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- PDB-8gzl: Crystal structure of Cd2+-bound DNA aptamer -

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Basic information

Entry
Database: PDB / ID: 8gzl
TitleCrystal structure of Cd2+-bound DNA aptamer
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: 3 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
C: 25-mer DNA
D: 25-mer DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,60411
Polymers30,7684
Non-polymers8377
Water543
1
A: 25-mer DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,0544
Polymers7,6921
Non-polymers3623
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area250 Å2
ΔGint-12 kcal/mol
Surface area4860 Å2
MethodPISA
2
B: 25-mer DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,9423
Polymers7,6921
Non-polymers2502
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area250 Å2
ΔGint-12 kcal/mol
Surface area4800 Å2
MethodPISA
3
C: 25-mer DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,8042
Polymers7,6921
Non-polymers1121
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area120 Å2
ΔGint-9 kcal/mol
Surface area4780 Å2
MethodPISA
4
D: 25-mer DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,8042
Polymers7,6921
Non-polymers1121
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area120 Å2
ΔGint-8 kcal/mol
Surface area4730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)26.800, 45.690, 147.020
Angle α, β, γ (deg.)90.000, 92.870, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B
31chain C
41chain D

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
1chain AAA
2chain BBB
3chain CCC
4chain DDD

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Components

#1: DNA chain
25-mer DNA


Mass: 7691.934 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cd / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-BA / BARIUM ION


Mass: 137.327 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ba / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / 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: 2.92 Å3/Da / Density % sol: 57.9 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 45% MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 1, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3→29.37 Å / Num. obs: 6161 / % possible obs: 84.3 % / Redundancy: 4.9 % / Biso Wilson estimate: 86.51 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.106 / Rpim(I) all: 0.051 / Rrim(I) all: 0.118 / Net I/σ(I): 7.3 / Num. measured all: 30010 / Scaling rejects: 46
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
3-3.184.40.45940969350.9760.2330.5181.881.7
9-29.374.80.05812492590.9970.030.06516.691.3

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Processing

Software
NameVersionClassification
Aimless0.5.29data scaling
PHENIX1.19.1_4122refinement
PDB_EXTRACT3.27data extraction
autoPROCdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8GZJ

8gzj


Resolution: 3→29.37 Å / SU ML: 0.56 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 40.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2841 301 5.06 %
Rwork0.2334 5652 -
obs0.2362 5953 81.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 188.03 Å2 / Biso mean: 95.6236 Å2 / Biso min: 30 Å2
Refinement stepCycle: final / Resolution: 3→29.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 2040 6 3 2049
Biso mean--110.39 30 -
Num. residues----101
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A984X-RAY DIFFRACTION17.078TORSIONAL
12B984X-RAY DIFFRACTION17.078TORSIONAL
13C984X-RAY DIFFRACTION17.078TORSIONAL
14D984X-RAY DIFFRACTION17.078TORSIONAL
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 (%)
3-3.780.45371400.34152627276776
3.78-29.370.23871610.20373025318687
Refinement TLS params.Method: refined / Origin x: 4.7191 Å / Origin y: 9.3045 Å / Origin z: 38.6643 Å
111213212223313233
T0.9686 Å2-0.3438 Å2-0.1401 Å2-0.8816 Å20.0861 Å2--0.7641 Å2
L-0.2476 °2-0.5282 °20.1581 °2--0.1034 °20.0017 °2--0.1747 °2
S-0.1135 Å °0.0521 Å °-0.0457 Å °0.1996 Å °0.0889 Å °-0.0472 Å °-0.8263 Å °0.1028 Å °-0.0092 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 25
2X-RAY DIFFRACTION1allB1 - 25
3X-RAY DIFFRACTION1allC1 - 25
4X-RAY DIFFRACTION1allD1 - 25
5X-RAY DIFFRACTION1allE1 - 5
6X-RAY DIFFRACTION1allF1 - 2
7X-RAY DIFFRACTION1allG1 - 3

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