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- PDB-2qus: Hammerhead Ribozyme G12A mutant pre-cleavage -

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Basic information

Entry
Database: PDB / ID: 2qus
TitleHammerhead Ribozyme G12A mutant pre-cleavage
ComponentsHammerhead ribozyme
KeywordsRNA / Hammerhead RNA / hammerhead ribozyme / catalytic RNA / satellite virus RNA / ribozyme
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 2.4 Å
AuthorsChi, Y.I. / Scott, W.G. / Kim, S.H.
CitationJournal: Plos Biol. / Year: 2008
Title: Capturing hammerhead ribozyme structures in action by modulating general base catalysis.
Authors: Chi, Y.I. / Martick, M. / Lares, M. / Kim, R. / Scott, W.G. / Kim, S.H.
History
DepositionAug 6, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 15, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_conn_type / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_conn_type.id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hammerhead ribozyme
B: Hammerhead ribozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,19718
Polymers44,8082
Non-polymers38916
Water2,360131
1
A: Hammerhead ribozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,5999
Polymers22,4041
Non-polymers1948
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Hammerhead ribozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,5999
Polymers22,4041
Non-polymers1948
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)27.926, 53.030, 71.963
Angle α, β, γ (deg.)74.570, 81.370, 75.610
Int Tables number1
Space group name H-MP1

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Components

#1: RNA chain Hammerhead ribozyme


Mass: 22404.166 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: in vitro T7 RNA polymerase transcription
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 131 / Source method: isolated from a natural source / Formula: H2O

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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: 2.21 Å3/Da / Density % sol: 44.39 %

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Data collection

Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→25.67 Å / Num. all: 12926 / Num. obs: 11632 / % possible obs: 86.05 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.054 / Net I/σ(I): 8

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PDB_EXTRACT3data extraction
RefinementStarting model: small helical fragments

Resolution: 2.4→25.67 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.917 / SU B: 18.854 / SU ML: 0.228 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.342 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.253 1294 10 %RANDOM
Rwork0.184 ---
obs0.191 12926 86.05 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 58.401 Å2
Baniso -1Baniso -2Baniso -3
1-0.77 Å20.71 Å2-0.09 Å2
2---0.34 Å2-0.19 Å2
3----0.66 Å2
Refinement stepCycle: LAST / Resolution: 2.4→25.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 2966 16 131 3113
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0213321
X-RAY DIFFRACTIONr_angle_refined_deg1.8535158
X-RAY DIFFRACTIONr_chiral_restr0.1050.2688
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021430
X-RAY DIFFRACTIONr_nbd_refined0.1890.21340
X-RAY DIFFRACTIONr_nbtor_refined0.2820.22053
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1940.2153
X-RAY DIFFRACTIONr_metal_ion_refined0.1170.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1620.236
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1960.217
X-RAY DIFFRACTIONr_scbond_it1.0834707
X-RAY DIFFRACTIONr_scangle_it1.7154.55158
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 61 -
Rwork0.26 548 -
all-609 -
obs--54.96 %
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)
10.19480.1881-0.2180.5630.15572.284-0.024-0.02660.0467-0.00380.0249-0.0788-0.24910.0312-0.0009-0.0130.0614-0.0428-0.0677-0.0039-0.0472-5.6144-7.63197.3737
20.04690.04110.41390.53360.13453.7554-0.09930.03210.09240.0475-0.0931-0.08870.2935-0.20940.19240.01160.03410.0183-0.0221-0.0453-0.03847.2385-28.803617.1906
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 691 - 69
2X-RAY DIFFRACTION2BB1 - 691 - 69

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