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- PDB-1q29: Hammerhead Ribozyme with 5'-5' G-G linkage: Conformational change... -

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Basic information

Entry
Database: PDB / ID: 1q29
TitleHammerhead Ribozyme with 5'-5' G-G linkage: Conformational change experiment
Components
  • 5'-R(*GP*GP*UP*GP*GP*UP*CP*UP*GP*AP*UP*GP*AP*GP*GP*CP*C)-3'
  • Ribozyme
KeywordsRNA / Hammerhead Ribozyme
Function / homology: / RNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsDunham, C.M. / Murray, J.B. / Scott, W.G.
CitationJournal: J.Mol.Biol. / Year: 2003
Title: A helical twist-induced conformational switch activates cleavage in the hammerhead ribozyme.
Authors: Dunham, C.M. / Murray, J.B. / Scott, W.G.
History
DepositionJul 23, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 24, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 24, 2019Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Refinement description
Category: pdbx_validate_polymer_linkage / software / struct_conn
Item: _software.classification / _software.name ..._software.classification / _software.name / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Feb 14, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 5'-R(*GP*GP*UP*GP*GP*UP*CP*UP*GP*AP*UP*GP*AP*GP*GP*CP*C)-3'
B: Ribozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,4857
Polymers13,1902
Non-polymers2955
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.689, 66.689, 140.528
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
DetailsHammerhead Ribozyme with 5'-5' G-G linkage at 5' end of enzyme strand

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Components

#1: RNA chain 5'-R(*GP*GP*UP*GP*GP*UP*CP*UP*GP*AP*UP*GP*AP*GP*GP*CP*C)-3'


Mass: 5515.309 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: RNA chain Ribozyme


Mass: 7674.670 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Chemical
ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Co

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 6.84 Å3/Da / Density % sol: 82.02 %
Crystal grow
*PLUS
Temperature: 16 ℃ / pH: 5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
11 mMribozyme1drop
250 mMsodium acetate1droppH5.0
31.8 M1dropLi2SO4
450 mMsodium acetate1reservoirpH5.0
51.8 M1reservoirLi2SO4
61.0 mMEDTA1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2
DetectorDetector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.99 Å / Lowest resolution: 100 Å / % possible obs: 98.6 % / Redundancy: 5.3 % / Num. measured all: 7686 / Rmerge(I) obs: 0.089
Reflection shell
*PLUS
% possible obs: 92.8 % / Redundancy: 5 % / Num. measured obs: 1017 / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 2.4

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Processing

Software
NameVersionClassification
REFMAC5.1refinement
SCALAdata scaling
CNSrefinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: NDB entry urx057

Resolution: 3→19.8 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.924 / SU B: 17.927 / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.385 / ESU R Free: 0.31
RfactorNum. reflection% reflectionSelection details
Rfree0.27914 744 9.8 %RANDOM
Rwork0.24196 ---
obs0.24559 6872 99.3 %-
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: 77.623 Å2
Baniso -1Baniso -2Baniso -3
1-0.19 Å20.09 Å20 Å2
2--0.19 Å20 Å2
3----0.28 Å2
Refinement stepCycle: LAST / Resolution: 3→19.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 872 5 0 877
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONr_bond_refined_d0.0119750.021
X-RAY DIFFRACTIONr_angle_refined_deg2.07715123
X-RAY DIFFRACTIONr_chiral_restr0.0921640.2
X-RAY DIFFRACTIONr_gen_planes_refined0.0064270.02
X-RAY DIFFRACTIONr_nbd_refined0.1963960.2
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.212140.2
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.195250.2
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.17340.2
X-RAY DIFFRACTIONr_scbond_it1.0879753
X-RAY DIFFRACTIONr_scangle_it1.72815124.5
LS refinement shellResolution: 3.001→3.077 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.412 55
Rwork0.438 474
Software
*PLUS
Version: 5.1.24 / Classification: refinement
Refinement
*PLUS
% reflection Rfree: 10 % / Rfactor obs: 0.23 / Rfactor Rfree: 0.26 / Rfactor Rwork: 0.23
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.012
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg2.518

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