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- PDB-2v6m: Crystal structure of lactate dehydrogenase from Thermus Thermophi... -

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Basic information

Entry
Database: PDB / ID: 2v6m
TitleCrystal structure of lactate dehydrogenase from Thermus Thermophilus HB8 (Apo form)
ComponentsL-LACTATE DEHYDROGENASE
KeywordsOXIDOREDUCTASE / PHOSPHORYLATION / NAD / LACTATE / CYTOPLASM / GLYCOLYSIS / THERMOPHILE
Function / homology
Function and homology information


L-lactate dehydrogenase / lactate metabolic process / L-lactate dehydrogenase activity / glycolytic process / cytoplasm
Similarity search - Function
L-lactate dehydrogenase active site. / L-lactate dehydrogenase / 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 active site. / L-lactate dehydrogenase / 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 THERMOPHILUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsCoquelle, N. / Fioravanti, E. / Weik, M. / Vellieux, F.
CitationJournal: J. Mol. Biol. / Year: 2007
Title: Activity, stability and structural studies of lactate dehydrogenases adapted to extreme thermal environments.
Authors: Coquelle, N. / Fioravanti, E. / Weik, M. / Vellieux, F. / Madern, D.
History
DepositionJul 19, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 25, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 28, 2018Group: Database references / Source and taxonomy / Category: citation / entity_src_gen
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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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)131,9087
Polymers131,3224
Non-polymers5863
Water9,242513
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13460 Å2
ΔGint-82.2 kcal/mol
Surface area54430 Å2
MethodPQS
Unit cell
Length a, b, c (Å)54.092, 135.296, 85.645
Angle α, β, γ (deg.)90.00, 94.04, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
L-LACTATE DEHYDROGENASE / L-LDH / LACTATE DEHYDROGENASE


Mass: 32830.582 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 / Plasmid: PTTHLDH12 / Production host: Escherichia coli DH5[alpha] (bacteria) / References: UniProt: Q5SJA1, L-lactate dehydrogenase
#2: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 513 / 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: 2.38 Å3/Da / Density % sol: 48.42 % / Description: NONE
Crystal growpH: 6 / Details: 0.1M MES PH 6 15% PEG 6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9393
DetectorType: ADSC CCD / Detector: CCD / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9393 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. obs: 61724 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 3.78 % / Biso Wilson estimate: 20.6 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 12.29
Reflection shellResolution: 2.2→2.25 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 3.38 / % possible all: 99.8

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Processing

Software
NameVersionClassification
CNS1.1refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1LDN

1ldn


Resolution: 2.2→29.22 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 2186103.32 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.218 3087 5 %RANDOM
Rwork0.196 ---
obs0.196 61724 99.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 45.7376 Å2 / ksol: 0.340268 e/Å3
Displacement parametersBiso mean: 33.1 Å2
Baniso -1Baniso -2Baniso -3
1-6.37 Å20 Å24.87 Å2
2---3.08 Å20 Å2
3----3.28 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.25 Å0.22 Å
Refinement stepCycle: LAST / Resolution: 2.2→29.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9084 0 36 513 9633
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
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_d21.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.05
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.831.5
X-RAY DIFFRACTIONc_mcangle_it2.582
X-RAY DIFFRACTIONc_scbond_it2.862
X-RAY DIFFRACTIONc_scangle_it3.942.5
LS refinement shellResolution: 2.2→2.28 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.281 293 5 %
Rwork0.245 5516 -
obs--93.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_JPP.PARAMPROTEIN_JPP.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER_REP.TOP
X-RAY DIFFRACTION3MES.PARAMMES.TOP

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