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- PDB-1ykv: Crystal structure of the Diels-Alder ribozyme complexed with the ... -

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Basic information

Entry
Database: PDB / ID: 1ykv
TitleCrystal structure of the Diels-Alder ribozyme complexed with the product of the reaction between N-pentylmaleimide and covalently attached 9-hydroxymethylanthracene
Components(Diels-Alder ribozyme) x 2
KeywordsRNA / carbon-carbon bond / catalytic mechanism / Diels-Alder reaction / ribozyme
Function / homologyChem-DAI / RNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsSerganov, A. / Keiper, S. / Malinina, L. / Tereshko, V. / Skripkin, E. / Hobartner, C. / Polonskaia, A. / Phan, A.T. / Wombacher, R. / Micura, R. ...Serganov, A. / Keiper, S. / Malinina, L. / Tereshko, V. / Skripkin, E. / Hobartner, C. / Polonskaia, A. / Phan, A.T. / Wombacher, R. / Micura, R. / Dauter, Z. / Jaschke, A. / Patel, D.J.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2005
Title: Structural basis for Diels-Alder ribozyme-catalyzed carbon-carbon bond formation.
Authors: Serganov, A. / Keiper, S. / Malinina, L. / Tereshko, V. / Skripkin, E. / Hobartner, C. / Polonskaia, A. / Phan, A.T. / Wombacher, R. / Micura, R. / Dauter, Z. / Jaschke, A. / Patel, D.J.
History
DepositionJan 18, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 22, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE The DAI hetgroup is connected to the 5' G of the 11-mer RNA via hexaethyleneglycol linker. ...SEQUENCE The DAI hetgroup is connected to the 5' G of the 11-mer RNA via hexaethyleneglycol linker. The linker is not visible in the electron density.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Diels-Alder ribozyme
B: Diels-Alder ribozyme
C: Diels-Alder ribozyme
D: Diels-Alder ribozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,44013
Polymers31,5194
Non-polymers9219
Water0
1
A: Diels-Alder ribozyme
B: Diels-Alder ribozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,2327
Polymers15,7592
Non-polymers4735
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Diels-Alder ribozyme
D: Diels-Alder ribozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,2086
Polymers15,7592
Non-polymers4484
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.288, 44.039, 79.998
Angle α, β, γ (deg.)90.00, 106.87, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12B
22D

NCS domain segments:

Component-ID: 1 / End auth comp-ID: C / End label comp-ID: C / Refine code: 6

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd label seq-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11DAIDAI11AE - A100 - 111
21DAIDAI11CJ - C100 - 111
12GGBB201 - 2381 - 38
22GGDD201 - 2381 - 38

NCS ensembles :
ID
1
2

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Components

#1: RNA chain Diels-Alder ribozyme


Mass: 3497.146 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: This RNA was chemically synthesized. The sequence was derived from the in vitro selected ribozyme catalysing Diels-Alder reaction between thethered anthracene and biotinylated maleimide
#2: RNA chain Diels-Alder ribozyme


Mass: 12262.333 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: This RNA was chemically synthesized. The sequence was derived from the in vitro selected ribozyme catalysing Diels-Alder reaction between thethered anthracene and biotinylated maleimide
#3: Chemical ChemComp-DAI / (3AS,9AS)-2-PENTYL-4-HYDROXYMETHYL-3A,4,9,9A-TETRAHYDRO-4,9[1',2']-BENZENO-1H-BENZ[F]ISOINDOLE-1,3(2H)-DIONE / (11S,12S)-9-HYDROXYMETHYL-11,12-(2-PENTYL-1,3-DIOXO-2-AZAPROPANO)-9,10-DIHYDRO-9,10-ETHANOANTHRACENE


Mass: 375.460 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H25NO3
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Mg

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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: 3.99 Å3/Da / Density % sol: 63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG400, sodium HEPES, magnesium chloride, ethylacetate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG40011
2sodium HEPES11
3H2O11
4PEG40012
5sodium HEPES12
6magnesium chloride12
7ethylacetate12
8H2O12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-D / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 3, 2002
Details: Si (111) double-crystal monochromator, Bent cylindrical Si-mirror (Rh coating)
RadiationMonochromator: Si (111) double-crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 3.3→20 Å / Num. all: 8607 / Num. obs: 8392 / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Rmerge(I) obs: 0.092 / Net I/σ(I): 14
Reflection shellResolution: 3.3→3.42 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.162 / Mean I/σ(I) obs: 8 / % possible all: 88.9

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Processing

Software
NameVersionClassification
REFMAC5.1.9999refinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: The Diels-Alder ribozyme structure from the Diels-Alder ribozyme-product complex, pdb entry 1YLS

1yls


Resolution: 3.3→20 Å / Cor.coef. Fo:Fc: 0.899 / Cor.coef. Fo:Fc free: 0.862 / SU B: 53.158 / SU ML: 0.383 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.474 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26206 388 4.9 %RANDOM
Rwork0.22802 ---
all0.22971 7910 --
obs0.22971 7522 97.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.884 Å2
Baniso -1Baniso -2Baniso -3
1-3.52 Å20 Å2-0.82 Å2
2---3.78 Å20 Å2
3----0.22 Å2
Refine analyzeLuzzati coordinate error obs: 0.607 Å
Refinement stepCycle: LAST / Resolution: 3.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 2092 63 0 2155
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0212404
X-RAY DIFFRACTIONr_bond_other_d0.0060.02846
X-RAY DIFFRACTIONr_angle_refined_deg1.4833734
X-RAY DIFFRACTIONr_angle_other_deg2.59732200
X-RAY DIFFRACTIONr_chiral_restr0.0940.2496
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021074
X-RAY DIFFRACTIONr_gen_planes_other0.0090.0216
X-RAY DIFFRACTIONr_nbd_refined0.1680.2593
X-RAY DIFFRACTIONr_nbd_other0.310.21154
X-RAY DIFFRACTIONr_nbtor_other0.1150.2589
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1410.246
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.3690.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2060.240
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2230.211
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.130.23
X-RAY DIFFRACTIONr_scbond_it0.63933432
X-RAY DIFFRACTIONr_scangle_it0.5994.53734
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A376loose positional0.35
2B1122loose positional0.385
1A376loose thermal0.410
2B1122loose thermal0.4410
LS refinement shellResolution: 3.3→3.383 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.297 35
Rwork0.326 568
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)
16.6386-0.1901-7.88452.694-1.182410.1018-0.03290.45670.38020.12150.61920.46550.032-0.8974-0.5863-0.0677-0.01680.2104-0.19840.1709-0.196228.294225.601234.0195
21.0523-0.402-1.31014.03710.68615.9779-0.03550.1519-0.0768-0.43170.28390.34780.2254-0.0508-0.2484-0.2742-0.1219-0.0152-0.30250.0803-0.337537.821826.750919.6474
310.113-0.68078.47522.29981.84779.6968-0.17070.48620.21520.10660.4069-0.53090.12340.7441-0.2362-0.0752-0.0343-0.2325-0.2747-0.15670.088365.8634.28133.9042
41.213-1.63981.91513.108-1.08095.57590.03320.39280.1433-0.38020.231-0.5544-0.09750.4293-0.2642-0.2679-0.1455-0.0531-0.1949-0.0477-0.119856.240133.404319.605
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A101 - 111
2X-RAY DIFFRACTION2B201 - 238
3X-RAY DIFFRACTION3C101 - 111
4X-RAY DIFFRACTION4D201 - 238

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