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- PDB-5hru: Crystal structure of Plasmodium vivax LDH in complex with a DNA a... -

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Basic information

Entry
Database: PDB / ID: 5hru
TitleCrystal structure of Plasmodium vivax LDH in complex with a DNA aptamer called pL1
Components
  • DNA (32-MER)
  • L-lactate dehydrogenase
KeywordsOXIDOREDUCTASE/DNA / DNA aptamer / Plasmodium LDH / malaria / DNA structural element / OXIDOREDUCTASE-DNA complex
Function / homology
Function and homology information


L-lactate dehydrogenase / L-lactate dehydrogenase (NAD+) activity / lactate 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)
Phylica emirnensis (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.71 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 24, 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_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 (32-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,2884
Polymers85,2643
Non-polymers241
Water9,476526
1
A: L-lactate dehydrogenase
B: L-lactate dehydrogenase
C: DNA (32-MER)
hetero molecules

A: L-lactate dehydrogenase
B: L-lactate dehydrogenase
C: DNA (32-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)170,5768
Polymers170,5276
Non-polymers492
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_465y-1,x+1,-z1
Buried area20090 Å2
ΔGint-154 kcal/mol
Surface area48050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.477, 84.477, 209.867
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

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


Mass: 37659.656 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium vivax (malaria parasite P. vivax)
Gene: LDH / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / References: UniProt: Q4PRK9, L-lactate dehydrogenase
#2: DNA chain DNA (32-MER)


Mass: 9944.372 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Phylica emirnensis (plant)
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 526 / 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: 43.98 %
Crystal growTemperature: 293.19 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: PEG-20K, NDSB-195, magnesium chloride

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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: 1.71→25 Å / Num. obs: 82531 / % possible obs: 99.8 % / Redundancy: 21.4 % / Rmerge(I) obs: 0.103 / Net I/av σ(I): 80.476 / Net I/σ(I): 15
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.71-1.7415.10.292199.9
1.74-1.7715.60.272199.9
1.77-1.8116.20.254199.9
1.81-1.8416.70.239199.9
1.84-1.8817.40.223199.9
1.88-1.93180.208199.9
1.93-1.9718.90.19199.9
1.97-2.0319.60.176199.9
2.03-2.0920.40.164199.9
2.09-2.1521.40.152199.8
2.15-2.23220.142199.9
2.23-2.3222.50.134199.9
2.32-2.4323.40.125199.8
2.43-2.5523.90.119199.9
2.55-2.7124.70.113199.8
2.71-2.9225.40.115199.9
2.92-3.2226.20.123199.9
3.22-3.6826.90.109199.9
3.68-4.6326.50.081199.9
4.63-2526.30.073199.3

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Processing

Software
NameVersionClassification
PHENIX1.9-1692refinement
HKL-2000data scaling
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2A92

2a92


Resolution: 1.71→24.96 Å
RfactorNum. reflection% reflection
Rfree0.1845 --
Rwork0.1598 --
obs-82462 99.84 %
Displacement parametersBiso max: 99.02 Å2 / Biso mean: 24.2256 Å2 / Biso min: 11.36 Å2
Refinement stepCycle: LAST / Resolution: 1.71→24.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3422 663 1203 526 5814
LS refinement shellResolution: 1.712→1.773 Å
RfactorNum. reflection% reflection
Rfree0.2317 --
Rwork0.1751 8064 -
obs--99.33 %

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