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- PDB-1pzh: T.gondii LDH1 ternary complex with NAD and oxalate -

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Basic information

Entry
Database: PDB / ID: 1pzh
TitleT.gondii LDH1 ternary complex with NAD and oxalate
Componentslactate dehydrogenase
KeywordsOXIDOREDUCTASE / NADH-dependent dehydrogenase / tetramer / Rossmann fold
Function / homology
Function and homology information


L-lactate dehydrogenase (NAD+) activity / lactate metabolic process / nucleotide binding
Similarity search - Function
Malate dehydrogenase, type 3 / 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 ...Malate dehydrogenase, type 3 / 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 / OXALATE ION / L-lactate dehydrogenase
Similarity search - Component
Biological speciesToxoplasma gondii (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsKavanagh, K.L. / Elling, R.A. / Wilson, D.K.
CitationJournal: Biochemistry / Year: 2004
Title: Structure of Toxoplasma gondii LDH1: Active-Site Differences from Human Lactate Dehydrogenases and the Structural Basis for Efficient APAD+ Use.
Authors: Kavanagh, K.L. / Elling, R.A. / Wilson, D.K.
History
DepositionJul 10, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 24, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Aug 16, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: lactate dehydrogenase
B: lactate dehydrogenase
C: lactate dehydrogenase
D: lactate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,96812
Polymers142,9624
Non-polymers3,0068
Water10,593588
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23740 Å2
ΔGint-101 kcal/mol
Surface area41620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.068, 125.121, 86.597
Angle α, β, γ (deg.)90.00, 106.08, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
lactate dehydrogenase / LDH


Mass: 35740.531 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Toxoplasma gondii (eukaryote) / Strain: ME49 / Gene: lactate dehydrogenase (LDH1) / Plasmid: pTYB2 / Production host: Escherichia coli (E. coli) / References: UniProt: P90613, L-lactate dehydrogenase
#2: Chemical
ChemComp-OXL / OXALATE ION


Mass: 88.019 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2O4
#3: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 588 / 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: 2.48 Å3/Da / Density % sol: 50.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 0.9 M ammonium sulfate, 100 mM acetate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 293 K / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
112 mg/mlprotein1drop
210 mMcosubstrate1drop
35 mMoxalate1dropor oxamate
40.85-0.90 Mammonium sulfate1reservoir
5100 mMacetate1reservoirpH4.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.97 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 3, 2002
RadiationMonochromator: crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. all: 109430 / Num. obs: 103102 / % possible obs: 94.2 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.071 / Net I/σ(I): 12.6
Reflection shellResolution: 1.9→1.93 Å / Rmerge(I) obs: 0.326 / % possible all: 91.8
Reflection
*PLUS
Num. measured all: 223205
Reflection shell
*PLUS
% possible obs: 91.8 % / Mean I/σ(I) obs: 3.1

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1PZE

1pze


Resolution: 1.9→30 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2 5142 4.7 %random
Rwork0.164 ---
obs0.164 103053 94.2 %-
all-109400 --
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.872 Å20 Å2-0.216 Å2
2--2.521 Å20 Å2
3----3.393 Å2
Refinement stepCycle: LAST / Resolution: 1.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9880 0 200 588 10668
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_bond_d0.015
X-RAY DIFFRACTIONc_mcbond_it1.5911.5
X-RAY DIFFRACTIONc_scbond_it2.6792
X-RAY DIFFRACTIONc_mcangle_it2.1692
X-RAY DIFFRACTIONc_scangle_it3.7792.5
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.paramCNS_TOPPAR:protein.top
X-RAY DIFFRACTION2par.oxltop.oxl
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.paramCNS_TOPPAR:water.top
X-RAY DIFFRACTION4CNS_TOPPAR:ion.paramCNS_TOPPAR:ion.top
X-RAY DIFFRACTION5par.nadtop.nad
Refinement
*PLUS
Rfactor Rfree: 0.2 / Rfactor Rwork: 0.1644
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_angle_deg / Dev ideal: 1.63

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