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- PDB-1y6j: L-Lactate Dehydrogenase from Clostridium Thermocellum Cth-1135 -

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Basic information

Entry
Database: PDB / ID: 1y6j
TitleL-Lactate Dehydrogenase from Clostridium Thermocellum Cth-1135
ComponentsL-lactate dehydrogenase
KeywordsOXIDOREDUCTASE / L-Lactate Dehydrogenase / CLOSTRIDIUM THERMOCELLUM / SOUTHEAST COLLABORATORY FOR STRUCTURAL GENOMICS / SECSG / PROTEIN STRUCTURE INITIATIVE / PSI
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 / 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 speciesClostridium thermocellum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.01 Å
AuthorsChen, L. / Yang, H. / Kataeva, I. / Chen, L.R. / Tempel, W. / Lee, D. / Habel, J. / Zhou, W. / Lin, D. / Ljungdahl, L. ...Chen, L. / Yang, H. / Kataeva, I. / Chen, L.R. / Tempel, W. / Lee, D. / Habel, J. / Zhou, W. / Lin, D. / Ljungdahl, L. / Liu, Z.-J. / Rose, J. / Wang, B.-C. / Southeast Collaboratory for Structural Genomics (SECSG)
CitationJournal: To be Published
Title: L-Lactate Dehydrogenase from Clostridium Thermocellum Cth-1135
Authors: Chen, L. / Yang, H. / Kataeva, I. / Chen, L.R. / Tempel, W. / Lee, D. / Habel, J. / Zhou, W. / Lin, D. / Ljungdahl, L. / Liu, Z.-J. / Rose, J. / Wang, B.-C.
History
DepositionDec 6, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 14, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 23, 2023Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: L-lactate dehydrogenase


Theoretical massNumber of molelcules
Total (without water)34,8721
Polymers34,8721
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: L-lactate dehydrogenase

A: L-lactate dehydrogenase


Theoretical massNumber of molelcules
Total (without water)69,7442
Polymers69,7442
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_663-y+1,-x+1,-z-3/21
Buried area3150 Å2
ΔGint-27 kcal/mol
Surface area24020 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)73.360, 73.360, 191.730
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein L-lactate dehydrogenase


Mass: 34872.137 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium thermocellum (bacteria) / Gene: Cth-1135 / Plasmid: pET15G / Production host: Escherichia coli (E. coli)
References: GenBank: 48858109, UniProt: A3DCA4*PLUS, L-lactate dehydrogenase

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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: 3.79 Å3/Da / Density % sol: 67 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 6.5
Details: NaCl, NaH2PO4, KH2PO4, pH 6.5, VAPOR DIFFUSION, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.9794 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 14, 2004
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. all: 11020 / Num. obs: 11020 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 16.6 % / Rmerge(I) obs: 0.131 / Rsym value: 0.131 / Net I/σ(I): 8.9
Reflection shellResolution: 3→3.11 Å / Redundancy: 10.4 % / Rmerge(I) obs: 0.795 / Mean I/σ(I) obs: 1.9 / Num. unique all: 1049 / Rsym value: 0.795 / % possible all: 98.2

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Processing

Software
NameVersionClassification
CNS1refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2LDB

2ldb


Resolution: 3.01→19.9 Å / Rfactor Rfree error: 0.013 / Data cutoff high absF: 274076.72 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.271 467 5.2 %RANDOM
Rwork0.229 ---
all0.252 10662 --
obs0.229 8967 81.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 29.4737 Å2 / ksol: 0.316081 e/Å3
Displacement parametersBiso mean: 68.4 Å2
Baniso -1Baniso -2Baniso -3
1-4.52 Å20 Å20 Å2
2--4.52 Å20 Å2
3----9.03 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.52 Å0.39 Å
Luzzati d res low-5 Å
Luzzati sigma a0.59 Å0.47 Å
Refinement stepCycle: LAST / Resolution: 3.01→19.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2214 0 0 0 2214
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d22.2
X-RAY DIFFRACTIONc_improper_angle_d0.84
X-RAY DIFFRACTIONc_mcbond_it1.411.5
X-RAY DIFFRACTIONc_mcangle_it2.532
X-RAY DIFFRACTIONc_scbond_it1.832
X-RAY DIFFRACTIONc_scangle_it3.032.5
LS refinement shellResolution: 3.01→3.19 Å / Rfactor Rfree error: 0.068 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.402 35 5.1 %
Rwork0.31 651 -
obs-651 38 %
Xplor fileSerial no: 1 / Param file: PROTEIN_REP.PARAM / Topol file: PROTEIN.TOP

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