---0.18 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.15 Å0.1 Å
Refinement stepCycle: LAST / Resolution: 1.8→29.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9256 0 12 795 10063
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
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_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.79
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it3.11.5
X-RAY DIFFRACTIONc_mcangle_it3.652
X-RAY DIFFRACTIONc_scbond_it4.892
X-RAY DIFFRACTIONc_scangle_it6.42.5
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.26 922 5 %
Rwork0.223 17391 -
obs--96.9 %
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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