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- PDB-2a94: Structure of Plasmodium falciparum lactate dehydrogenase complexe... -

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Basic information

Entry
Database: PDB / ID: 2a94
TitleStructure of Plasmodium falciparum lactate dehydrogenase complexed to APADH.
ComponentsL-lactate dehydrogenase
KeywordsOXIDOREDUCTASE / Rossmann fold
Function / homology
Function and homology information


L-lactate dehydrogenase / L-lactate dehydrogenase (NAD+) activity / lactate metabolic process / pyruvate 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
ACETYL PYRIDINE ADENINE DINUCLEOTIDE, REDUCED / L-lactate dehydrogenase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsChaikuad, A. / Fairweather, V. / Conners, R. / Joseph-Horne, T. / Turgut-Balik, D. / Brady, R.L.
CitationJournal: Biochemistry / Year: 2005
Title: Structure of Lactate Dehydrogenase from Plasmodium vivax: Complexes with NADH and APADH.
Authors: Chaikuad, A. / Fairweather, V. / Conners, R. / Joseph-Horne, T. / Turgut-Balik, D. / Brady, R.L.
History
DepositionJul 11, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 10, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 11, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_residues / software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Aug 23, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_residues / 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
Revision 2.0Sep 20, 2023Group: Data collection / Non-polymer description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / entity / pdbx_validate_chiral
Item: _chem_comp.formula / _chem_comp.formula_weight / _entity.formula_weight

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: L-lactate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,5112
Polymers34,8461
Non-polymers6641
Water3,855214
1
A: L-lactate dehydrogenase
hetero molecules

A: L-lactate dehydrogenase
hetero molecules

A: L-lactate dehydrogenase
hetero molecules

A: L-lactate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,0438
Polymers139,3864
Non-polymers2,6584
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-x+1,y,-z1
crystal symmetry operation4_565x,-y+1,-z1
Buried area19990 Å2
ΔGint-128 kcal/mol
Surface area41080 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)80.183, 86.208, 90.826
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
DetailsBiological unit is a tetramer

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Components

#1: Protein L-lactate dehydrogenase / LDH-P


Mass: 34846.387 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Gene: LDH / Plasmid: pKK223-3 / Production host: Escherichia coli (E. coli) / Strain (production host): DH5alpha / References: UniProt: Q27743, L-lactate dehydrogenase
#2: Chemical ChemComp-AP0 / ACETYL PYRIDINE ADENINE DINUCLEOTIDE, REDUCED


Mass: 664.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H30N6O14P2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 214 / 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: 2.31 Å3/Da / Density % sol: 46.33 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: MPD, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.2 / Wavelength: 0.978 / Wavelength: 0.978 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 24, 2001
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.5→30 Å / Num. all: 51103 / Num. obs: 50501 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 4.5 % / Rmerge(I) obs: 0.031 / Χ2: 1.037 / Net I/σ(I): 37.4
Reflection shellResolution: 1.5→1.62 Å / % possible obs: 99.5 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.133 / Mean I/σ(I) obs: 7.3 / Num. measured obs: 10030 / Χ2: 0.778 / % possible all: 99.5

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5refinement
PDB_EXTRACT1.7data extraction
HKL-2000data reduction
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry 1T2C

1t2c


Resolution: 1.5→29.36 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.957 / SU B: 1.473 / SU ML: 0.055 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.066 / ESU R Free: 0.064 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.176 2452 5.1 %RANDOM
Rwork0.16 ---
all0.16 50719 --
obs0.16 48267 95.28 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 10.543 Å2
Baniso -1Baniso -2Baniso -3
1--0.9 Å20 Å20 Å2
2--1.08 Å20 Å2
3----0.18 Å2
Refinement stepCycle: LAST / Resolution: 1.5→29.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2383 0 44 214 2641
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0222342
X-RAY DIFFRACTIONr_bond_other_d0.0010.022202
X-RAY DIFFRACTIONr_angle_refined_deg1.5331.9943180
X-RAY DIFFRACTIONr_angle_other_deg1.54335141
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.0683298
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.57915427
X-RAY DIFFRACTIONr_chiral_restr0.0910.2386
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022534
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02392
X-RAY DIFFRACTIONr_nbd_refined0.2250.3500
X-RAY DIFFRACTIONr_nbd_other0.190.32069
X-RAY DIFFRACTIONr_nbtor_other0.5820.53
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1120.5179
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1980.319
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2070.364
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3320.522
X-RAY DIFFRACTIONr_mcbond_it0.7141.51484
X-RAY DIFFRACTIONr_mcangle_it1.36222398
X-RAY DIFFRACTIONr_scbond_it2.263858
X-RAY DIFFRACTIONr_scangle_it3.7414.5782
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.211 154 -
Rwork0.17 3217 -
all-3371 -
obs--99.5 %

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