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- PDB-6jq5: The structure of Hatchet Ribozyme -

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Basic information

Entry
Database: PDB / ID: 6jq5
TitleThe structure of Hatchet Ribozyme
ComponentsRNA (82-MER)
KeywordsRNA / Ribozyme / non-coding RNA / hatchet / cleavage / catalysis
Function / homologyRNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.059 Å
AuthorsRen, A. / Zheng, L.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (China) China
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2019
Title: Hatchet ribozyme structure and implications for cleavage mechanism.
Authors: Zheng, L. / Falschlunger, C. / Huang, K. / Mairhofer, E. / Yuan, S. / Wang, J. / Patel, D.J. / Micura, R. / Ren, A.
History
DepositionMar 29, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 12, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA (82-MER)
B: RNA (82-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,7863
Polymers52,7612
Non-polymers241
Water1,42379
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4400 Å2
ΔGint13 kcal/mol
Surface area24380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.582, 104.275, 126.862
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: RNA chain RNA (82-MER)


Mass: 26380.668 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 79 / 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: 2.54 Å3/Da / Density % sol: 51.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.10M HEPES, pH 6.8, 2.0M (NH4)2SO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 26, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 33380 / % possible obs: 99.6 % / Redundancy: 12.1 % / Rpim(I) all: 0.036 / Net I/σ(I): 31.9
Reflection shellResolution: 2→2.18 Å / Num. unique obs: 1867 / Rpim(I) all: 0.9

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6JQ6

6jq6


Resolution: 2.059→33.523 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.2
RfactorNum. reflection% reflection
Rfree0.2308 1628 4.89 %
Rwork0.1929 --
obs0.1947 33267 97.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.059→33.523 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 3472 1 79 3552
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073919
X-RAY DIFFRACTIONf_angle_d1.0346099
X-RAY DIFFRACTIONf_dihedral_angle_d14.6861963
X-RAY DIFFRACTIONf_chiral_restr0.048818
X-RAY DIFFRACTIONf_plane_restr0.009164
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0587-2.11930.3322980.29311867X-RAY DIFFRACTION70
2.1193-2.18770.34071130.30142651X-RAY DIFFRACTION99
2.1877-2.26580.46371280.352662X-RAY DIFFRACTION98
2.2658-2.35650.34891540.29822622X-RAY DIFFRACTION99
2.3565-2.46380.3371300.28652670X-RAY DIFFRACTION99
2.4638-2.59360.3741460.26792675X-RAY DIFFRACTION100
2.5936-2.7560.30691430.28332679X-RAY DIFFRACTION100
2.756-2.96870.30281440.2642695X-RAY DIFFRACTION100
2.9687-3.26720.24781320.19712727X-RAY DIFFRACTION100
3.2672-3.73950.20911540.16622725X-RAY DIFFRACTION100
3.7395-4.70930.16881410.15092761X-RAY DIFFRACTION100
4.7093-33.52730.16891450.14262905X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -32.5384 Å / Origin y: -15.4974 Å / Origin z: -15.8258 Å
111213212223313233
T0.2835 Å2-0.0136 Å20.0232 Å2-0.3313 Å2-0.03 Å2--0.3314 Å2
L0.0155 °20.2424 °20.154 °2-2.5432 °20.5004 °2--0.4898 °2
S-0.0004 Å °0.0411 Å °-0.0139 Å °0.216 Å °0.0454 Å °-0.0579 Å °-0.0987 Å °-0.0102 Å °-0.0511 Å °
Refinement TLS groupSelection details: all

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