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

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Basic information

Entry
Database: PDB / ID: 8gzj
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 / SAD / Resolution: 2.093 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)23,95910
Polymers23,0733
Non-polymers8877
Water30617
1
A: 25-mer DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,0784
Polymers7,6911
Non-polymers3873
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area310 Å2
ΔGint-15 kcal/mol
Surface area4740 Å2
MethodPISA
2
B: 25-mer DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,9413
Polymers7,6911
Non-polymers2502
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area310 Å2
ΔGint-14 kcal/mol
Surface area4860 Å2
MethodPISA
3
C: 25-mer DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,9413
Polymers7,6911
Non-polymers2502
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area290 Å2
ΔGint-13 kcal/mol
Surface area4550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.474, 41.932, 73.247
Angle α, β, γ (deg.)90.000, 106.200, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 1 through 23 or (resid 24 and (name P or name OP1 or name OP2 or name O5))))
21(chain B and (resid 1 through 23 or (resid 24 and (name P or name OP1 or name OP2 or name O5))))
31chain C

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: DG / Beg label comp-ID: DG / End auth comp-ID: DT / End label comp-ID: DT / Auth seq-ID: 1 - 24 / Label seq-ID: 1 - 24

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1(chain A and (resid 1 through 23 or (resid 24 and (name P or name OP1 or name OP2 or name O5))))AA
2(chain B and (resid 1 through 23 or (resid 24 and (name P or name OP1 or name OP2 or name O5))))BB
3chain CCC

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Components

#1: DNA chain 25-mer DNA


Mass: 7690.945 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-CD / CADMIUM ION


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


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


Mass: 18.015 Da / Num. of mol.: 17 / 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: 2.6 Å3/Da / Density % sol: 52.76 % / 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: BL17U1 / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Dec 10, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.09→30 Å / Num. obs: 13259 / % possible obs: 93.5 % / Redundancy: 6 % / Biso Wilson estimate: 29.34 Å2 / Rmerge(I) obs: 0.061 / Rpim(I) all: 0.027 / Rrim(I) all: 0.067 / Χ2: 0.881 / Net I/σ(I): 13
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.1-2.1840.6611230.9040.3040.730.88580.4
2.18-2.264.60.54512640.9580.2470.6010.91191.8
2.26-2.375.40.55713690.9660.2380.6071.22798.1
2.37-2.496.10.38414020.9740.1660.4190.95596.9
2.49-2.656.60.21213700.9930.0880.230.92198.1
2.65-2.857.10.14114070.9950.0570.1520.88998.9
2.85-3.146.80.07413950.9950.0310.0810.89899.1
3.14-3.596.40.06513540.9880.0290.0720.85394.6
3.59-4.526.30.04213370.9950.0180.0450.66393.4
4.52-305.70.03812380.9940.0180.0420.61483.7

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.12_2829refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.093→23.446 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 30.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2735 494 4.9 %
Rwork0.2321 9581 -
obs0.2342 10075 70.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 180.9 Å2 / Biso mean: 43.5926 Å2 / Biso min: 9.72 Å2
Refinement stepCycle: final / Resolution: 2.093→23.446 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1465 6 17 1488
Biso mean--111.33 27.55 -
Num. residues----75
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111640
X-RAY DIFFRACTIONf_angle_d1.1662531
X-RAY DIFFRACTIONf_chiral_restr0.062284
X-RAY DIFFRACTIONf_plane_restr0.00871
X-RAY DIFFRACTIONf_dihedral_angle_d31.833704
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A684X-RAY DIFFRACTION10.876TORSIONAL
12B684X-RAY DIFFRACTION10.876TORSIONAL
13C684X-RAY DIFFRACTION10.876TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.093-2.30350.3756730.3162116935
2.3035-2.63640.35731010.3005200560
2.6364-3.32010.31181700.2595331098
3.3201-23.4460.21471500.1896309789
Refinement TLS params.Method: refined / Origin x: 21.2867 Å / Origin y: -13.4068 Å / Origin z: 31.7707 Å
111213212223313233
T0.3655 Å20.0905 Å20.1105 Å2-0.3843 Å20.066 Å2--0.2884 Å2
L-0.2933 °20.1157 °2-0.2584 °2--0.577 °2-0.2413 °2--2.6929 °2
S0.0689 Å °0.0762 Å °0.1538 Å °-0.1015 Å °-0.0523 Å °-0.0862 Å °-0.0866 Å °0.2733 Å °0.0203 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 25
2X-RAY DIFFRACTION1allB1 - 25
3X-RAY DIFFRACTION1allC1 - 24
4X-RAY DIFFRACTION1allX1 - 3
5X-RAY DIFFRACTION1allD1 - 4
6X-RAY DIFFRACTION1allE1 - 17

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