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- PDB-1oc4: Lactate dehydrogenase from Plasmodium berghei -

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Basic information

Entry
Database: PDB / ID: 1oc4
TitleLactate dehydrogenase from Plasmodium berghei
ComponentsL-LACTATE DEHYDROGENASE
KeywordsOXIDOREDUCTASE / LACTATE DEHYDROGENASE / GLYCOLYSIS / INTERCONVERSION OF PYRUVATE AND LACTATE / 3-LAYER (ABA) SANDWICH
Function / homology
Function and homology information


pyruvate biosynthetic process / L-lactate dehydrogenase / carboxylic acid metabolic process / L-lactate dehydrogenase (NAD+) activity / lactate metabolic process / glycolytic process / NAD binding / carbohydrate metabolic process / oxidoreductase activity
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 / OXAMIC ACID / L-lactate dehydrogenase / L-lactate dehydrogenase
Similarity search - Component
Biological speciesPLASMODIUM BERGHEI (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsWinter, V.J. / Brady, R.L.
CitationJournal: Mol.Biochem.Parasitol. / Year: 2003
Title: Crystal Structure of Plasmodium Berghei Lactate Dehydrogenase Indicates the Unique Structural Differences of These Enzymes are Shared Across the Plasmodium Genus
Authors: Winter, V.J. / Cameron, A. / Tranter, R. / Sessions, R.B. / Brady, R.L.
History
DepositionFeb 5, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 18, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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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)72,2818
Polymers70,5922
Non-polymers1,6896
Water3,513195
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)144,56216
Polymers141,1844
Non-polymers3,37812
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
MethodPQS
Unit cell
Length a, b, c (Å)103.586, 71.528, 94.540
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1113A1 - 315
2113B1 - 315

NCS oper: (Code: given
Matrix: (0.511, -0.859, -0.003), (-0.859, -0.511), (-0.002, 0.003, -1)
Vector: -0.05382, 0.00813, 55.58175)

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Components

#1: Protein L-LACTATE DEHYDROGENASE


Mass: 35295.930 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: NICOTINAMIDE-ADENINE-DINUCLEOTIDE COFACTOR, OXAMIC ACID INHIBITOR
Source: (gene. exp.) PLASMODIUM BERGHEI (eukaryote) / Strain: ANKA / Plasmid: PKK223-3 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): JM105
References: UniProt: Q4Z783, UniProt: Q7SI97*PLUS, L-lactate dehydrogenase
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical ChemComp-OXM / OXAMIC ACID


Mass: 89.050 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3NO3
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 195 / 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: 43.3 %
Crystal growpH: 7.5 / Details: 32% PEG 1500, pH 7.50
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
12.5 mMNADH1drop
232-34 %PEG15001reservoir
365 %MPD1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.1 / Wavelength: 1.488
DetectorType: ADSC CCD / Detector: CCD / Date: Jan 15, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.488 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. obs: 31653 / % possible obs: 98.8 % / Redundancy: 5.49 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 18.11
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 5 % / Rmerge(I) obs: 0.281 / Mean I/σ(I) obs: 4.01 / % possible all: 98
Reflection
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 30 Å / Redundancy: 5.49 % / Num. measured all: 173810 / Rmerge(I) obs: 0.087
Reflection shell
*PLUS
Highest resolution: 2.3 Å / Rmerge(I) obs: 0.281

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Processing

Software
NameVersionClassification
REFMAC5refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1LDG

1ldg


Resolution: 2.3→29.49 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.888 / SU B: 8.163 / SU ML: 0.203 / Cross valid method: THROUGHOUT / ESU R: 0.394 / ESU R Free: 0.266 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.268 1540 5.1 %RANDOM
Rwork0.219 ---
obs0.222 28850 95 %-
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: 33.41 Å2
Baniso -1Baniso -2Baniso -3
1--1.91 Å20 Å20 Å2
2---1.03 Å20 Å2
3---2.95 Å2
Refinement stepCycle: LAST / Resolution: 2.3→29.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4808 0 112 195 5115
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0224883
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4271.9886601
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.0913613
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.84715872
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0910.2785
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023510
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021
X-RAY DIFFRACTIONr_nbd_refined0.2780.32362
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2070.5369
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2610.366
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined1.080.511
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6591.53073
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.25324950
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.81631810
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.8564.51651
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
1238tight positional0.070.05
1087loose positional0.455
1238tight thermal0.330.5
1087loose thermal2.2110
LS refinement shellResolution: 2.29→2.35 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.335 95
Rwork0.246 1938
Refinement
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 30 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.011
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.428

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