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- PDB-7d33: The Pb2+ complexed structure of TBA G8C mutant -

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Basic information

Entry
Database: PDB / ID: 7d33
TitleThe Pb2+ complexed structure of TBA G8C mutant
ComponentsDNA (5'-D(*GP*GP*TP*TP*GP*GP*TP*CP*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: 2.117 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*CP*TP*GP*GP*TP*TP*GP*G)-3')
B: DNA (5'-D(*GP*GP*TP*TP*GP*GP*TP*CP*TP*GP*GP*TP*TP*GP*G)-3')
C: DNA (5'-D(*GP*GP*TP*TP*GP*GP*TP*CP*TP*GP*GP*TP*TP*GP*G)-3')
D: DNA (5'-D(*GP*GP*TP*TP*GP*GP*TP*CP*TP*GP*GP*TP*TP*GP*G)-3')
E: DNA (5'-D(*GP*GP*TP*TP*GP*GP*TP*CP*TP*GP*GP*TP*TP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,55110
Polymers23,5155
Non-polymers1,0365
Water1,26170
1
A: DNA (5'-D(*GP*GP*TP*TP*GP*GP*TP*CP*TP*GP*GP*TP*TP*GP*G)-3')
B: DNA (5'-D(*GP*GP*TP*TP*GP*GP*TP*CP*TP*GP*GP*TP*TP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,8204
Polymers9,4062
Non-polymers4142
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: DNA (5'-D(*GP*GP*TP*TP*GP*GP*TP*CP*TP*GP*GP*TP*TP*GP*G)-3')
D: DNA (5'-D(*GP*GP*TP*TP*GP*GP*TP*CP*TP*GP*GP*TP*TP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,8204
Polymers9,4062
Non-polymers4142
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: DNA (5'-D(*GP*GP*TP*TP*GP*GP*TP*CP*TP*GP*GP*TP*TP*GP*G)-3')
hetero molecules

E: DNA (5'-D(*GP*GP*TP*TP*GP*GP*TP*CP*TP*GP*GP*TP*TP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,8204
Polymers9,4062
Non-polymers4142
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Unit cell
Length a, b, c (Å)78.765, 51.941, 57.063
Angle α, β, γ (deg.)90.000, 113.590, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11D-202-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B
31chain C
41chain D
51chain E

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

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Components

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


Mass: 4703.027 Da / Num. of mol.: 5 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical
ChemComp-PB / LEAD (II) ION


Mass: 207.200 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Pb / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 70 / 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: 2.27 Å3/Da / Density % sol: 45.92 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 10% v/v MPD, 40 mM sodium cacodylate pH 7.0, 28 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: BL18U1 / Wavelength: 0.9793 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Mar 22, 2020
RadiationMonochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.117→37.37 Å / Num. obs: 22836 / % possible obs: 96.9 % / Redundancy: 6.7 % / Biso Wilson estimate: 24.59 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.239 / Rpim(I) all: 0.099 / Rrim(I) all: 0.259 / Net I/σ(I): 6.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.12-2.236.70.9991166917440.7730.4121.0822.499.3
6.69-37.376.10.10723863940.9930.0460.11712.697.6

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
PHENIX1.12_2829refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7D31

7d31


Resolution: 2.117→25.338 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 23.98 / Stereochemistry target values: ML
Details: the entry contains Friedel pairs in F_Plus/Minus and I_Plus/Minus columns
RfactorNum. reflection% reflection
Rfree0.2398 2283 10 %
Rwork0.2122 20553 -
obs0.2149 22836 96.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 43.26 Å2 / Biso mean: 24.5362 Å2 / Biso min: 16.06 Å2
Refinement stepCycle: final / Resolution: 2.117→25.338 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1560 5 70 1635
Biso mean--26.04 25.71 -
Num. residues----75
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051745
X-RAY DIFFRACTIONf_angle_d0.7512700
X-RAY DIFFRACTIONf_chiral_restr0.034295
X-RAY DIFFRACTIONf_plane_restr0.00575
X-RAY DIFFRACTIONf_dihedral_angle_d32.066730
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A730X-RAY DIFFRACTION0.588TORSIONAL
12B730X-RAY DIFFRACTION0.588TORSIONAL
13C730X-RAY DIFFRACTION0.588TORSIONAL
14D730X-RAY DIFFRACTION0.588TORSIONAL
15E730X-RAY DIFFRACTION0.588TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.117-2.16260.27241490.26481349100
2.1626-2.21290.30071460.2602129499
2.2129-2.26820.353790.272571654
2.2682-2.32950.28761510.2507132699
2.3295-2.3980.24711370.2606127199
2.398-2.47530.24221550.2441372100
2.4753-2.56370.24371460.21731306100
2.5637-2.66620.26161450.20811333100
2.6662-2.78740.26741470.21721323100
2.7874-2.93420.2761480.23131322100
2.9342-3.11770.28791500.2471326100
3.1177-3.35790.22431430.20491339100
3.3579-3.69490.26811450.19941318100
3.6949-4.22750.19821460.19051310100
4.2275-5.31810.21291460.15641326100
5.3181-25.3380.16451500.16132299
Refinement TLS params.Method: refined / Origin x: -6.0568 Å / Origin y: -24.7696 Å / Origin z: -7.0574 Å
111213212223313233
T0.1975 Å2-0.0101 Å2-0.0224 Å2-0.1767 Å2-0.0024 Å2--0.2218 Å2
L0.7144 °2-0.2019 °2-0.9002 °2-0.0581 °20.2338 °2--2.2827 °2
S-0.0234 Å °0.0937 Å °-0.0463 Å °-0.028 Å °-0.0528 Å °0.0221 Å °-0.0837 Å °-0.2493 Å °0.078 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 15
2X-RAY DIFFRACTION1allB1 - 15
3X-RAY DIFFRACTION1allC1 - 15
4X-RAY DIFFRACTION1allD1 - 15
5X-RAY DIFFRACTION1allE1 - 15
6X-RAY DIFFRACTION1allP1 - 5
7X-RAY DIFFRACTION1allS1 - 70

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