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- PDB-2a92: Crystal structure of lactate dehydrogenase from Plasmodium vivax:... -

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Basic information

Entry
Database: PDB / ID: 2a92
TitleCrystal structure of lactate dehydrogenase from Plasmodium vivax: complex with NADH
ComponentsL-lactate dehydrogenase
KeywordsOXIDOREDUCTASE / rossmann fold
Function / homology
Function and homology information


lactate metabolic process / L-lactate dehydrogenase activity / pyruvate 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
1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / : / L-lactate dehydrogenase
Similarity search - Component
Biological speciesPlasmodium vivax (malaria parasite P. vivax)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.04 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: Advisory / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: 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: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)142,4968
Polymers139,8344
Non-polymers2,6624
Water8,647480
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20730 Å2
ΔGint-124 kcal/mol
Surface area43460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.593, 128.636, 130.580
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is a tetramer and is the same as the asymmetric unit

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Components

#1: Protein
L-lactate dehydrogenase


Mass: 34958.621 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium vivax (malaria parasite P. vivax)
Gene: LDH / Plasmid: pKK223-3 / Production host: Escherichia coli (E. coli) / Strain (production host): DH5alpha
References: GenBank: 66967948, UniProt: Q4PRK9*PLUS, L-lactate dehydrogenase
#2: Chemical
ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH


Mass: 665.441 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H29N7O14P2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 480 / 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: 2.39 Å3/Da / Density % sol: 48.05 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.1
Details: PEG 5000 monoethylether, Ammonium Sulphate, Mes, pH 6.1, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.1 / Wavelength: 1.488 / Wavelength: 1.488 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 24, 2004
RadiationMonochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.488 Å / Relative weight: 1
ReflectionResolution: 2→91.29 Å / Num. all: 98204 / Num. obs: 98204 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 3.9 % / Biso Wilson estimate: 26.95 Å2 / Rmerge(I) obs: 0.108 / Χ2: 1.039 / Net I/σ(I): 11.8
Reflection shellResolution: 2→2.1 Å / % possible obs: 97.3 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.434 / Mean I/σ(I) obs: 2.4 / Num. measured obs: 9595 / Num. unique all: 9639 / Χ2: 0.675 / % possible all: 97.5

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Processing

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

1t2c


Resolution: 2.04→91.29 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.908 / SU B: 7.82 / SU ML: 0.114 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.205 / ESU R Free: 0.175 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.236 4299 5 %RANDOM
Rwork0.194 ---
all0.197 90148 --
obs0.197 85849 97.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 9.716 Å2
Baniso -1Baniso -2Baniso -3
1-1.44 Å20 Å20 Å2
2---1.85 Å20 Å2
3---0.41 Å2
Refinement stepCycle: LAST / Resolution: 2.04→91.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9596 0 176 480 10252
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0229938
X-RAY DIFFRACTIONr_angle_refined_deg1.5252.00213490
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.11251262
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.52926.164365
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.824151801
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.0511524
X-RAY DIFFRACTIONr_chiral_restr0.1080.21621
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.027116
X-RAY DIFFRACTIONr_nbd_refined0.2010.24491
X-RAY DIFFRACTIONr_nbtor_refined0.2960.26747
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1460.2551
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2090.229
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1570.29
X-RAY DIFFRACTIONr_mcbond_it0.7211.56500
X-RAY DIFFRACTIONr_mcangle_it1.08210162
X-RAY DIFFRACTIONr_scbond_it1.933889
X-RAY DIFFRACTIONr_scangle_it2.7524.53327
LS refinement shellResolution: 2.042→2.095 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 276 -
Rwork0.223 5508 -
all-5784 -
obs--90.66 %
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)
10.47130.1917-0.01011.18220.41240.91560.0847-0.01080.0897-0.029-0.04140.0785-0.0901-0.0264-0.0433-0.26640.00240.0221-0.10250.0054-0.1363-17.719-0.06918.839
20.61860.08870.25360.01270.0370.80910.03310.0022-0.00050.1033-0.0125-0.02820.02950.2156-0.02060-0.00010-0.000100-7.4246.76324.209
30.72640.19640.02550.85850.31640.80640.06990.02220.1267-0.0155-0.03730.1119-0.0772-0.0175-0.0326-0.2334-0.0030.0274-0.11140.0028-0.1236-17.457-0.18518.892
40.64830.2850.07490.78150.23080.69890.05230.01530.1911-0.0183-0.03020.126-0.0682-0.0148-0.0221-0.22540.00530.0229-0.1130.0016-0.0849-17.44-0.518.957
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA21 - 984 - 79
21BB21 - 984 - 79
31CC21 - 984 - 79
41DD21 - 984 - 79
52AA99 - 11680 - 101
62BB99 - 11680 - 101
72CC99 - 11680 - 101
82DD99 - 11680 - 101
93AA117 - 285102 - 272
103BB117 - 285102 - 272
113CC117 - 285102 - 272
123DD117 - 285102 - 272
134AA286 - 330273 - 316
144BB286 - 329273 - 315
154CC288 - 330275 - 316
164DD286 - 329273 - 315

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