PDB-3ok4: Crystal structure of the ANA:RNA decamer suffering from lattice t...

ID or keywords:

Entry

Database: PDB / ID: 3ok4

Title

Crystal structure of the ANA:RNA decamer suffering from lattice translocation defects

Components

ANA
RNA

Keywords

RNA / altritol / sugar modification / lattice translocation defect

Function / homology

OTHER / OTHER (> 10) / RNA

Function and homology information

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.149 Å

Authors

Ovaere, M. / Van Meervelt, L.

Citation

Journal: To be Published
Title: Crystal structure of the ANA:RNA decamer suffering from lattice translocation defects
Authors: Ovaere, M. / Van Meervelt, L.

History

Deposition	Aug 24, 2010	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 30, 2011	Provider: repository / Type: Initial release
Revision 1.1	Dec 12, 2018	Group: Advisory / Data collection / Derived calculations Category: ndb_struct_na_base_pair / ndb_struct_na_base_pair_step ...ndb_struct_na_base_pair / ndb_struct_na_base_pair_step / pdbx_distant_solvent_atoms / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_conn_type
Revision 1.2	Feb 21, 2024	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 / struct_conn / struct_ncs_dom_lim 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.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.pdbx_value_order / _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_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_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_alt_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_alt_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

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	3ok4.cif.gz	177.4 KB	Display	PDBx/mmCIF format
PDB format	pdb3ok4.ent.gz	161.1 KB	Display	PDB format
PDBx/mmJSON format	3ok4.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	3ok4_validation.pdf.gz	639 KB	Display	wwPDB validaton report
Full document	3ok4_full_validation.pdf.gz	746.5 KB	Display
Data in XML	3ok4_validation.xml.gz	27 KB	Display
Data in CIF	3ok4_validation.cif.gz	34.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ok/3ok4 ftp://data.pdbj.org/pub/pdb/validation_reports/ok/3ok4	HTTPS FTP

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Related structure data

Related structure data	3ok2
Similar structure data	6va4-d 3r1d-1 4mcf-2 6wy3-2 2ro2-d 2m44-d 1di2-3 2rlu-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) 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) 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) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

Related structure data

3ok2

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: ANA

C: ANA

E: ANA

B: RNA

D: RNA

F: RNA

G: ANA

I: ANA

K: ANA

H: RNA

J: RNA

L: RNA

M: ANA

O: ANA

Q: ANA

N: RNA

P: RNA

R: RNA

S: ANA

U: ANA

W: ANA

T: RNA

V: RNA

X: RNA

Y: ANA

1: ANA

3: ANA

Z: RNA

2: RNA

4: RNA

98.6 kDa, 30 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: ANA

B: RNA

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

2

C: ANA

D: RNA

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

3

E: ANA

F: RNA

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

4

G: ANA

H: RNA

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

5

I: ANA

J: RNA

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

6

K: ANA

L: RNA

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

7

M: ANA

N: RNA

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

8

O: ANA

P: RNA

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

9

Q: ANA

R: RNA

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

10

S: ANA

T: RNA

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

11

U: ANA

V: RNA

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

12

W: ANA

X: RNA

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

13

Y: ANA

Z: RNA

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

14

1: ANA

2: RNA

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

15

3: ANA

4: RNA

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

Unit cell

Length a, b, c (Å)	34.220, 34.210, 170.920
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Component-ID: 1 / Refine code: 1 / Auth seq-ID: 1 - 10 / Label seq-ID: 1 - 10

Dom-ID	Ens-ID	Beg auth comp-ID	Beg label alt-ID	Beg label comp-ID	End auth comp-ID	End label alt-ID	End label comp-ID	Auth asym-ID	Label asym-ID
1	1	A6C	A	A6C	A6C	A	A6C	A	A
2	1	A6C	B	A6C	A6C	B	A6C	G	G
3	1	A6C	C	A6C	A6C	C	A6C	M	M
4	1	A6C	D	A6C	A6C	D	A6C	S	S
5	1	A6C	E	A6C	A6C	E	A6C	Y	Y
1	2	A6C	A	A6C	A6C	A	A6C	C	B
2	2	A6C	B	A6C	A6C	B	A6C	I	H
3	2	A6C	C	A6C	A6C	C	A6C	O	N
4	2	A6C	D	A6C	A6C	D	A6C	U	T
5	2	A6C	E	A6C	A6C	E	A6C	1	Z
1	3	A6C	A	A6C	A6C	A	A6C	E	C
2	3	A6C	B	A6C	A6C	B	A6C	K	I
3	3	A6C	C	A6C	A6C	C	A6C	Q	O
4	3	A6C	D	A6C	A6C	D	A6C	W	U
5	3	A6C	E	A6C	A6C	E	A6C	3	AA
1	4	G	A	G	G	A	G	B	D
2	4	G	B	G	G	B	G	H	J
3	4	G	C	G	G	C	G	N	P
4	4	G	D	G	G	D	G	T	V
5	4	G	E	G	G	E	G	Z	BA
1	5	G	A	G	G	A	G	D	E
2	5	G	B	G	G	B	G	J	K
3	5	G	C	G	G	C	G	P	Q
4	5	G	D	G	G	D	G	V	W
5	5	G	E	G	G	E	G	2	CA
1	6	G	A	G	G	A	G	F	F
2	6	G	B	G	G	B	G	L	L
3	6	G	C	G	G	C	G	R	R
4	6	G	D	G	G	D	G	X	X
5	6	G	E	G	G	E	G	4	DA

NCS ensembles :

ID
1
2
3
4
5
6

#1: Other	ANA Mass: 3354.144 Da / Num. of mol.: 15 / Source method: obtained synthetically / Details: The molecule was synthesized
#2: RNA chain	RNA Mass: 3216.973 Da / Num. of mol.: 15 / Source method: obtained synthetically / Details: The molecule was synthesized
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 375 / 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 grow	Temperature: 289 K / Method: vapor diffusion, hanging drop Details: ammonium sulphate, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

SLS

/ Beamline: X06DA / Wavelength: 1 Å

Detector

Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 29, 2008

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1 Å / Relative weight: 1

Reflection twin

Crystal-ID	ID	Operator	Domain-ID	Fraction
1	1	1.000H, 1.000K, L	1	0.507
1	1	1.000K, 1.000H, -L	2	0.493

Reflection

Resolution: 1.149→85.46 Å / Num. all: 70276 / Num. obs: 70276 / % possible obs: 97.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.1 % / R_sym value: 0.081 / Net I/σ(I): 13.6

Reflection shell

Resolution (Å)	R_sym value	Diffraction-ID	% possible all
1.149-1.21	0.587	1	95.3
1.29-1.37	0.285	1	96.7
1.48-1.63	0.131	1	97.9
1.82-2.1	0.064	1	99.1
3.64-85.46	0.056	1	93.1

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Processing

Software

Name	Version	Classification
SHELX	D/E	model building
REFMAC	5.5.0072	refinement
MOSFLM		data reduction
SCALA		data scaling
SHELX	D/E	phasing

Refinement

Method to determine structure:

SAD / Resolution: 1.149→85.46 Å / Cor.coef. F_o:F_c: 0.946 / Cor.coef. F_o:F_c free: 0.936 / SU B: 0.81 / SU ML: 0.038 / Cross valid method: THROUGHOUT / ESU R: 0.023 / ESU R Free: 0.02 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.25288	3612	5.1 %	RANDOM
R_work	0.22126	-	-	-
obs	0.22295	66626	96.53 %	-
all	-	66705	-	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 9.274 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-3.14 Å²	0 Å²	0 Å²
2-	-	3.43 Å²	0 Å²
3-	-	-	-0.29 Å²

Refinement step

Cycle: LAST / Resolution: 1.149→85.46 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	0	6510	0	375	6885

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.021	7230
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	2.06	3	11145
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	0.083	0.2	1245
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	3090
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_scbond_it	0.337	3	7230
X-RAY DIFFRACTION	r_scangle_it	0.476	4.5	11145
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

Ens-ID	Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	1	A	217	TIGHT POSITIONAL	0.04	0.05
1	2	G	217	TIGHT POSITIONAL	0.04	0.05
1	3	M	217	TIGHT POSITIONAL	0.04	0.05
1	4	S	217	TIGHT POSITIONAL	0.05	0.05
1	5	Y	217	TIGHT POSITIONAL	0.04	0.05
1	1	A	217	TIGHT THERMAL	0.18	0.5
1	2	G	217	TIGHT THERMAL	0.14	0.5
1	3	M	217	TIGHT THERMAL	0.16	0.5
1	4	S	217	TIGHT THERMAL	0.18	0.5
1	5	Y	217	TIGHT THERMAL	0.12	0.5
2	1	C	217	TIGHT POSITIONAL	0.06	0.05
2	2	I	217	TIGHT POSITIONAL	0.07	0.05
2	3	O	217	TIGHT POSITIONAL	0.06	0.05
2	4	U	217	TIGHT POSITIONAL	0.07	0.05
2	5	1	217	TIGHT POSITIONAL	0.07	0.05
2	1	C	217	TIGHT THERMAL	0.21	0.5
2	2	I	217	TIGHT THERMAL	0.29	0.5
2	3	O	217	TIGHT THERMAL	0.28	0.5
2	4	U	217	TIGHT THERMAL	0.23	0.5
2	5	1	217	TIGHT THERMAL	0.27	0.5
3	1	E	217	TIGHT POSITIONAL	0.05	0.05
3	2	K	217	TIGHT POSITIONAL	0.05	0.05
3	3	Q	217	TIGHT POSITIONAL	0.05	0.05
3	4	W	217	TIGHT POSITIONAL	0.05	0.05
3	5	3	217	TIGHT POSITIONAL	0.06	0.05
3	1	E	217	TIGHT THERMAL	0.2	0.5
3	2	K	217	TIGHT THERMAL	0.2	0.5
3	3	Q	217	TIGHT THERMAL	0.2	0.5
3	4	W	217	TIGHT THERMAL	0.17	0.5
3	5	3	217	TIGHT THERMAL	0.18	0.5
4	1	B	213	TIGHT POSITIONAL	0.05	0.05
4	2	H	213	TIGHT POSITIONAL	0.05	0.05
4	3	N	213	TIGHT POSITIONAL	0.04	0.05
4	4	T	213	TIGHT POSITIONAL	0.05	0.05
4	5	Z	213	TIGHT POSITIONAL	0.04	0.05
4	1	B	213	TIGHT THERMAL	0.14	0.5
4	2	H	213	TIGHT THERMAL	0.13	0.5
4	3	N	213	TIGHT THERMAL	0.16	0.5
4	4	T	213	TIGHT THERMAL	0.16	0.5
4	5	Z	213	TIGHT THERMAL	0.14	0.5
5	1	D	213	TIGHT POSITIONAL	0.05	0.05
5	2	J	213	TIGHT POSITIONAL	0.07	0.05
5	3	P	213	TIGHT POSITIONAL	0.05	0.05
5	4	V	213	TIGHT POSITIONAL	0.06	0.05
5	5	2	213	TIGHT POSITIONAL	0.07	0.05
5	1	D	213	TIGHT THERMAL	0.27	0.5
5	2	J	213	TIGHT THERMAL	0.27	0.5
5	3	P	213	TIGHT THERMAL	0.22	0.5
5	4	V	213	TIGHT THERMAL	0.3	0.5
5	5	2	213	TIGHT THERMAL	0.27	0.5
6	1	F	213	TIGHT POSITIONAL	0.05	0.05
6	2	L	213	TIGHT POSITIONAL	0.05	0.05
6	3	R	213	TIGHT POSITIONAL	0.04	0.05
6	4	X	213	TIGHT POSITIONAL	0.04	0.05
6	5	4	213	TIGHT POSITIONAL	0.04	0.05
6	1	F	213	TIGHT THERMAL	0.17	0.5
6	2	L	213	TIGHT THERMAL	0.14	0.5
6	3	R	213	TIGHT THERMAL	0.16	0.5
6	4	X	213	TIGHT THERMAL	0.13	0.5
6	5	4	213	TIGHT THERMAL	0.16	0.5

LS refinement shell

Resolution: 1.149→1.179 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.264	275	-
R_work	0.256	4694	-
obs	-	-	92.58 %

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