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- PDB-1nyi: Crosslinked Hammerhead Ribozyme Initial State -

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Basic information

Entry
Database: PDB / ID: 1nyi
TitleCrosslinked Hammerhead Ribozyme Initial State
Components
  • 5'-R(*GP*CP*CP*GP*AP*AP*AP*CP*UP*CP*GP*UP*AP*AP*GP*AP*GP*UP*CP*AP*CP*CP*AP*C)-3'
  • 5'-R(P*GP*UP*GP*GP*UP*CP*UP*GP*AP*UP*GP*AP*GP*GP*CP*C)-3'
KeywordsRNA / Hammerhead Ribozyme crosslink conformational change
Function / homologyGUANOSINE-5'-MONOPHOSPHATE / : / RNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.85 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
DepositionFeb 12, 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 1.3Jan 31, 2018Group: Advisory / Category: pdbx_unobs_or_zero_occ_atoms
Revision 1.4Feb 28, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.5Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.name ..._software.classification / _software.name / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.6Feb 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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.7Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 2.0Oct 16, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Source and taxonomy / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / ndb_struct_conf_na / ndb_struct_na_base_pair / pdbx_entity_nonpoly / pdbx_entity_src_syn / pdbx_entry_details / pdbx_nonpoly_scheme / pdbx_validate_close_contact / struct_conn / struct_site
Item: _atom_site.auth_comp_id / _atom_site.label_comp_id ..._atom_site.auth_comp_id / _atom_site.label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _ndb_struct_na_base_pair.hbond_type_12 / _ndb_struct_na_base_pair.propeller / _pdbx_entity_nonpoly.comp_id / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_validate_close_contact.auth_comp_id_2 / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_label_comp_id / _struct_site.details / _struct_site.pdbx_auth_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)13,4447
Polymers12,8452
Non-polymers5995
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.639, 65.639, 137.475
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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


Mass: 5170.103 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: RNA chain 5'-R(*GP*CP*CP*GP*AP*AP*AP*CP*UP*CP*GP*UP*AP*AP*GP*AP*GP*UP*CP*AP*CP*CP*AP*C)-3'


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


Mass: 58.933 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Co
#4: Chemical ChemComp-5GP / GUANOSINE-5'-MONOPHOSPHATE


Mass: 363.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O8P
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

Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 1.8 M Lithium sulphate and 50 mM sodium cacodylate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 20.0K
Components of the solutions
IDNameCrystal-IDSol-ID
1LiSO411
2sodium cacodylate11
3LiSO412
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 / Wavelength: 1.15 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 1, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.15 Å / Relative weight: 1
ReflectionResolution: 2.85→19.76 Å / Num. all: 7544 / Num. obs: 7544 / % possible obs: 99.53 % / Observed criterion σ(I): 0 / Redundancy: 5.2 % / Rmerge(I) obs: 0.072 / Rsym value: 0.064 / Net I/σ(I): 13.8
Reflection shellResolution: 2.85→2.923 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.349 / Mean I/σ(I) obs: 2.2 / Num. unique all: 565 / Rsym value: 0.316 / % possible all: 99.3
Reflection
*PLUS
Lowest resolution: 100 Å / % possible obs: 99.3 % / Num. measured all: 8413
Reflection shell
*PLUS
% possible obs: 99.3 % / Num. measured obs: 1192

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Processing

Software
NameVersionClassification
REFMAC5.1refinement
SCALAdata scaling
CNSrefinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: urx 057

Resolution: 2.85→19.76 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.939 / SU B: 10.15 / SU ML: 0.184 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.28 / ESU R Free: 0.234 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflection
Rfree0.23241 840 10 %
Rwork0.20332 --
all0.20607 7544 -
obs0.20607 7544 99.53 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso mean: 41.892 Å2
Baniso -1Baniso -2Baniso -3
1-0.12 Å20.06 Å20 Å2
2--0.12 Å20 Å2
3----0.18 Å2
Refine analyzeLuzzati coordinate error obs: 0.28 Å
Refinement stepCycle: LAST / Resolution: 2.85→19.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 873 4 0 877
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.021976
X-RAY DIFFRACTIONr_angle_refined_deg2.00731515
X-RAY DIFFRACTIONr_chiral_restr0.0970.2164
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02428
X-RAY DIFFRACTIONr_nbd_refined0.2030.2427
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2280.228
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2240.239
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1520.25
X-RAY DIFFRACTIONr_scbond_it1.343976
X-RAY DIFFRACTIONr_scangle_it2.1524.51515
LS refinement shellResolution: 2.85→2.923 Å / Rfactor Rfree error: 0.468 / Total num. of bins used: 20 /
RfactorNum. reflection
Rwork0.479 514
Rfree-64
Refinement
*PLUS
Lowest resolution: 19.75 Å / Rfactor obs: 0.21 / Rfactor Rfree: 0.23 / Rfactor Rwork: 0.2
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.01
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg2.007

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