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- PDB-5yta: Pig Heart Lactate Dehydrogenase in complex with NADH and Oxamate -

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Basic information

Entry
Database: PDB / ID: 5yta
TitlePig Heart Lactate Dehydrogenase in complex with NADH and Oxamate
ComponentsL-lactate dehydrogenase B chain
KeywordsOXIDOREDUCTASE / lactate dehydrogenase / NADH / oxamate
Function / homology
Function and homology information


Pyruvate metabolism / L-lactate dehydrogenase / lactate metabolic process / L-lactate dehydrogenase activity / pyruvate metabolic process / mitochondrial inner membrane / mitochondrion
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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / OXAMIC ACID / L-lactate dehydrogenase B chain
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsHo, M.C.
CitationJournal: To Be Published
Title: pig heart lactate dehydrogenase in complex with NADH and oxamate
Authors: Ho, M.C.
History
DepositionNov 17, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 21, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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 B chain
B: L-lactate dehydrogenase B chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,3196
Polymers72,8142
Non-polymers1,5054
Water3,657203
1
A: L-lactate dehydrogenase B chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,1593
Polymers36,4071
Non-polymers7522
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1220 Å2
ΔGint-6 kcal/mol
Surface area15660 Å2
MethodPISA
2
B: L-lactate dehydrogenase B chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,1593
Polymers36,4071
Non-polymers7522
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1210 Å2
ΔGint-7 kcal/mol
Surface area15900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.788, 130.788, 111.909
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein L-lactate dehydrogenase B chain / LDH-B / LDH heart subunit / LDH-H


Mass: 36406.910 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: P00336, L-lactate dehydrogenase
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical ChemComp-OXM / OXAMIC ACID


Mass: 89.050 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3NO3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 203 / 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: 3.79 Å3/Da / Density % sol: 67.59 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.1M BisTris pH6.5 and 45% PEG 400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 12, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 63058 / % possible obs: 96.4 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.103 / Χ2: 1.103 / Net I/σ(I): 12.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
2.1-2.184.60.78361421.207195.1
2.18-2.264.70.58861821.276195.3
2.26-2.374.70.42461821.144195.2
2.37-2.494.80.3361661.182194.9
2.49-2.654.90.24361981.082195.4
2.65-2.854.90.18662121.038195.3
2.85-3.1450.13862631.006195.8
3.14-3.5950.10464021.059197.9
3.59-4.5250.08365741.017199.5
4.52-5050.0767371.061198.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data scaling
REFMAC5.5.0109refinement
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→50 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.95 / SU B: 4.045 / SU ML: 0.107 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.159 / ESU R Free: 0.149
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2288 3199 5.1 %RANDOM
Rwork0.1946 ---
obs0.1963 59445 95.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso max: 88.08 Å2 / Biso mean: 43.003 Å2 / Biso min: 26.24 Å2
Baniso -1Baniso -2Baniso -3
1-0.14 Å20.07 Å20 Å2
2--0.14 Å20 Å2
3----0.21 Å2
Refinement stepCycle: final / Resolution: 2.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5100 0 100 203 5403
Biso mean--36.67 41.23 -
Num. residues----664
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0225288
X-RAY DIFFRACTIONr_angle_refined_deg1.3911.9917188
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8955662
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.98225.98204
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.54715950
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.8851516
X-RAY DIFFRACTIONr_chiral_restr0.0940.2860
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213816
LS refinement shellResolution: 2.091→2.145 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 245 -
Rwork0.268 4141 -
all-4386 -
obs--91.6 %

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