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- PDB-6txr: Structural insights into cubane-modified aptamer recognition of a... -

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Basic information

Entry
Database: PDB / ID: 6txr
TitleStructural insights into cubane-modified aptamer recognition of a malaria biomarker
ComponentsL-lactate dehydrogenase
KeywordsDNA / Aptamer / Cubamer / PvLDH
Function / homology
Function and homology information


L-lactate dehydrogenase (NAD+) activity / lactate metabolic process / 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
2'-DEOXYADENOSINE-5'-MONOPHOSPHATE / 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE / 2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE / 2'-DEOXYURIDINE-5'-MONOPHOSPHATE / Chem-O0Q / L-lactate dehydrogenase
Similarity search - Component
Biological speciesPlasmodium vivax (malaria parasite P. vivax)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsCheung, Y. / Roethlisberger, P. / Mechaly, A. / Weber, P. / Wong, A. / Lo, Y. / Haouz, A. / Savage, P. / Hollenstein, M. / Tanner, J.
Funding support France, Hong Kong, 2items
OrganizationGrant numberCountry
Pasteur Institute France
Shirley Boyde Foundation Hong Kong
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: Evolution of abiotic cubane chemistries in a nucleic acid aptamer allows selective recognition of a malaria biomarker.
Authors: Cheung, Y.W. / Rothlisberger, P. / Mechaly, A.E. / Weber, P. / Levi-Acobas, F. / Lo, Y. / Wong, A.W.C. / Kinghorn, A.B. / Haouz, A. / Savage, G.P. / Hollenstein, M. / Tanner, J.A.
History
DepositionJan 14, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 15, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 5, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jan 24, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)161,14680
Polymers137,0444
Non-polymers24,10276
Water1,874104
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18850 Å2
ΔGint-72 kcal/mol
Surface area50170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.720, 80.720, 504.770
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
12
22

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain 'A' and (resid 3 through 53 or resid 55...A3 - 53
121(chain 'A' and (resid 3 through 53 or resid 55...A55 - 57
131(chain 'A' and (resid 3 through 53 or resid 55...A59 - 84
141(chain 'A' and (resid 3 through 53 or resid 55...A95 - 167
151(chain 'A' and (resid 3 through 53 or resid 55...A169 - 316
261(chain 'B' and (resid 3 through 53 or resid 55...B3 - 53
271(chain 'B' and (resid 3 through 53 or resid 55...B55 - 57
281(chain 'B' and (resid 3 through 53 or resid 55...B59 - 84
291(chain 'B' and (resid 3 through 53 or resid 55...B95 - 167
2101(chain 'B' and (resid 3 through 53 or resid 55...B169 - 316
3111(chain 'C' and (resid 3 through 53 or resid 55...C3 - 53
3121(chain 'C' and (resid 3 through 53 or resid 55...C55 - 57
3131(chain 'C' and (resid 3 through 53 or resid 55...C59 - 84
3141(chain 'C' and (resid 3 through 53 or resid 55...C95 - 167
3151(chain 'C' and (resid 3 through 53 or resid 55...C169 - 316
4161(chain 'D' and (resid 3 through 53 or resid 55...D3 - 53
4171(chain 'D' and (resid 3 through 53 or resid 55...D55 - 57
4181(chain 'D' and (resid 3 through 53 or resid 55...D59 - 84
4191(chain 'D' and (resid 3 through 53 or resid 55...D95 - 167
4201(chain 'D' and (resid 3 through 53 or resid 55...D169 - 316
1212chain 'F'F1 - 34
2222chain 'J'J1 - 34

NCS ensembles :
ID
1
2

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Components

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Protein , 1 types, 4 molecules ABCD

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


Mass: 34260.945 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium vivax (malaria parasite P. vivax)
Gene: LDH, ldh, PVC01_120033300, PVP01_1229700, PVT01_120033900
Production host: Escherichia coli (E. coli) / References: UniProt: Q4PRK9, L-lactate dehydrogenase

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Non-polymers , 6 types, 180 molecules

#2: Chemical
ChemComp-O0Q / ~{N}-[2-(1,2,3-triazol-1-yl)ethyl]cubane-1-carboxamide


Mass: 242.276 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C13H14N4O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical...
ChemComp-DG / 2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE


Type: DNA linking / Mass: 347.221 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: dGMP*YM
#4: Chemical
ChemComp-DU / 2'-DEOXYURIDINE-5'-MONOPHOSPHATE


Type: DNA linking / Mass: 308.182 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C9H13N2O8P
#5: Chemical
ChemComp-DA / 2'-DEOXYADENOSINE-5'-MONOPHOSPHATE


Type: DNA linking / Mass: 331.222 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C10H14N5O6P / Comment: dAMP*YM
#6: Chemical
ChemComp-DC / 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE


Type: DNA linking / Mass: 307.197 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C9H14N3O7P / Comment: dCMP*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 3 Å3/Da / Density % sol: 59 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 45% (v/v) 2-Methyl-2,4-pentanediol, 0,2 M Ammonium acetate and 0,1 M Hepes pH 7,5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 13, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.496→40.23 Å / Num. obs: 59822 / % possible obs: 99.64 % / Redundancy: 20 % / Biso Wilson estimate: 61.55 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.1715 / Rrim(I) all: 0.176 / Net I/σ(I): 13.25
Reflection shellResolution: 2.5→2.65 Å / Mean I/σ(I) obs: 1.43 / Num. unique obs: 9400 / CC1/2: 0.73 / Rrim(I) all: 2.036 / Rsym value: 1.986 / % possible all: 99.4

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ZH2

3zh2


Resolution: 2.5→40.23 Å / SU ML: 0.3852 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 31.2002
RfactorNum. reflection% reflectionSelection details
Rfree0.2427 2985 5 %Random selection
Rwork0.2029 ---
obs0.2049 59696 99.68 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 66.2 Å2
Refinement stepCycle: LAST / Resolution: 2.5→40.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9248 0 1498 104 10850
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.010411100
X-RAY DIFFRACTIONf_angle_d1.463215374
X-RAY DIFFRACTIONf_chiral_restr0.0741882
X-RAY DIFFRACTIONf_plane_restr0.00771692
X-RAY DIFFRACTIONf_dihedral_angle_d26.54494712
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.540.46891350.41652578X-RAY DIFFRACTION96.21
2.54-2.580.33181390.33112629X-RAY DIFFRACTION100
2.58-2.630.37361390.30452649X-RAY DIFFRACTION99.96
2.63-2.680.34671390.29342645X-RAY DIFFRACTION99.93
2.68-2.730.3541410.29182657X-RAY DIFFRACTION99.79
2.73-2.790.33371400.26932659X-RAY DIFFRACTION99.89
2.79-2.860.29561400.26692659X-RAY DIFFRACTION99.96
2.86-2.930.34061390.28572644X-RAY DIFFRACTION99.93
2.93-3.010.31231420.29262704X-RAY DIFFRACTION99.93
3.01-3.10.33181400.25422652X-RAY DIFFRACTION99.79
3.1-3.20.28771400.2432647X-RAY DIFFRACTION99.86
3.2-3.310.32251400.23252662X-RAY DIFFRACTION99.86
3.31-3.440.24831420.21582696X-RAY DIFFRACTION99.89
3.44-3.60.25891420.20292706X-RAY DIFFRACTION100
3.6-3.790.21051420.18352697X-RAY DIFFRACTION99.72
3.79-4.030.23351430.17542726X-RAY DIFFRACTION99.97
4.03-4.340.20151430.15862719X-RAY DIFFRACTION100
4.34-4.770.18971460.15022774X-RAY DIFFRACTION99.93
4.77-5.460.1931470.16752775X-RAY DIFFRACTION100
5.46-6.870.25511480.19712823X-RAY DIFFRACTION99.97
6.88-40.230.17341580.16553010X-RAY DIFFRACTION98.81
Refinement TLS params.Method: refined / Origin x: 0.102997940093 Å / Origin y: 36.9991453643 Å / Origin z: -33.2394426756 Å
111213212223313233
T0.57178719469 Å2-0.00686120213455 Å2-0.0191101468289 Å2-0.270112016876 Å2-0.0370599451523 Å2--0.390451156165 Å2
L0.437283962821 °2-0.0188575946701 °2-0.0809834227602 °2-0.733127804924 °20.00367073245515 °2--0.442163393491 °2
S-0.0175495204725 Å °0.0338333819888 Å °0.024548501859 Å °-0.31689680614 Å °-0.00951330675124 Å °-0.000562164779478 Å °0.00693332005086 Å °-0.0128651256153 Å °0.0211131262688 Å °
Refinement TLS groupSelection details: all

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