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- PDB-9fn2: Crystal structure of the alkyltransferase ribozyme SAMURI co-crys... -

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Basic information

Entry
Database: PDB / ID: 9fn2
TitleCrystal structure of the alkyltransferase ribozyme SAMURI co-crystallized with SAM
ComponentsSAMURI-SAM
KeywordsRNA / Alkylation ribozyme / SAM / methylation / SAMURI
Function / homologyS-ADENOSYL-L-HOMOCYSTEINE / RNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsChen, H.-A. / Okuda, T. / Lenz, A.-K. / Scheitl, C.P.M. / Schindelin, H. / Hoebartner, C.
Funding support Germany, European Union, 2items
OrganizationGrant numberCountry
German Research Foundation (DFG) Germany
European Research Council (ERC)European Union
CitationJournal: Nat.Chem.Biol. / Year: 2025
Title: Structure and catalytic activity of the SAM-utilizing ribozyme SAMURI.
Authors: Chen, H.A. / Okuda, T. / Lenz, A.K. / Scheitl, C.P.M. / Schindelin, H. / Hobartner, C.
History
DepositionJun 7, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 22, 2025Provider: repository / Type: Initial release
Revision 2.0Feb 5, 2025Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Refinement description
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / pdbx_nonpoly_scheme / pdbx_refine_tls_group / pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_conn
Item: _atom_site.auth_seq_id / _atom_site_anisotrop.pdbx_auth_seq_id ..._atom_site.auth_seq_id / _atom_site_anisotrop.pdbx_auth_seq_id / _pdbx_nonpoly_scheme.pdb_seq_num / _pdbx_refine_tls_group.end_auth_seq_id / _pdbx_refine_tls_group.end_label_asym_id / _pdbx_refine_tls_group.end_label_seq_id / _pdbx_refine_tls_group.selection_details / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SAMURI-SAM
B: SAMURI-SAM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,55911
Polymers37,6202
Non-polymers9399
Water72140
1
A: SAMURI-SAM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,2926
Polymers18,8101
Non-polymers4825
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: SAMURI-SAM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,2675
Polymers18,8101
Non-polymers4574
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.444, 75.444, 73.150
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number77
Space group name H-MP42
Space group name HallP4c
Symmetry operation#1: x,y,z
#2: -y,x,z+1/2
#3: y,-x,z+1/2
#4: -x,-y,z

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Components

#1: RNA chain SAMURI-SAM


Mass: 18810.168 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: In vitro transcription with T7 polymerase / Source: (synth.) synthetic construct (others)
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 40 / Source method: isolated from a natural source / Formula: H2O
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: 2.64 Å3/Da / Density % sol: 70 % / Description: Rod-shaped, 200-300 micrometer
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 50 mM MES pH6.5 100 mM NaCl 100 mM LiCl 15 mM MgCl2 39% MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 17, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.9→43.1 Å / Num. obs: 9208 / % possible obs: 99.9 % / Redundancy: 13.9 % / Biso Wilson estimate: 113 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.051 / Rpim(I) all: 0.015 / Rrim(I) all: 0.052 / Χ2: 1.01 / Net I/σ(I): 24.9
Reflection shellResolution: 2.9→3.08 Å / Redundancy: 14 % / Rmerge(I) obs: 1.18 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 1471 / CC1/2: 0.833 / Rpim(I) all: 0.326 / Rrim(I) all: 1.223 / Χ2: 1.05 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHENIX1.20.1_4487phasing
Coot0.9.4.1model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→33.74 Å / SU ML: 0.264 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.5253
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2303 489 5.32 %
Rwork0.2042 8699 -
obs0.2056 9188 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 52.09 Å2
Refinement stepCycle: LAST / Resolution: 2.9→33.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 2494 59 40 2593
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00182842
X-RAY DIFFRACTIONf_angle_d0.55634426
X-RAY DIFFRACTIONf_chiral_restr0.026590
X-RAY DIFFRACTIONf_plane_restr0.0021122
X-RAY DIFFRACTIONf_dihedral_angle_d17.15321402
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-3.320.29741390.25632895X-RAY DIFFRACTION99.97
3.32-4.180.23831770.19882877X-RAY DIFFRACTION100
4.18-33.740.18921730.1762927X-RAY DIFFRACTION99.74
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)
10.927295245457-0.325750259007-0.3075323691050.6036561170030.3230526469971.31136590665-0.1627518417790.0942984560015-0.06542684738370.113860288444-0.159645913207-0.0283778787231-0.01825136170890.269025713524-0.7178755361740.192000473159-0.03833029671790.2342246509110.256200897086-0.02435266813150.30062951163528.863075409827.4250949856-1.73462077171
20.593254979171-0.110024754924-0.005519912766090.810566532893-0.4488698986630.3758534411230.1802561216410.03083385044070.1296405721680.145928051965-0.09657519763250.0163372937058-0.135728576659-0.081485886041-0.02959339886790.3008026837630.0453419468463-0.02305153991230.0856511959162-0.02599743711790.23147110535912.32711769113.55751224270.372259185457
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and resid 1 through 58)AA1 - 58
2X-RAY DIFFRACTION2(chain 'B' and resid 1 through 58)BB1 - 58

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