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- PDB-1sow: T. gondii bradyzoite-specific LDH (LDH2) in complex with NAD and ... -

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Basic information

Entry
Database: PDB / ID: 1sow
TitleT. gondii bradyzoite-specific LDH (LDH2) in complex with NAD and oxalate
ComponentsL-lactate dehydrogenaseLactate dehydrogenase
KeywordsOXIDOREDUCTASE / Rossmann fold / tetramer / NAD-binding
Function / homology
Function and homology information


L-lactate dehydrogenase / L-lactate dehydrogenase activity / carboxylic acid metabolic process
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. / Wilson, D.K.
CitationJournal: To be Published
Title: Structure of apo and ternary forms of Toxoplasma gondii LDH2
Authors: Kavanagh, K.L. / Wilson, D.K.
History
DepositionMar 15, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 15, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 23, 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
Remark 999SEQUENCE Authors informed that the primary sequence corresponds to the sequence published in Gene ...SEQUENCE Authors informed that the primary sequence corresponds to the sequence published in Gene (1997)184:1-12. This sequence has an Asn at residue 209A and not Ser.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: L-lactate dehydrogenase
B: L-lactate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,5636
Polymers71,0612
Non-polymers1,5034
Water5,963331
1
A: L-lactate dehydrogenase
B: L-lactate dehydrogenase
hetero molecules

A: L-lactate dehydrogenase
B: L-lactate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,12712
Polymers142,1214
Non-polymers3,0068
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
Buried area23670 Å2
ΔGint-83 kcal/mol
Surface area40640 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)140.712, 140.712, 74.740
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321
Components on special symmetry positions
IDModelComponents
11A-519-

HOH

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Components

#1: Protein L-lactate dehydrogenase / Lactate dehydrogenase / LDH / LDH2


Mass: 35530.262 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Toxoplasma gondii (eukaryote) / Plasmid: pTYB12 / Production host: Escherichia coli (E. coli) / References: UniProt: Q27797, L-lactate dehydrogenase
#2: Chemical ChemComp-OXL / OXALATE ION / Oxalate


Mass: 88.019 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2O4
#3: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 331 / 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: 3.01 Å3/Da / Density % sol: 59.08 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 10% PEG-MME 5000, 0.6 M magnesium acetate, 100 mM sodium acetate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 18, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. all: 67210 / Num. obs: 67007 / % possible obs: 99.7 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 4.3 % / Rmerge(I) obs: 0.044 / Net I/σ(I): 28
Reflection shellResolution: 1.9→1.93 Å / Rmerge(I) obs: 0.342 / Mean I/σ(I) obs: 3.97 / % possible all: 99.6

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1sov, chain A

1sov


Resolution: 1.9→30 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.212 3378 -random
Rwork0.185 ---
obs0.185 67007 99.7 %-
all-67212 --
Refinement stepCycle: LAST / Resolution: 1.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4898 0 100 331 5329
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.47
X-RAY DIFFRACTIONc_bond_d0.01
LS refinement shellResolution: 1.9→1.93 Å

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