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- PDB-7d32: The TBA-Pb2+ complex in P41212 space group -

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Basic information

Entry
Database: PDB / ID: 7d32
TitleThe TBA-Pb2+ complex in P41212 space group
ComponentsDNA (5'-D(*GP*GP*TP*TP*GP*GP*TP*GP*TP*GP*GP*TP*TP*GP*G)-3')
KeywordsDNA / Quadruplex / Pb2+-binding / DNA aptamer
Function / homologyLEAD (II) ION / DNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.707 Å
AuthorsLiu, H.H. / Gao, Y.Q. / Sheng, J. / Gan, J.H.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2019FY101506 China
CitationJournal: Sci Rep / Year: 2022
Title: Structure-guided development of Pb 2+ -binding DNA aptamers.
Authors: Liu, H. / Gao, Y. / Mathivanan, J. / Shen, F. / Chen, X. / Li, Y. / Shao, Z. / Zhang, Y. / Shao, Q. / Sheng, J. / Gan, J.
History
DepositionSep 18, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 22, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 6, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA (5'-D(*GP*GP*TP*TP*GP*GP*TP*GP*TP*GP*GP*TP*TP*GP*G)-3')
B: DNA (5'-D(*GP*GP*TP*TP*GP*GP*TP*GP*TP*GP*GP*TP*TP*GP*G)-3')
C: DNA (5'-D(*GP*GP*TP*TP*GP*GP*TP*GP*TP*GP*GP*TP*TP*GP*G)-3')
D: DNA (5'-D(*GP*GP*TP*TP*GP*GP*TP*GP*TP*GP*GP*TP*TP*GP*G)-3')
E: DNA (5'-D(*GP*GP*TP*TP*GP*GP*TP*GP*TP*GP*GP*TP*TP*GP*G)-3')
F: DNA (5'-D(*GP*GP*TP*TP*GP*GP*TP*GP*TP*GP*GP*TP*TP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,70212
Polymers28,4586
Non-polymers1,2436
Water1,53185
1
A: DNA (5'-D(*GP*GP*TP*TP*GP*GP*TP*GP*TP*GP*GP*TP*TP*GP*G)-3')
B: DNA (5'-D(*GP*GP*TP*TP*GP*GP*TP*GP*TP*GP*GP*TP*TP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,9014
Polymers9,4862
Non-polymers4142
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: DNA (5'-D(*GP*GP*TP*TP*GP*GP*TP*GP*TP*GP*GP*TP*TP*GP*G)-3')
D: DNA (5'-D(*GP*GP*TP*TP*GP*GP*TP*GP*TP*GP*GP*TP*TP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,9014
Polymers9,4862
Non-polymers4142
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: DNA (5'-D(*GP*GP*TP*TP*GP*GP*TP*GP*TP*GP*GP*TP*TP*GP*G)-3')
F: DNA (5'-D(*GP*GP*TP*TP*GP*GP*TP*GP*TP*GP*GP*TP*TP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,9014
Polymers9,4862
Non-polymers4142
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)27.301, 53.107, 152.492
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B
31chain C
41chain D
51chain E
61chain F

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: DG / Beg label comp-ID: DG / End auth comp-ID: DG / End label comp-ID: DG / Auth seq-ID: 1 - 15 / Label seq-ID: 1 - 15

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1chain AAA
2chain BBB
3chain CCC
4chain DDD
5chain EEE
6chain FFF

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Components

#1: DNA chain
DNA (5'-D(*GP*GP*TP*TP*GP*GP*TP*GP*TP*GP*GP*TP*TP*GP*G)-3')


Mass: 4743.051 Da / Num. of mol.: 6 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical
ChemComp-PB / LEAD (II) ION


Mass: 207.200 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Pb / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 85 / Source method: isolated from a natural source / Formula: H2O
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: 1.94 Å3/Da / Density % sol: 36.67 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 10% v/v MPD, 40 mM sodium cacodylate pH 7.0, 12 mM spermine tetra-HCl, and 80 mM sodium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 25, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.7→30 Å / Num. obs: 24087 / % possible obs: 96 % / Redundancy: 5.7 % / Biso Wilson estimate: 12.41 Å2 / Rmerge(I) obs: 0.146 / Rpim(I) all: 0.059 / Rrim(I) all: 0.159 / Χ2: 0.885 / Net I/σ(I): 5.5 / Num. measured all: 137260
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.7-1.762.60.43220320.1640.2810.520.884.4
1.76-1.833.10.42222820.270.2570.4980.78792
1.83-1.913.40.40523070.4680.230.470.83794.5
1.91-2.024.50.43323680.5120.2160.4880.85796.5
2.02-2.145.30.4124470.6170.1870.4530.91198.3
2.14-2.315.60.36524560.80.160.40.94598.2
2.31-2.546.30.26624510.9430.1080.2880.90998.7
2.54-2.917.80.19625080.9770.070.2080.95799.2
2.91-3.6680.11425210.9960.040.1210.91498.5
3.66-3090.07927150.9920.0270.0840.80499.1

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.12_2829refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7D31

7d31


Resolution: 1.707→26.447 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.52 / Phase error: 19.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2146 1050 5.07 %
Rwork0.1885 19671 -
obs0.1898 20721 82.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 41.98 Å2 / Biso mean: 19.6314 Å2 / Biso min: 9.38 Å2
Refinement stepCycle: final / Resolution: 1.707→26.447 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1890 6 85 1981
Biso mean--16 18.28 -
Num. residues----90
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062118
X-RAY DIFFRACTIONf_angle_d0.9183282
X-RAY DIFFRACTIONf_chiral_restr0.047354
X-RAY DIFFRACTIONf_plane_restr0.00690
X-RAY DIFFRACTIONf_dihedral_angle_d32.599876
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A876X-RAY DIFFRACTION7.417TORSIONAL
12B876X-RAY DIFFRACTION7.417TORSIONAL
13C876X-RAY DIFFRACTION7.417TORSIONAL
14D876X-RAY DIFFRACTION7.417TORSIONAL
15E876X-RAY DIFFRACTION7.417TORSIONAL
16F876X-RAY DIFFRACTION7.417TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.707-1.79680.285480.2668104432
1.7968-1.90940.29931200.2776212764
1.9094-2.05670.2671520.267300089
2.0567-2.26360.26291650.2305322396
2.2636-2.59090.24511750.1986331198
2.5909-3.26330.2451920.1719339199
3.2633-26.4470.1351980.1291357599
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)
12.4973-0.9425-0.1844.43091.04862.4549-0.0711-0.2761-0.11890.27010.08850.2651-0.0430.08990.00050.1475-0.00640.00060.20810.00080.0977-19.138919.2929218.7703
24.1691-0.07060.33692.3061-0.97793.65850.0466-0.07670.15280.0531-0.04640.087-0.0996-0.07450.00670.1297-0.00930.00460.129-0.02560.1092-19.636526.5161208.8027
32.8348-0.07640.5871.07130.32492.63180.0049-0.0770.0615-0.005-0.00140.07190.0752-0.0582-0.00060.1479-0.01140.00160.08820.01970.1149-20.493923.7087193.3266
43.30210.56340.05931.6695-0.00873.104-0.07130.1203-0.0255-0.0850.029-0.24250.11710.02120.03830.12540.0093-0.00790.0637-0.00910.0955-11.871823.6173184.3424
53.1003-0.3454-0.6153.40570.60163.8139-0.0889-0.14490.1893-0.13270.07170.2059-0.08340.27520.01460.1052-0.0001-0.01740.13720.02060.1342-14.429353.1581212.298
62.3855-0.18751.37773.90390.30883.85630.1648-0.3589-0.18660.38290.05780.18860.49660.0244-0.20950.2047-0.0054-0.01030.24340.03940.1172-13.530547.2608222.9932
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resseq 1:15)A1 - 15
2X-RAY DIFFRACTION2(chain B and resseq 1:15)B1 - 15
3X-RAY DIFFRACTION3(chain C and resseq 1:15)C1 - 15
4X-RAY DIFFRACTION4(chain D and resseq 1:15)D1 - 15
5X-RAY DIFFRACTION5(chain E and resseq 1:15)E1 - 15
6X-RAY DIFFRACTION6(chain F and resseq 1:15)F1 - 15

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