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- PDB-5es3: Co-crystal structure of LDH liganded with oxamate -

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Basic information

Entry
Database: PDB / ID: 5es3
TitleCo-crystal structure of LDH liganded with oxamate
ComponentsL-lactate dehydrogenase A chain
KeywordsOXIDOREDUCTASE / Lactate dehydrogenase / allostery
Function / homology
Function and homology information


lactate dehydrogenase activity / Pyruvate metabolism / Regulation of pyruvate metabolism / sperm fibrous sheath / pyruvate catabolic process / L-lactate dehydrogenase / oxidoreductase complex / NAD metabolic process / lactate metabolic process / L-lactate dehydrogenase activity ...lactate dehydrogenase activity / Pyruvate metabolism / Regulation of pyruvate metabolism / sperm fibrous sheath / pyruvate catabolic process / L-lactate dehydrogenase / oxidoreductase complex / NAD metabolic process / lactate metabolic process / L-lactate dehydrogenase activity / glucose catabolic process to lactate via pyruvate / pyruvate metabolic process / response to glucose / skeletal muscle tissue development / response to cAMP / response to nutrient / liver development / response to hydrogen peroxide / response to organic cyclic compound / kinase binding / response to estrogen / NAD binding / response to hypoxia / positive regulation of apoptotic process / response to xenobiotic stimulus / mitochondrion / identical protein binding / cytosol
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
OXAMIC ACID / L-lactate dehydrogenase A chain
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.29 Å
AuthorsNowicki, M.W. / Wear, M.A. / McNae, I.W. / Blackburn, E.A.
CitationJournal: Plos One / Year: 2015
Title: A Streamlined, Automated Protocol for the Production of Milligram Quantities of Untagged Recombinant Rat Lactate Dehydrogenase A Using AKTAxpressTM.
Authors: Nowicki, M.W. / Blackburn, E.A. / McNae, I.W. / Wear, M.A.
History
DepositionNov 16, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 13, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 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 / diffrn_source / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: L-lactate dehydrogenase A chain
C: L-lactate dehydrogenase A chain
E: L-lactate dehydrogenase A chain
F: L-lactate dehydrogenase A chain
D: L-lactate dehydrogenase A chain
H: L-lactate dehydrogenase A chain
B: L-lactate dehydrogenase A chain
G: L-lactate dehydrogenase A chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)291,61816
Polymers290,9068
Non-polymers7128
Water23,7981321
1
A: L-lactate dehydrogenase A chain
C: L-lactate dehydrogenase A chain
D: L-lactate dehydrogenase A chain
B: L-lactate dehydrogenase A chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,8098
Polymers145,4534
Non-polymers3564
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21500 Å2
ΔGint-126 kcal/mol
Surface area45900 Å2
MethodPISA
2
E: L-lactate dehydrogenase A chain
F: L-lactate dehydrogenase A chain
H: L-lactate dehydrogenase A chain
G: L-lactate dehydrogenase A chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,8098
Polymers145,4534
Non-polymers3564
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21280 Å2
ΔGint-122 kcal/mol
Surface area46320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.080, 146.630, 284.900
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
L-lactate dehydrogenase A chain / LDH-A / LDH muscle subunit / LDH-M


Mass: 36363.238 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Ldha, Ldh-1, Ldh1 / Plasmid: pDEST-14 / Production host: Escherichia coli (E. coli) / Strain (production host): C41 BL21(DE3) / References: UniProt: P04642, L-lactate dehydrogenase
#2: Chemical
ChemComp-OXM / OXAMIC ACID


Mass: 89.050 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H3NO3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1321 / 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: 3.02 Å3/Da / Density % sol: 59.25 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1 M Tris/Bicine pH 8.5, 20 % ethylene glycol, 10 % PEG 8000, 0.02 M of each of sodium formate, ammonium acetate, tri-sodium citrate, sodium/potassium tartrate and sodium oxamate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Feb 13, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.29→80.642 Å / Num. obs: 158462 / % possible obs: 99.7 % / Redundancy: 7.5 % / Rmerge(I) obs: 0.127 / Net I/σ(I): 11.9

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Processing

Software
NameVersionClassification
PHENIXrefinement
xia2data scaling
PDB_EXTRACT3.15data extraction
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4AJE

4aje


Resolution: 2.29→80.642 Å / SU ML: 0.22 / Cross valid method: NONE / σ(F): 1.35 / Phase error: 19.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2028 7940 5.01 %
Rwork0.17 150413 -
obs0.1716 158353 99.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 109.79 Å2 / Biso mean: 32.7418 Å2 / Biso min: 13.54 Å2
Refinement stepCycle: final / Resolution: 2.29→80.642 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20267 0 64 1321 21652
Biso mean--50.26 35.47 -
Num. residues----2625
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00720651
X-RAY DIFFRACTIONf_angle_d0.84527959
X-RAY DIFFRACTIONf_chiral_restr0.0543291
X-RAY DIFFRACTIONf_plane_restr0.0053529
X-RAY DIFFRACTIONf_dihedral_angle_d14.9087685
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.29-2.3160.28072530.223549745227100
2.316-2.34330.26612660.22144860512698
2.3433-2.37190.27732540.21824881513599
2.3719-2.40190.25532740.212150075281100
2.4019-2.43350.27622710.210449195190100
2.4335-2.46680.25522770.204949605237100
2.4668-2.50210.24872610.197649905251100
2.5021-2.53940.22652670.194349945261100
2.5394-2.57910.23982440.195949535197100
2.5791-2.62140.25382820.199650165298100
2.6214-2.66660.25022650.249565221100
2.6666-2.71510.21932660.185850575323100
2.7151-2.76730.2312850.183849295214100
2.7673-2.82380.20852470.184650245271100
2.8238-2.88520.24652910.184949615252100
2.8852-2.95230.22752210.18749905211100
2.9523-3.02620.22042560.189650435299100
3.0262-3.1080.22452560.18550235279100
3.108-3.19940.22732560.184950245280100
3.1994-3.30270.20272520.17750085260100
3.3027-3.42080.21432880.17724885517397
3.4208-3.55770.1882710.167550105281100
3.5577-3.71960.20462610.168950485309100
3.7196-3.91570.18052620.155550575319100
3.9157-4.16110.17922760.14950625338100
4.1611-4.48230.15242540.130150955349100
4.4823-4.93330.14232820.127650865368100
4.9333-5.6470.17082620.152551485410100
5.647-7.1140.18952680.16015042531098
7.114-80.69150.16092720.142654115683100

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