PDB-4qjd: Crystal Structure of Twister with the Nucleotide 5'- to the Cleav...

ID or keywords:

Entry

Database: PDB / ID: 4qjd

Title

Crystal Structure of Twister with the Nucleotide 5'- to the Cleavage Site Disordered at 3.1 A Resolution

Components

(Twister RNA sequence) x 2

Keywords

RNA / self-cleaving ribozyme / 2' deoxy subsitution / nucleotide 5 (U)

Function / homology

RNA / RNA (> 10)

Function and homology information

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.1 Å

Authors

Eiler, D.R. / Wang, J. / Steitz, T.A.

Citation

Journal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Structural basis for the fast self-cleavage reaction catalyzed by the twister ribozyme.
Authors: Eiler, D. / Wang, J. / Steitz, T.A.

History

Deposition	Jun 3, 2014	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 3, 2014	Provider: repository / Type: Initial release
Revision 1.1	Sep 10, 2014	Group: Database references
Revision 1.2	Sep 24, 2014	Group: Database references
Revision 1.3	Sep 20, 2023	Group: 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.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_label_asym_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4qjd.cif.gz	167.2 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	4qjd_validation.pdf.gz	464.7 KB	Display	wwPDB validaton report
Full document	4qjd_full_validation.pdf.gz	484.9 KB	Display
Data in XML	4qjd_validation.xml.gz	13.4 KB	Display
Data in CIF	4qjd_validation.cif.gz	18.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/qj/4qjd ftp://data.pdbj.org/pub/pdb/validation_reports/qj/4qjd	HTTPS FTP

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Related structure data

Related structure data	4qjhSC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	4nf9-2 2gnx-d 5xtm-1 4qjh-2 4qjh-3 16vp-d 4wi0-d 6cso-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

Related structure data

4qjhSC

S: Starting model for refinement

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#121 - Jan 2010 70S Ribosomes similarity (1) #130 - Oct 2010 Riboswitches similarity (1) #16 - Apr 2001 Aminoacyl-tRNA Synthetases similarity (1) #157 - Jan 2013 Transfer-Messenger RNA similarity (1) #181 - Jan 2015 Cascade and CRISPR similarity (1) #229 - Jan 2019 Fluorescent RNA Aptamers similarity (1) #253 - Jan 2021 Expressome similarity (1) #260 - Aug 2021 Ribonuclease P similarity (1) #146 - Feb 2012 Aminoglycoside Antibiotics similarity (1) #15 - Mar 2001 Transfer RNA similarity (1) #249 - Sep 2020 SARS-CoV-2 RNA-dependent RNA Polymerase similarity (1) #10 - Oct 2000 Ribosome similarity (1) #210 - Jun 2017 Adenine Riboswitch in Action similarity (1) #87 - Mar 2007 Zinc Fingers similarity (1) #105 - Sep 2008 Ribonuclease A similarity (1) #226 - Oct 2018 Aminoglycoside Antibiotics and Resistance similarity (1) #245 - May 2020 Spliceosomes similarity (1) #262 - Oct 2021 Fifty Years of Open Access to PDB Structures similarity (1) #65 - May 2005 Self-splicing RNA similarity (1) #98 - Feb 2008 Small Interfering RNA similarity (1) #104 - Aug 2008 Selenocysteine Synthase similarity (1) #106 - Oct 2008 Poly(A) Polymerase similarity (1) #143 - Nov 2011 Toll-like Receptors similarity (1) #161 - May 2013 Ricin similarity (1) #227 - Nov 2018 Telomerase similarity (1) #230 - Feb 2019 Initiation Factor eIF4E similarity (1) #266 - Feb 2022 Oligosaccharyltransferase similarity (1) #81 - Sep 2006 Elongation Factors similarity (1) #89 - May 2007 Aconitase and Iron Regulatory Protein 1 similarity (1) #241 - Jan 2020 Twenty Years of Molecules similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#121 - Jan 2010
70S Ribosomes
similarity (1)
#130 - Oct 2010
Riboswitches
similarity (1)
#16 - Apr 2001
Aminoacyl-tRNA Synthetases
similarity (1)
#157 - Jan 2013
Transfer-Messenger RNA
similarity (1)
#181 - Jan 2015
Cascade and CRISPR
similarity (1)
#229 - Jan 2019
Fluorescent RNA Aptamers
similarity (1)
#253 - Jan 2021
Expressome
similarity (1)
#260 - Aug 2021
Ribonuclease P
similarity (1)
#146 - Feb 2012
Aminoglycoside Antibiotics
similarity (1)
#15 - Mar 2001
Transfer RNA
similarity (1)
#249 - Sep 2020
SARS-CoV-2 RNA-dependent RNA Polymerase
similarity (1)
#10 - Oct 2000
Ribosome
similarity (1)
#210 - Jun 2017
Adenine Riboswitch in Action
similarity (1)
#87 - Mar 2007
Zinc Fingers
similarity (1)
#105 - Sep 2008
Ribonuclease A
similarity (1)
#226 - Oct 2018
Aminoglycoside Antibiotics and Resistance
similarity (1)
#245 - May 2020
Spliceosomes
similarity (1)
#262 - Oct 2021
Fifty Years of Open Access to PDB Structures
similarity (1)
#65 - May 2005
Self-splicing RNA
similarity (1)
#98 - Feb 2008
Small Interfering RNA
similarity (1)
#104 - Aug 2008
Selenocysteine Synthase
similarity (1)
#106 - Oct 2008
Poly(A) Polymerase
similarity (1)
#143 - Nov 2011
Toll-like Receptors
similarity (1)
#161 - May 2013
Ricin
similarity (1)
#227 - Nov 2018
Telomerase
similarity (1)
#230 - Feb 2019
Initiation Factor eIF4E
similarity (1)
#266 - Feb 2022
Oligosaccharyltransferase
similarity (1)
#81 - Sep 2006
Elongation Factors
similarity (1)
#89 - May 2007
Aconitase and Iron Regulatory Protein 1
similarity (1)
#241 - Jan 2020
Twenty Years of Molecules
similarity (1)

Deposited unit

A: Twister RNA sequence

B: Twister RNA sequence

C: Twister RNA sequence

D: Twister RNA sequence

E: Twister RNA sequence

F: Twister RNA sequence

G: Twister RNA sequence

H: Twister RNA sequence

hetero molecules

94.6 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Twister RNA sequence

B: Twister RNA sequence

hetero molecules

defined by author&software
23.7 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: Twister RNA sequence

D: Twister RNA sequence

defined by author&software
23.6 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

E: Twister RNA sequence

F: Twister RNA sequence

hetero molecules

defined by author&software
23.7 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

G: Twister RNA sequence

H: Twister RNA sequence

hetero molecules

defined by author&software
23.7 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	70.910, 53.070, 106.750
Angle α, β, γ (deg.)	90.00, 106.86, 90.00
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Component-ID: _ / Refine code: _

Dom-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	U	U	U	U	A	A	3 - 24	3 - 24
2	1	U	U	U	U	C	C	3 - 24	3 - 24
1	2	U	U	U	U	A	A	3 - 25	3 - 25
2	2	U	U	U	U	E	E	3 - 25	3 - 25
1	3	U	U	U	U	A	A	3 - 24	3 - 24
2	3	U	U	U	U	G	G	3 - 24	3 - 24
1	4	U	U	U	U	B	B	28 - 72	2 - 46
2	4	U	U	U	U	D	D	28 - 72	2 - 46
1	5	U	U	U	U	B	B	28 - 72	2 - 46
2	5	U	U	U	U	F	F	28 - 72	2 - 46
1	6	GTP	GTP	A	A	B	B	27 - 73	1 - 47
2	6	GTP	GTP	A	A	H	H	27 - 73	1 - 47
1	7	U	U	U	U	C	C	1 - 24	1 - 24
2	7	U	U	U	U	E	E	1 - 24	1 - 24
1	8	U	U	U	U	C	C	1 - 25	1 - 25
2	8	U	U	U	U	G	G	1 - 25	1 - 25
1	9	U	U	A	A	D	D	28 - 73	2 - 47
2	9	U	U	A	A	F	F	28 - 73	2 - 47
1	10	U	U	U	U	D	D	28 - 72	2 - 46
2	10	U	U	U	U	H	H	28 - 72	2 - 46
1	11	U	U	U	U	E	E	1 - 24	1 - 24
2	11	U	U	U	U	G	G	1 - 24	1 - 24
1	12	U	U	U	U	F	F	28 - 72	2 - 46
2	12	U	U	U	U	H	H	28 - 72	2 - 46

NCS ensembles :

ID
1
2
3
4
5
6
7
8
9
10
11
12

#1: RNA chain	Twister RNA sequence Mass: 8163.825 Da / Num. of mol.: 4 / Source method: obtained synthetically
#2: RNA chain	Twister RNA sequence Mass: 15474.196 Da / Num. of mol.: 4 / Source method: obtained synthetically Details: RNA was prepared by in vitro transcription with T7 RNA polymerase.
#3: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.03 Å³/Da / Density % sol: 39.5 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.5 Details: 100 mM sodium acetate, pH 4.5, 200 mM ammonium sulfate, 30% PEG4000, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 24-ID-C / Wavelength: 1.605 Å

Detector

Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 9, 2013

Radiation

Monochromator: cryo-cooled double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1.605 Å / Relative weight: 1

Reflection

Resolution: 3.056→104.828 Å / Num. all: 13691 / Num. obs: 11987 / % possible obs: 97.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.7 % / R_merge(I) obs: 0.111 / Net I/σ(I): 7.01

Reflection shell

Resolution (Å)	R_merge(I) obs	Mean I/σ(I) obs	Diffraction-ID	% possible all
3.056-3.22	1.02	2	1	98.5
3.22-3.31			1	97
3.31-3.41			1	96.2
3.41-3.52			1	95.1
3.52-3.65			1	97.9
3.65-50			1	96.5

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Processing

Software

Name	Version	Classification
XDS		data scaling
PHASER		phasing
REFMAC	5.8.0073	refinement
XDS		data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4QJH

4qjh

Resolution: 3.1→102.37 Å / Cor.coef. F_o:F_c: 0.968 / Cor.coef. F_o:F_c free: 0.916 / SU B: 34.659 / SU ML: 0.571 / Cross valid method: THROUGHOUT / ESU R Free: 0.707 / Stereochemistry target values: MAXIMUM LIKELIHOOD

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.28745	616	5.1 %	RANDOM
R_work	0.19009	-	-	-
obs	0.19505	11370	84.93 %	-
all	-	13644	-	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 80.877 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	4.36 Å²	0 Å²	-0.23 Å²
2-	-	-1.19 Å²	0 Å²
3-	-	-	-2.57 Å²

Refinement step

Cycle: LAST / Resolution: 3.1→102.37 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	0	6168	4	16	6188

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.011	6897
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.805	1.298	10727
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg
X-RAY DIFFRACTION	r_dihedral_angle_2_deg
X-RAY DIFFRACTION	r_dihedral_angle_3_deg
X-RAY DIFFRACTION	r_dihedral_angle_4_deg
X-RAY DIFFRACTION	r_chiral_restr	0.146	0.2	1148
X-RAY DIFFRACTION	r_gen_planes_refined	0.01	0.02	2986
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	6.941	8.093	6897
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined	16.492	80.12	13144
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-ID	Dom-ID	Auth asym-ID	Number	Rms dev position (Å)
1	1	A	887	0.06
1	2	C	887	0.06
2	1	A	899	0.06
2	2	E	899	0.06
3	1	A	855	0.09
3	2	G	855	0.09
4	1	B	2486	0.08
4	2	D	2486	0.08
5	1	B	2539	0.05
5	2	F	2539	0.05
6	1	B	2707	0.04
6	2	H	2707	0.04
7	1	C	996	0.07
7	2	E	996	0.07
8	1	C	931	0.11
8	2	G	931	0.11
9	1	D	2614	0.06
9	2	F	2614	0.06
10	1	D	2485	0.08
10	2	H	2485	0.08
11	1	E	921	0.12
11	2	G	921	0.12
12	1	F	2550	0.06
12	2	H	2550	0.06

LS refinement shell

Resolution: 3.1→3.181 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.204	6	-
R_work	0.343	143	-
obs	-	-	14.61 %

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