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- PDB-1pze: T.gondii LDH1 apo form -

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Basic information

Entry
Database: PDB / ID: 1pze
TitleT.gondii LDH1 apo form
Componentslactate dehydrogenase
KeywordsOXIDOREDUCTASE / NADH-dependent / 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
L-lactate dehydrogenase
Similarity search - Component
Biological speciesToxoplasma gondii (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 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: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Aug 16, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: lactate dehydrogenase


Theoretical massNumber of molelcules
Total (without water)35,7411
Polymers35,7411
Non-polymers00
Water1,802100
1
A: lactate dehydrogenase

A: lactate dehydrogenase

A: lactate dehydrogenase

A: lactate dehydrogenase


Theoretical massNumber of molelcules
Total (without water)142,9624
Polymers142,9624
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_556-y,-x,-z+11
crystal symmetry operation10_555-x,-y,z1
crystal symmetry operation15_556y,x,-z+11
Buried area18020 Å2
ΔGint-82 kcal/mol
Surface area42830 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)77.459, 77.459, 218.577
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122

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Components

#1: Protein lactate dehydrogenase / LDH


Mass: 35740.531 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Toxoplasma gondii (eukaryote) / Strain: ME49 / Gene: lactate dehydrogenase / Plasmid: pTYB2 / Production host: Escherichia coli (E. coli) / References: UniProt: P90613, L-lactate dehydrogenase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 100 / 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: 2.29 Å3/Da / Density % sol: 46.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.2
Details: 24% PEG 1K, 100 mM phosphate-citrate, pH 4.2, 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
16 mg/mlprotein1drop
21 mMgossylic iminolactone1drop
312 %(w/v)PEG10001drop
450 mMphosphate-citrate1droppH4.2
524 %(w/v)PEG10001reservoir
6100 mMphosphate-citrate1reservoirpH4.2

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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 4, 2002
RadiationMonochromator: crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.95→30 Å / Num. all: 24807 / Num. obs: 24776 / % possible obs: 99.9 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 5.7 % / Rmerge(I) obs: 0.043
Reflection shellResolution: 1.95→1.98 Å / Rmerge(I) obs: 0.349 / Mean I/σ(I) obs: 4.5 / % possible all: 99.8
Reflection
*PLUS
Num. measured all: 141594
Reflection shell
*PLUS
% possible obs: 99.8 %

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Processing

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

1ldg


Resolution: 1.95→30 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.222 1236 5 %random
Rwork0.188 ---
obs0.188 24745 99.8 %-
all-24791 --
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.654 Å20 Å20 Å2
2---1.654 Å20 Å2
3---3.309 Å2
Refinement stepCycle: LAST / Resolution: 1.95→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2438 0 0 100 2538
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.16
X-RAY DIFFRACTIONc_angle_deg1.64
X-RAY DIFFRACTIONc_mcbond_it1.8241.5
X-RAY DIFFRACTIONc_scbond_it2.9542
X-RAY DIFFRACTIONc_mcangle_it2.5142
X-RAY DIFFRACTIONc_scangle_it4.0922.5
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.paramCNS_TOPPAR:dna-rna.top
X-RAY DIFFRACTION2CNS_TOPPAR:dna-rna_rep.paramCNS_TOPPAR:dna-rna.top
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.paramCNS_TOPPAR:water.top
X-RAY DIFFRACTION4CNS_CNS_TOPPAR:ion.paramCNS_TOPPAR:ion.top
Refinement
*PLUS
Rfactor Rfree: 0.222 / Rfactor Rwork: 0.1876
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_bond_d / Dev ideal: 0.016

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