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- PDB-8aml: Crystal structure of AUGUGGCAU duplex with cadmium ions -

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Basic information

Entry
Database: PDB / ID: 8aml
TitleCrystal structure of AUGUGGCAU duplex with cadmium ions
ComponentsRNA (5'-R(*AP*UP*GP*UP*GP*GP*CP*AP*U)-3')
KeywordsRNA / UG wobble / Cd ions / UGG repeats
Function / homology: / RNA
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsKiliszek, A. / Rypniewski, W.
Funding support Poland, 1items
OrganizationGrant numberCountry
Other government Poland
CitationJournal: Rna / Year: 2022
Title: Structure and thermodynamics of a UGG motif interacting with Ba2+ and other metal ions: accommodating changes in the RNA structure and the presence of a G(syn)-G(syn) pair.
Authors: Kiliszek, A. / Pluta, M. / Bejger, M. / Rypniewski, W.
History
DepositionAug 3, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 23, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 1, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA (5'-R(*AP*UP*GP*UP*GP*GP*CP*AP*U)-3')
B: RNA (5'-R(*AP*UP*GP*UP*GP*GP*CP*AP*U)-3')
C: RNA (5'-R(*AP*UP*GP*UP*GP*GP*CP*AP*U)-3')
D: RNA (5'-R(*AP*UP*GP*UP*GP*GP*CP*AP*U)-3')
E: RNA (5'-R(*AP*UP*GP*UP*GP*GP*CP*AP*U)-3')
F: RNA (5'-R(*AP*UP*GP*UP*GP*GP*CP*AP*U)-3')
G: RNA (5'-R(*AP*UP*GP*UP*GP*GP*CP*AP*U)-3')
H: RNA (5'-R(*AP*UP*GP*UP*GP*GP*CP*AP*U)-3')
I: RNA (5'-R(*AP*UP*GP*UP*GP*GP*CP*AP*U)-3')
J: RNA (5'-R(*AP*UP*GP*UP*GP*GP*CP*AP*U)-3')
K: RNA (5'-R(*AP*UP*GP*UP*GP*GP*CP*AP*U)-3')
L: RNA (5'-R(*AP*UP*GP*UP*GP*GP*CP*AP*U)-3')
M: RNA (5'-R(*AP*UP*GP*UP*GP*GP*CP*AP*U)-3')
N: RNA (5'-R(*AP*UP*GP*UP*GP*GP*CP*AP*U)-3')
O: RNA (5'-R(*AP*UP*GP*UP*GP*GP*CP*AP*U)-3')
P: RNA (5'-R(*AP*UP*GP*UP*GP*GP*CP*AP*U)-3')
Q: RNA (5'-R(*AP*UP*GP*UP*GP*GP*CP*AP*U)-3')
R: RNA (5'-R(*AP*UP*GP*UP*GP*GP*CP*AP*U)-3')
S: RNA (5'-R(*AP*UP*GP*UP*GP*GP*CP*AP*U)-3')
T: RNA (5'-R(*AP*UP*GP*UP*GP*GP*CP*AP*U)-3')
U: RNA (5'-R(*AP*UP*GP*UP*GP*GP*CP*AP*U)-3')
V: RNA (5'-R(*AP*UP*GP*UP*GP*GP*CP*AP*U)-3')
Y: RNA (5'-R(*AP*UP*GP*UP*GP*GP*CP*AP*U)-3')
Z: RNA (5'-R(*AP*UP*GP*UP*GP*GP*CP*AP*U)-3')
a: RNA (5'-R(*AP*UP*GP*UP*GP*GP*CP*AP*U)-3')
b: RNA (5'-R(*AP*UP*GP*UP*GP*GP*CP*AP*U)-3')
c: RNA (5'-R(*AP*UP*GP*UP*GP*GP*CP*AP*U)-3')
d: RNA (5'-R(*AP*UP*GP*UP*GP*GP*CP*AP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,77431
Polymers80,43728
Non-polymers3373
Water181
1
A: RNA (5'-R(*AP*UP*GP*UP*GP*GP*CP*AP*U)-3')
B: RNA (5'-R(*AP*UP*GP*UP*GP*GP*CP*AP*U)-3')


Theoretical massNumber of molelcules
Total (without water)5,7462
Polymers5,7462
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area850 Å2
ΔGint-4 kcal/mol
Surface area3420 Å2
2
C: RNA (5'-R(*AP*UP*GP*UP*GP*GP*CP*AP*U)-3')
D: RNA (5'-R(*AP*UP*GP*UP*GP*GP*CP*AP*U)-3')


Theoretical massNumber of molelcules
Total (without water)5,7462
Polymers5,7462
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area840 Å2
ΔGint-3 kcal/mol
Surface area3410 Å2
3
E: RNA (5'-R(*AP*UP*GP*UP*GP*GP*CP*AP*U)-3')
F: RNA (5'-R(*AP*UP*GP*UP*GP*GP*CP*AP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,8583
Polymers5,7462
Non-polymers1121
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1040 Å2
ΔGint-14 kcal/mol
Surface area3380 Å2
4
G: RNA (5'-R(*AP*UP*GP*UP*GP*GP*CP*AP*U)-3')
H: RNA (5'-R(*AP*UP*GP*UP*GP*GP*CP*AP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,8583
Polymers5,7462
Non-polymers1121
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1020 Å2
ΔGint-15 kcal/mol
Surface area3360 Å2
5
I: RNA (5'-R(*AP*UP*GP*UP*GP*GP*CP*AP*U)-3')
J: RNA (5'-R(*AP*UP*GP*UP*GP*GP*CP*AP*U)-3')


Theoretical massNumber of molelcules
Total (without water)5,7462
Polymers5,7462
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area860 Å2
ΔGint-4 kcal/mol
Surface area3440 Å2
6
K: RNA (5'-R(*AP*UP*GP*UP*GP*GP*CP*AP*U)-3')
L: RNA (5'-R(*AP*UP*GP*UP*GP*GP*CP*AP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,8583
Polymers5,7462
Non-polymers1121
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1000 Å2
ΔGint-14 kcal/mol
Surface area3390 Å2
7
M: RNA (5'-R(*AP*UP*GP*UP*GP*GP*CP*AP*U)-3')
N: RNA (5'-R(*AP*UP*GP*UP*GP*GP*CP*AP*U)-3')


Theoretical massNumber of molelcules
Total (without water)5,7462
Polymers5,7462
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area840 Å2
ΔGint-4 kcal/mol
Surface area3410 Å2
8
O: RNA (5'-R(*AP*UP*GP*UP*GP*GP*CP*AP*U)-3')
P: RNA (5'-R(*AP*UP*GP*UP*GP*GP*CP*AP*U)-3')


Theoretical massNumber of molelcules
Total (without water)5,7462
Polymers5,7462
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area860 Å2
ΔGint-3 kcal/mol
Surface area3430 Å2
9
Q: RNA (5'-R(*AP*UP*GP*UP*GP*GP*CP*AP*U)-3')
R: RNA (5'-R(*AP*UP*GP*UP*GP*GP*CP*AP*U)-3')


Theoretical massNumber of molelcules
Total (without water)5,7462
Polymers5,7462
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area850 Å2
ΔGint-3 kcal/mol
Surface area3420 Å2
10
S: RNA (5'-R(*AP*UP*GP*UP*GP*GP*CP*AP*U)-3')
T: RNA (5'-R(*AP*UP*GP*UP*GP*GP*CP*AP*U)-3')


Theoretical massNumber of molelcules
Total (without water)5,7462
Polymers5,7462
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area880 Å2
ΔGint-3 kcal/mol
Surface area3430 Å2
11
U: RNA (5'-R(*AP*UP*GP*UP*GP*GP*CP*AP*U)-3')
V: RNA (5'-R(*AP*UP*GP*UP*GP*GP*CP*AP*U)-3')


Theoretical massNumber of molelcules
Total (without water)5,7462
Polymers5,7462
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area830 Å2
ΔGint-3 kcal/mol
Surface area3390 Å2
12
Y: RNA (5'-R(*AP*UP*GP*UP*GP*GP*CP*AP*U)-3')
Z: RNA (5'-R(*AP*UP*GP*UP*GP*GP*CP*AP*U)-3')


Theoretical massNumber of molelcules
Total (without water)5,7462
Polymers5,7462
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area830 Å2
ΔGint-3 kcal/mol
Surface area3400 Å2
13
a: RNA (5'-R(*AP*UP*GP*UP*GP*GP*CP*AP*U)-3')
b: RNA (5'-R(*AP*UP*GP*UP*GP*GP*CP*AP*U)-3')


Theoretical massNumber of molelcules
Total (without water)5,7462
Polymers5,7462
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area840 Å2
ΔGint-4 kcal/mol
Surface area3390 Å2
14
c: RNA (5'-R(*AP*UP*GP*UP*GP*GP*CP*AP*U)-3')
d: RNA (5'-R(*AP*UP*GP*UP*GP*GP*CP*AP*U)-3')


Theoretical massNumber of molelcules
Total (without water)5,7462
Polymers5,7462
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area820 Å2
ΔGint-2 kcal/mol
Surface area3390 Å2
Unit cell
Length a, b, c (Å)28.193, 90.600, 139.623
Angle α, β, γ (deg.)90.000, 91.504, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: RNA chain ...
RNA (5'-R(*AP*UP*GP*UP*GP*GP*CP*AP*U)-3')


Mass: 2872.751 Da / Num. of mol.: 28 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / 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: 2.22 Å3/Da / Density % sol: 44.5 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.08 M NaCl 0.02 M CdCl2 0.04 M cacodylate sodium 45% MPD 0.012 M spermine

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.917143 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 28, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.917143 Å / Relative weight: 1
ReflectionResolution: 2.75→46.53 Å / Num. obs: 18088 / % possible obs: 98.6 % / Redundancy: 3.8 % / Biso Wilson estimate: 76.89 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.045 / Net I/σ(I): 16.31
Reflection shellResolution: 2.75→2.92 Å / Rmerge(I) obs: 0.703 / Mean I/σ(I) obs: 1.63 / Num. unique obs: 2861 / CC1/2: 0.731

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8AMI

8ami


Resolution: 2.75→46.52 Å / SU ML: 0.5039 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 33.693
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2666 1789 9.92 %
Rwork0.2185 16240 -
obs0.2234 18029 98.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 91.89 Å2
Refinement stepCycle: LAST / Resolution: 2.75→46.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 5320 3 1 5324
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00185936
X-RAY DIFFRACTIONf_angle_d0.47929212
X-RAY DIFFRACTIONf_chiral_restr0.02021232
X-RAY DIFFRACTIONf_plane_restr0.0022252
X-RAY DIFFRACTIONf_dihedral_angle_d10.13682912
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.75-2.830.43951430.37571242X-RAY DIFFRACTION95.85
2.83-2.910.37681290.3391211X-RAY DIFFRACTION98.6
2.91-30.38541410.32471245X-RAY DIFFRACTION99.21
3-3.110.35681450.30521278X-RAY DIFFRACTION98.82
3.11-3.240.34371270.27551236X-RAY DIFFRACTION98.98
3.24-3.380.35431370.2771240X-RAY DIFFRACTION98.15
3.38-3.560.37081340.27721265X-RAY DIFFRACTION97.76
3.56-3.780.31781410.26851218X-RAY DIFFRACTION98.76
3.78-4.080.28661380.24331276X-RAY DIFFRACTION98.67
4.08-4.490.25591380.21721228X-RAY DIFFRACTION98.7
4.49-5.130.3121390.20921243X-RAY DIFFRACTION98.01
5.13-6.470.21831360.18181273X-RAY DIFFRACTION99.02
6.47-46.520.15361410.13341285X-RAY DIFFRACTION97.6

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