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- PDB-8gzk: Crystal structure of Cd2+-bound DNA aptamer T10A mutant -

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Basic information

Entry
Database: PDB / ID: 8gzk
TitleCrystal structure of Cd2+-bound DNA aptamer T10A mutant
Components25-mer DNA
KeywordsDNA / DNA aptamer / Cd2+-binding / complex
Function / homology: / : / DNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.94 Å
AuthorsGan, J.H. / Liu, H.H. / Gao, Y.Q.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32171197 China
CitationJournal: Nucleic Acids Res. / Year: 2023
Title: Crystal structures and identification of novel Cd2+-specific DNA aptamer.
Authors: Liu, H. / Gao, Y. / Mathivanan, J. / Armour-Garb, Z. / Shao, Z. / Zhang, Y. / Zhao, X. / Shao, Q. / Zhang, W. / Yang, J. / Cao, C. / Li, H. / Sheng, J. / Gan, J.
History
DepositionSep 27, 2022Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Aug 9, 2023Provider: repository / Type: Initial release
Revision 1.1May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 25-mer DNA
B: 25-mer DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,3119
Polymers15,4002
Non-polymers9117
Water362
1
A: 25-mer DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,2245
Polymers7,7001
Non-polymers5244
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 25-mer DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,0874
Polymers7,7001
Non-polymers3873
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)28.708, 136.379, 51.133
Angle α, β, γ (deg.)90.000, 104.390, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 1 through 9 or resid 11 through 25))
21(chain B and (resid 1 through 9 or resid 11 through 25))

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: DG / Beg label comp-ID: DG / End auth comp-ID: DC / End label comp-ID: DC / Auth seq-ID: 1 - 25 / Label seq-ID: 1 - 25

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1(chain A and (resid 1 through 9 or resid 11 through 25))AA
2(chain B and (resid 1 through 9 or resid 11 through 25))BB

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Components

#1: DNA chain 25-mer DNA


Mass: 7699.959 Da / Num. of mol.: 2 / Mutation: T10A / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cd / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-BA / BARIUM ION


Mass: 137.327 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ba / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 3.15 Å3/Da / Density % sol: 60.93 % / Description: Rod
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 10% MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Dec 1, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.94→30 Å / Num. obs: 3980 / % possible obs: 97.4 % / Redundancy: 5.1 % / Biso Wilson estimate: 37.38 Å2 / Rmerge(I) obs: 0.091 / Rpim(I) all: 0.045 / Rrim(I) all: 0.102 / Χ2: 0.897 / Net I/σ(I): 11.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.95-3.063.40.4153730.7410.2390.4820.87191.4
3.06-3.183.50.2173870.9710.1190.2490.90293
3.18-3.324.80.1383820.9930.0630.1520.89697.2
3.32-3.55.10.124090.9950.0550.1321.02898.3
3.5-3.725.10.1253880.9970.0570.1380.99197.7
3.72-45.30.1254070.9890.0570.1381.06599
4-4.45.50.0963950.9930.0420.1050.92598.5
4.4-5.0460.0814120.9920.0340.0880.89299.5
5.04-6.345.90.0684110.9960.030.0750.75100
6.34-306.50.094160.9860.0450.1010.72399.5

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.19.1_4122refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8GZJ

8gzj


Resolution: 2.94→28.08 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.47 / Phase error: 28.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2894 307 8.45 %
Rwork0.2329 3327 -
obs0.2365 3634 89.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 111.39 Å2 / Biso mean: 54.3181 Å2 / Biso min: 14.14 Å2
Refinement stepCycle: final / Resolution: 2.94→28.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1022 6 2 1030
Biso mean--92.15 51.28 -
Num. residues----51
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A466X-RAY DIFFRACTION12.626TORSIONAL
12B466X-RAY DIFFRACTION12.626TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 2

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.94-3.710.30761590.25441463162280
3.71-28.080.27721480.21661864201299
Refinement TLS params.Method: refined / Origin x: 0.6685 Å / Origin y: 27.7067 Å / Origin z: 12.8518 Å
111213212223313233
T0.3032 Å2-1.3108 Å2-0.3752 Å2-0.0528 Å2-0.0884 Å2--0.359 Å2
L0.5951 °20.6489 °20.2018 °2-0.4213 °20.1508 °2---0.0697 °2
S-0.212 Å °0.1464 Å °0.4555 Å °-0.1393 Å °-0.0139 Å °0.0113 Å °-0.6825 Å °0.4039 Å °-0.0099 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 25
2X-RAY DIFFRACTION1allB1 - 25
3X-RAY DIFFRACTION1allC1 - 2
4X-RAY DIFFRACTION1allD1 - 5
5X-RAY DIFFRACTION1allE1 - 2

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