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- PDB-8za4: Crystal structure of OR4K15 ribozyme mutant - chainBDF C2U -

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Basic information

Entry
Database: PDB / ID: 8za4
TitleCrystal structure of OR4K15 ribozyme mutant - chainBDF C2U
Components
  • RNA (5'-R(*CP*UP*UP*GP*CP*GP*CP*UP*CP*AP*AP*CP*CP*AP*GP*A)-3')
  • RNA (5'-R(*UP*CP*UP*GP*GP*GP*CP*CP*AP*GP*GP*CP*AP*GP*G)-3')
KeywordsRNA / ribozyme / OR4K15
Function / homologyRNA / RNA (> 10)
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsRen, Y. / Huang, L.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32171191 China
CitationJournal: Nucleic Acids Res. / Year: 2025
Title: A general strategy for engineering GU base pairs to facilitate RNA crystallization.
Authors: Ren, Y. / Lin, X. / Liao, W. / Peng, X. / Deng, J. / Zhang, Z. / Zhan, J. / Zhou, Y. / Westhof, E. / Lilley, D.M.J. / Wang, J. / Huang, L.
History
DepositionApr 24, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Mar 19, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA (5'-R(*UP*CP*UP*GP*GP*GP*CP*CP*AP*GP*GP*CP*AP*GP*G)-3')
B: RNA (5'-R(*CP*UP*UP*GP*CP*GP*CP*UP*CP*AP*AP*CP*CP*AP*GP*A)-3')
C: RNA (5'-R(*UP*CP*UP*GP*GP*GP*CP*CP*AP*GP*GP*CP*AP*GP*G)-3')
D: RNA (5'-R(*CP*UP*UP*GP*CP*GP*CP*UP*CP*AP*AP*CP*CP*AP*GP*A)-3')
E: RNA (5'-R(*UP*CP*UP*GP*GP*GP*CP*CP*AP*GP*GP*CP*AP*GP*G)-3')
F: RNA (5'-R(*CP*UP*UP*GP*CP*GP*CP*UP*CP*AP*AP*CP*CP*AP*GP*A)-3')


Theoretical massNumber of molelcules
Total (without water)29,7606
Polymers29,7606
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.170, 37.354, 116.136
Angle α, β, γ (deg.)90.00, 91.88, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 4862.954 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: RNA chain RNA (5'-R(*CP*UP*UP*GP*CP*GP*CP*UP*CP*AP*AP*CP*CP*AP*GP*A)-3')


Mass: 5057.072 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
Has protein modificationN

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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: 2.67 Å3/Da / Density % sol: 53.85 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Sodium Acetate trihydrate 0.1 M Tris Hydrochloride pH pH 5.8 25%w/v Polyethylene Glycol 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.979183 Å
DetectorType: DECTRIS EIGER2 X 4M / Detector: PIXEL / Date: Aug 29, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979183 Å / Relative weight: 1
ReflectionResolution: 2.85→35.21 Å / Num. obs: 7477 / % possible obs: 99.2 % / Redundancy: 5.7 % / CC1/2: 0.992 / Net I/σ(I): 7.6
Reflection shellResolution: 2.85→3.01 Å / Num. unique obs: 1069 / CC1/2: 0.951

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.85→35.21 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2066 361 4.9 %
Rwork0.1977 --
obs0.1981 7371 97.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.85→35.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1965 0 0 1965
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082193
X-RAY DIFFRACTIONf_angle_d1.4323408
X-RAY DIFFRACTIONf_dihedral_angle_d11.2131086
X-RAY DIFFRACTIONf_chiral_restr0.053456
X-RAY DIFFRACTIONf_plane_restr0.00993
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.85-3.270.30041200.26562248X-RAY DIFFRACTION96
3.27-4.120.19411060.19392366X-RAY DIFFRACTION98
4.12-35.210.17411350.16812396X-RAY DIFFRACTION99

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