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- PDB-5hto: Crystal structure of Plasmodium Vivax LDH in complex with a DNA a... -

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Basic information

Entry
Database: PDB / ID: 5hto
TitleCrystal structure of Plasmodium Vivax LDH in complex with a DNA aptamer called pL1 (tetrameric LDH in an asymmetric unit)
Components
  • DNA (30-MER)
  • DNA (34-MER)
  • L-lactate dehydrogenase
KeywordsOXIDOREDUCTASE/DNA / LDH / malaria / DNA aptamer / aptamer / structural element / OXIDOREDUCTASE-DNA complex
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
DNA / DNA (> 10) / L-lactate dehydrogenase
Similarity search - Component
Biological speciesPlasmodium vivax (malaria parasite P. vivax)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsChoi, S.J. / Ban, C.
Funding support Korea, Republic Of, 2items
OrganizationGrant numberCountry
National Research Foundation of KoreaNRF- 2015027587 Korea, Republic Of
National Research Foundation of KoreaNRF-2014K1B1A1073720 Korea, Republic Of
CitationJournal: Sci Rep / Year: 2016
Title: Crystal structure of a DNA aptamer bound to PvLDH elucidates novel single-stranded DNA structural elements for folding and recognition
Authors: Choi, S.J. / Ban, C.
History
DepositionJan 27, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 19, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2016Group: Database references
Revision 1.2Nov 8, 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_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_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: DNA (34-MER)
D: L-lactate dehydrogenase
E: L-lactate dehydrogenase
F: DNA (30-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)170,5768
Polymers170,5276
Non-polymers492
Water16,177898
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19760 Å2
ΔGint-159 kcal/mol
Surface area48020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.512, 86.539, 209.128
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
L-lactate dehydrogenase / Lactate dehydrogenase / Parasite lactate dehydrogenase


Mass: 37659.656 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium vivax (malaria parasite P. vivax)
Gene: LDH / Production host: Escherichia coli (E. coli) / Strain (production host): ER2566 / References: UniProt: Q4PRK9, L-lactate dehydrogenase
#2: DNA chain DNA (34-MER)


Mass: 10561.771 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Plasmodium vivax (malaria parasite P. vivax)
#3: DNA chain DNA (30-MER)


Mass: 9326.973 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Plasmodium vivax (malaria parasite P. vivax)
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 898 / 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: 2.27 Å3/Da / Density % sol: 45.79 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: PEG-20K, magnesium ion, HEPES, Tirs, PEG-400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9796 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 2, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 1.9→25 Å / Num. obs: 122668 / % possible obs: 100 % / Redundancy: 14.6 % / Biso Wilson estimate: 17.93 Å2 / Rmerge(I) obs: 0.083 / Net I/av σ(I): 64.423 / Net I/σ(I): 16.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.9-1.9314.40.2881100
1.93-1.9714.50.2521100
1.97-2.0114.50.2211100
2.01-2.0514.60.1951100
2.05-2.0914.70.1691100
2.09-2.1414.70.151100
2.14-2.1914.70.1331100
2.19-2.2514.80.1221100
2.25-2.3214.80.1131100
2.32-2.3914.80.11100
2.39-2.4814.80.11100
2.48-2.5814.80.0951100
2.58-2.714.70.0891100
2.7-2.8414.70.0921100
2.84-3.0114.70.0961100
3.01-3.2514.60.1011100
3.25-3.5714.50.0861100
3.57-4.0914.20.0631100
4.09-5.1414.20.0481100
5.14-2513.80.042199.6

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.9_1692refinement
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2A92

2a92


Resolution: 1.9→24.999 Å / SU ML: 0.17 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 19.86
RfactorNum. reflection% reflection
Rfree0.2001 6161 5.03 %
Rwork0.169 --
obs0.1706 122528 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 84.23 Å2 / Biso mean: 19.8186 Å2 / Biso min: 6.45 Å2
Refinement stepCycle: final / Resolution: 1.9→24.999 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9182 1264 64 898 11408
Biso mean--62.06 23.43 -
Num. residues----1275
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00910813
X-RAY DIFFRACTIONf_angle_d1.1114917
X-RAY DIFFRACTIONf_chiral_restr0.0451798
X-RAY DIFFRACTIONf_plane_restr0.0051665
X-RAY DIFFRACTIONf_dihedral_angle_d16.7294113
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9-1.92150.26321710.20063725389698
1.9215-1.94410.29161970.194738384035100
1.9441-1.96780.27092020.187338864088100
1.9678-1.99270.22132370.187838034040100
1.9927-2.01890.24971940.181138324026100
2.0189-2.04660.22251870.170438464033100
2.0466-2.07580.20622080.161838444052100
2.0758-2.10680.22222120.1738314043100
2.1068-2.13970.21852030.166638824085100
2.1397-2.17470.22692130.170238304043100
2.1747-2.21220.19971950.171538554050100
2.2122-2.25240.23091850.171338954080100
2.2524-2.29570.22512110.168838324043100
2.2957-2.34250.21451940.176838734067100
2.3425-2.39340.22932170.172738454062100
2.3934-2.44910.20882100.172538464056100
2.4491-2.51030.21151950.179138824077100
2.5103-2.57810.19252050.179138624067100
2.5781-2.65380.22322030.174138794082100
2.6538-2.73940.20682390.176838304069100
2.7394-2.83720.17931810.173639054086100
2.8372-2.95060.20542200.182439034123100
2.9506-3.08470.2091930.186238924085100
3.0847-3.2470.19992160.190238664082100
3.247-3.44990.2111940.17939404134100
3.4499-3.71550.18832100.160239384148100
3.7155-4.08790.16192240.148939144138100
4.0879-4.67610.15022140.138539474161100
4.6761-5.87880.18272030.154640174220100
5.8788-25.00110.17512280.16094129435799

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