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- PDB-2x8l: Plasmodium falciparum lactate dehydrogenase apo structure -

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Basic information

Entry
Database: PDB / ID: 2x8l
TitlePlasmodium falciparum lactate dehydrogenase apo structure
ComponentsL-LACTATE DEHYDROGENASE
KeywordsOXIDOREDUCTASE / NAD / PYRUVATE / GLYCOLYSIS
Function / homology
Function and homology information


L-lactate dehydrogenase / L-lactate dehydrogenase (NAD+) activity / lactate metabolic process / metal ion 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 / L-lactate dehydrogenase
Similarity search - Component
Biological speciesPLASMODIUM FALCIPARUM (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsBirkinshaw, R.W. / Brady, R.L.
CitationJournal: To be Published
Title: The Apo Crystal Structure of Plasmodium Falciparum Lactate Dehydrogenase
Authors: Birkinshaw, R.W. / Brady, R.L.
History
DepositionMar 10, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 23, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jan 30, 2019Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / pdbx_struct_special_symmetry / pdbx_unobs_or_zero_occ_atoms
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.3Feb 6, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.4Dec 20, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / 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 / pdbx_unobs_or_zero_occ_atoms / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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

Downloads & links

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Assembly

Deposited unit
A: L-LACTATE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,0702
Polymers34,9781
Non-polymers921
Water5,729318
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)140,2798
Polymers139,9104
Non-polymers3684
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_555x,-y,-z1
crystal symmetry operation2_555-x,-y,z1
Buried area16920 Å2
ΔGint-94.3 kcal/mol
Surface area42220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.120, 85.410, 91.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-2187-

HOH

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Components

#1: Protein L-LACTATE DEHYDROGENASE / LDH-P


Mass: 34977.586 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PLASMODIUM FALCIPARUM (malaria parasite P. falciparum)
Description: MALARIA PARASITE / Plasmid: PKK223 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): JM109
References: UniProt: Q27743, UniProt: Q71T02*PLUS, L-lactate dehydrogenase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 318 / 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: 2.2 Å3/Da / Density % sol: 45 % / Description: NONE
Crystal growTemperature: 275 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: MPD, HEPES, IMIDAZOLE, PH 7.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 26, 2009
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.6→62.5 Å / Num. obs: 41592 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 5 % / Biso Wilson estimate: 12.411 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 13.8
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 2 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1T24

1t24


Resolution: 1.6→62.5 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.966 / SU B: 3.12 / SU ML: 0.047 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.069 / ESU R Free: 0.073 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.U VALUES RESIDUAL ONLY. THE ACTIVE SITE LOOP IS DISORDERED (NOT OBSERVED) AND HAS BEEN OMITTED FROM THE MODEL ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1674 2087 5 %RANDOM
Rwork0.1357 ---
obs0.13726 39452 99.87 %-
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: 4.807 Å2
Baniso -1Baniso -2Baniso -3
1--1.44 Å20 Å20 Å2
2--2.1 Å20 Å2
3----0.66 Å2
Refinement stepCycle: LAST / Resolution: 1.6→62.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2362 0 6 318 2686
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0222518
X-RAY DIFFRACTIONr_bond_other_d0.0010.021632
X-RAY DIFFRACTIONr_angle_refined_deg1.7431.9613433
X-RAY DIFFRACTIONr_angle_other_deg1.0434054
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8945336
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.33625.769104
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.31915443
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.376156
X-RAY DIFFRACTIONr_chiral_restr0.120.2407
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0212827
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02447
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9031.51604
X-RAY DIFFRACTIONr_mcbond_other0.3451.5656
X-RAY DIFFRACTIONr_mcangle_it1.34322608
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.3563914
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.5664.5817
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
LS refinement shellResolution: 1.603→1.645 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.25 153 -
Rwork0.225 2888 -
obs--99.61 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.587-0.0687-0.1515.9553-1.13545.90010.0961-0.1181-0.00860.18470.02130.30990.0921-0.1606-0.11740.01690.0113-0.00240.0547-0.02660.0353-0.13814.976514.4989
22.05260.59680.47290.972-0.11871.73520.0185-0.0480.0440.0325-0.01130.0116-0.0667-0.0297-0.00720.03050.00590.00910.0249-0.00260.0172-5.786715.21638.4725
32.4764-1.76880.14614.18070.92623.8697-0.027-0.32580.02240.19590.02990.0294-0.0352-0.309-0.00280.0504-0.01730.0280.0768-0.01880.0573-3.721818.766920.8736
46.56847.2982-1.047917.9784-4.15095.8399-0.14080.31370.4844-0.24110.0541-0.1395-0.60040.19480.08670.10940.0079-0.01160.0920.0180.09189.150525.656713.5723
515.8902-2.46064.487411.7401-15.2720.0725-0.07010.90621.403-0.2999-0.4102-0.40860.24880.60190.48030.3033-0.02710.17240.09730.05070.379718.315234.535612.6706
64.84074.1091-4.41667.1184-3.63944.87650.1718-0.09630.29050.2117-0.08410.0776-0.37-0.0384-0.08770.0987-0.0065-0.01960.0674-0.04450.07999.754326.914223.4567
74.7361.5895-1.35892.3067-0.4611.85590.0215-0.15240.08880.03540.02670.0032-0.00690.0256-0.04830.04320.0064-0.00670.0242-0.02640.035112.664118.910219.7766
81.2962-0.3458-1.50220.89871.13936.380.0153-0.03660.0756-0.01850.0081-0.0177-0.0498-0.0435-0.02330.0057-0.0031-0.01120.00550.00070.042916.843513.798.5728
91.1195-0.053-0.0941.51791.42372.0112-0.0089-0.01340.041-0.06880.0331-0.1251-0.05170.1143-0.02420.0564-0.00390.00690.03340.02390.035525.52438.6617-2.591
103.8249-2.7161-2.92935.71083.67334.90990.07450.01860.2327-0.10820.0512-0.3159-0.08990.1915-0.12570.0572-0.0281-0.01480.06640.03430.064727.786215.4556-8.7989
1110.9265-3.87343.61449.96571.18659.0641-0.24220.47650.6058-0.15270.2106-0.2076-0.53770.04420.03160.1036-0.02620.0090.06270.03220.107814.133528.2607-5.981
121.116-0.44680.20814.7368-3.71935.92650.00660.04950.03980.02380.09960.1822-0.1198-0.0953-0.10620.00350.002-0.00060.0414-0.01820.0288.212713.58666.2446
131.90730.4560.10761.38560.5531.06890.0358-0.2127-0.09430.1137-0.0138-0.11810.04740.1049-0.0220.04860.0046-0.00760.04080.00430.026322.5658.16615.6982
144.2393-4.5416-2.27338.39253.62373.19680.0364-0.0990.3560.02350.1-0.3095-0.10390.2142-0.13630.0487-0.037-0.0210.07-0.01760.06630.478522.39513.3349
154.81989.3528-11.636318.1511-22.5828.0988-0.1376-0.6554-0.6613-0.1273-1.3669-1.26260.17681.55481.50450.4927-0.0459-0.25870.3682-0.01060.381819.723440.963123.5223
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A18 - 31
2X-RAY DIFFRACTION2A32 - 75
3X-RAY DIFFRACTION3A76 - 90
4X-RAY DIFFRACTION4A91 - 100
5X-RAY DIFFRACTION5A101 - 102
6X-RAY DIFFRACTION6A108 - 118
7X-RAY DIFFRACTION7A119 - 141
8X-RAY DIFFRACTION8A142 - 169
9X-RAY DIFFRACTION9A170 - 209D
10X-RAY DIFFRACTION10A210A - 238
11X-RAY DIFFRACTION11A239 - 246
12X-RAY DIFFRACTION12A247 - 266
13X-RAY DIFFRACTION13A267 - 308
14X-RAY DIFFRACTION14A309 - 331
15X-RAY DIFFRACTION15A332 - 334

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