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- PDB-8zau: Crystal structure of a methyl transferase ribozyme mutant - C29U ... -

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Basic information

Entry
Database: PDB / ID: 8zau
TitleCrystal structure of a methyl transferase ribozyme mutant - C29U and A59G
ComponentsRNA (69-MER)
KeywordsRNA / ribozyme / methyl transferase
Function / homology: / GUANINE / PHOSPHATE ION / RNA / RNA (> 10)
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.43 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 25, 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

Downloads & links

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Assembly

Deposited unit
A: RNA (69-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,22510
Polymers22,2461
Non-polymers9799
Water32418
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.400, 52.588, 100.784
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number17
Space group name H-MP2221
Components on special symmetry positions
IDModelComponents
11A-104-

BA

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Components

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RNA chain , 1 types, 1 molecules A

#1: RNA chain RNA (69-MER)


Mass: 22246.322 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Non-polymers , 5 types, 27 molecules

#2: Chemical ChemComp-GUN / GUANINE


Mass: 151.126 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H5N5O
#3: Chemical
ChemComp-BA / BARIUM ION


Mass: 137.327 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ba
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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: 2.94 Å3/Da / Density % sol: 58.2 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.08 M Potassium chloride 0.02 M Barium chloride dihydrate 0.04 M Sodium cacodylate trihydrate pH 6.8 32% v/v (+/-)-2-Methyl-2,4-pentanediol 0.012 M Spermine tetrahydrochloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER2 X 4M / Detector: PIXEL / Date: Jul 20, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.43→52.59 Å / Num. obs: 18690 / % possible obs: 99.3 % / Observed criterion σ(I): 3.5 / Redundancy: 7.1 % / CC1/2: 0.996 / Rmerge(I) obs: 0.121 / Rpim(I) all: 0.065 / Net I/σ(I): 12.6
Reflection shellResolution: 2.43→2.56 Å / Rmerge(I) obs: 0.666 / Num. unique obs: 1429 / CC1/2: 0.786 / Rpim(I) all: 0.398

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.43→25.2 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 36.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2835 921 4.93 %
Rwork0.2391 --
obs0.2414 18690 97.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.43→25.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1464 23 18 1505
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091652
X-RAY DIFFRACTIONf_angle_d1.6032571
X-RAY DIFFRACTIONf_dihedral_angle_d12.355816
X-RAY DIFFRACTIONf_chiral_restr0.061342
X-RAY DIFFRACTIONf_plane_restr0.01169
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.43-2.560.42221260.46662403X-RAY DIFFRACTION93
2.56-2.720.46091120.41872547X-RAY DIFFRACTION97
2.72-2.930.3974880.36152599X-RAY DIFFRACTION98
2.93-3.220.27431530.25932518X-RAY DIFFRACTION99
3.22-3.680.26191400.20472561X-RAY DIFFRACTION99
3.69-4.640.25341580.18842585X-RAY DIFFRACTION100
4.64-25.20.26871440.20492556X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.4658-1.32580.76261.76290.74344.1393-0.12170.17190.304-0.0013-0.1797-0.2842-0.28330.09450.18830.4673-0.0954-0.09570.34220.08690.417130.18717.786142.704
23.0562-3.36972.48533.7621-2.34465.0087-0.53210.4931-0.77870.3269-0.2148-0.68630.30160.43530.5060.48730.18570.42160.5473-0.01230.613341.0758-9.655635.5938
32.59020.3675-1.07520.0594-0.09990.92590.160.76990.1971-0.3135-0.1247-0.2513-0.1224-0.0906-0.4961.9073-0.0371.53480.9408-0.18442.021344.0516-15.302321.0079
43.26470.21790.32884.42010.69143.2822-0.22460.1237-0.4731-0.91150.1031-0.62240.10360.44320.32780.55420.08310.15850.3981-0.00870.418734.7835-2.935234.1424
51.6177-1.75251.06642.3814-1.56172.78-0.4530.18310.6077-0.4160.08610.7042-0.1619-0.44670.17830.52230.0722-0.3050.3735-0.07810.671813.453717.369335.5356
64.1436-1.1213-2.03563.3904-0.70981.81520.01040.25380.2794-0.70410.2105-0.23550.2466-0.3021-0.17260.70330.0247-0.27240.65320.17740.783611.150221.393931.8996
75.75661.01650.45811.30272.40224.8747-0.13830.24590.92390.7318-0.5447-0.2836-1.1059-0.00540.61160.9716-0.0425-0.44430.26230.08970.747529.207618.842953.5282
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 16 )
2X-RAY DIFFRACTION2chain 'A' and (resid 17 through 21 )
3X-RAY DIFFRACTION3chain 'A' and (resid 22 through 26 )
4X-RAY DIFFRACTION4chain 'A' and (resid 27 through 36 )
5X-RAY DIFFRACTION5chain 'A' and (resid 37 through 56 )
6X-RAY DIFFRACTION6chain 'A' and (resid 57 through 61 )
7X-RAY DIFFRACTION7chain 'A' and (resid 62 through 69 )

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