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- PDB-8gzm: Crystal structure of Cd2+-bound DNA aptamer T22C mutant -

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Basic information

Entry
Database: PDB / ID: 8gzm
TitleCrystal structure of Cd2+-bound DNA aptamer T22C 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: 2.55 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,3146
Polymers7,6771
Non-polymers6375
Water905
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area570 Å2
ΔGint-25 kcal/mol
Surface area4710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.388, 46.388, 107.301
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: DNA chain 25-mer DNA


Mass: 7676.922 Da / Num. of mol.: 1 / Mutation: T22C / 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.: 3 / Source method: obtained synthetically / Formula: Ba / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / 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: 3.76 Å3/Da / Density % sol: 67.28 % / Description: Rod-like
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 10% 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: Jun 8, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.55→30 Å / Num. obs: 4194 / % possible obs: 99.1 % / Redundancy: 22.4 % / Biso Wilson estimate: 50.03 Å2 / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.018 / Rrim(I) all: 0.08 / Χ2: 1.117 / Net I/σ(I): 14.2 / Num. measured all: 94083
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.55-2.6421.20.6683910.8430.6980.7440.908100
2.64-2.7522.40.6034240.9270.4270.6490.969100
2.75-2.8725.80.5683960.9770.2320.4910.908100
2.87-3.0224.60.4244090.9890.1070.5350.967100
3.02-3.2124.30.2084060.9970.0420.2121.016100
3.21-3.46230.1084230.9930.0240.1110.98399.8
3.46-3.8123.80.094230.9980.0190.0921.078100
3.81-4.3621.60.0694230.9970.0160.071.279100
4.36-5.4820.80.0594390.9890.0140.0611.47998.2
5.48-3017.40.0554600.9860.0150.0571.7293.9

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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: 2.55→22.67 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2052 206 5.41 %
Rwork0.1936 3604 -
obs0.1969 3810 90.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 156.88 Å2 / Biso mean: 54.2886 Å2 / Biso min: 20.24 Å2
Refinement stepCycle: final / Resolution: 2.55→22.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 509 5 5 519
Biso mean--101.48 32.55 -
Num. residues----25
LS refinement shellResolution: 2.55→22.67 Å / Rfactor Rfree error: 0 / Total num. of bins used: 1
RfactorNum. reflection% reflection
Rfree0.2022 206 -
Rwork0.1966 3604 -
all-3810 -
obs--91 %
Refinement TLS params.Method: refined / Origin x: -3.9855 Å / Origin y: 20.2266 Å / Origin z: -8.5624 Å
111213212223313233
T0.3739 Å2-0.1441 Å20.0513 Å2-0.3433 Å2-0.0368 Å2--0.366 Å2
L2.1743 °20.9537 °20.9461 °2-4.7361 °2-0.3717 °2--5.1106 °2
S0.518 Å °-0.3462 Å °0.1079 Å °0.4315 Å °-0.0576 Å °0.389 Å °0.2206 Å °0.3591 Å °-0.4542 Å °
Refinement TLS groupSelection details: (chain A and resseq 1:25)

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