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- PDB-1ykq: Crystal structure of Diels-Alder ribozyme -

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Basic information

Entry
Database: PDB / ID: 1ykq
TitleCrystal structure of Diels-Alder ribozyme
Components(Diels-Alder ribozyme) x 2
KeywordsRNA / carbon-carbon bond / catalytic mechanism / RNA crystal structure / Diels-Alder reaction / ribozyme
Function / homology: / RNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 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.end_auth_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)32,25116
Polymers31,5194
Non-polymers73212
Water0
1
A: Diels-Alder ribozyme
B: Diels-Alder ribozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,1708
Polymers15,7592
Non-polymers4106
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)16,0828
Polymers15,7592
Non-polymers3226
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.690, 44.240, 79.640
Angle α, β, γ (deg.)90.00, 107.12, 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 / Beg auth comp-ID: G / Beg label comp-ID: G / End auth comp-ID: C / End label comp-ID: C / Refine code: 6

Dom-IDEns-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA101 - 1111 - 11
21CC101 - 1111 - 11
12BB201 - 2381 - 38
22DD201 - 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 sequence was derived from the in vitro selected ribozyme catalyzing Diels-Alder reaction between tethered anthracene and biotinylated maleimide
#2: RNA chain Diels-Alder ribozyme


Mass: 12262.333 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: This sequence was derived from the in vitro selected ribozyme catalyzing Diels-Alder reaction between tethered anthracene and biotinylated maleimide
#3: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cd
#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: 4.04 Å3/Da / Density % sol: 63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG400, sodium cacodylate, magnesium acetate, 1,6-hexandiol, sodium chloride, cadmium chloride, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG40011
2sodium cacodylate11
3H2O11
4PEG40012
5sodium cacodylate12
6magnesium acetate12
71,6-hexandiol12
8sodium chloride12
9cadmium chloride12
10H2O12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 13, 2004
RadiationMonochromator: Si(111),(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 3.5→20 Å / Num. all: 6902 / Num. obs: 6744 / % possible obs: 97.7 % / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Rmerge(I) obs: 0.154 / Net I/σ(I): 8.1
Reflection shellResolution: 3.5→3.62 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.729 / Mean I/σ(I) obs: 1.8 / Num. unique all: 673 / % possible all: 98.2

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Processing

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

1yls


Resolution: 3.5→20 Å / Cor.coef. Fo:Fc: 0.896 / Cor.coef. Fo:Fc free: 0.852 / SU B: 109.285 / SU ML: 0.73 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: overall / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.671 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.3238 312 4.8 %random
Rwork0.2857 ---
obs0.2875 6563 97.6 %-
all-6564 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 40 Å2
Baniso -1Baniso -2Baniso -3
1-2.45 Å20 Å21.26 Å2
2---8.91 Å20 Å2
3---7.2 Å2
Refine analyzeLuzzati coordinate error obs: 0.755 Å
Refinement stepCycle: LAST / Resolution: 3.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 2078 12 0 2090
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0212320
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.61233610
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0850.2480
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021018
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2620.21209
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2180.271
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0980.21
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1840.242
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2620.23
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it033325
X-RAY DIFFRACTIONr_scangle_it04.53610
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

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

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A230loose positional0.485
2B809loose positional0.385
1A230loose thermal010
2B809loose thermal010
LS refinement shellResolution: 3.5→3.588 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.326 24
Rwork0.364 447
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)
11.9947-0.0839-1.10693.8868-0.13124.1616-0.20320.3208-0.0009-0.16770.50060.51160.4317-0.0485-0.2973-0.1432-0.10550.0076-0.03350.0686-0.21434.890326.316523.0536
22.32-0.62452.56012.5376-0.87964.4194-0.25390.2170.3499-0.40120.3263-0.4412-0.5310.2039-0.0724-0.0431-0.08490.02270.0349-0.1458-0.163858.188733.343822.9837
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A101 - 111
2X-RAY DIFFRACTION1B201 - 238
3X-RAY DIFFRACTION1A249
4X-RAY DIFFRACTION1B240 - 246
5X-RAY DIFFRACTION2C101 - 111
6X-RAY DIFFRACTION2D201 - 238
7X-RAY DIFFRACTION2D340 - 348
8X-RAY DIFFRACTION2C349

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