PDB-5knn: Evolutionary gain of alanine mischarging to non-cognate tRNAs wit...

ID or keywords:

Entry

Database: PDB / ID: 5knn

Title

Evolutionary gain of alanine mischarging to non-cognate tRNAs with a G4:U69 base pair

Components

Alanine--tRNA ligase, cytoplasmic

Keywords

LIGASE / tRNA synthetase

Function / homology

Function and homology information

Ser-tRNA(Ala) deacylase activity / peptide lactyltransferase (ATP-dependent) activity / regulation of cytoplasmic translational fidelity / Ligases / alanine-tRNA ligase / alanine-tRNA ligase activity / alanyl-tRNA aminoacylation / positive regulation of hippo signaling / Cytosolic tRNA aminoacylation / cerebellar Purkinje cell layer development ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.68 Å

Authors

Sun, L. / He, W. / Yang, X.-L.

Citation

Journal: J.Am.Chem.Soc. / Year: 2016
Title: Evolutionary Gain of Alanine Mischarging to Noncognate tRNAs with a G4:U69 Base Pair.
Authors: Sun, L. / Gomes, A.C. / He, W. / Zhou, H. / Wang, X. / Pan, D.W. / Schimmel, P. / Pan, T. / Yang, X.L.

History

Deposition	Jun 28, 2016	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 28, 2016	Provider: repository / Type: Initial release
Revision 1.1	Oct 19, 2016	Group: Database references
Revision 1.2	Sep 27, 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 / pdbx_reflns_twin / pdbx_struct_oper_list / struct_ncs_dom_lim Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_reflns_twin.operator / _pdbx_struct_oper_list.symmetry_operation / _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

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5knn.cif.gz	696 KB	Display	PDBx/mmCIF format
PDB format	pdb5knn.ent.gz	575.3 KB	Display	PDB format
PDBx/mmJSON format	5knn.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5knn_validation.pdf.gz	2.6 MB	Display	wwPDB validaton report
Full document	5knn_full_validation.pdf.gz	2.7 MB	Display
Data in XML	5knn_validation.xml.gz	84.1 KB	Display
Data in CIF	5knn_validation.cif.gz	120.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/kn/5knn ftp://data.pdbj.org/pub/pdb/validation_reports/kn/5knn	HTTPS FTP

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Related structure data

Related structure data	3hxuS S: Starting model for refinement
Similar structure data	3m2j-d 3hy1-1 3soi-d 4n9l-d 4pq9-d 6quh-d 6q5f-2 2e18-d 5dok-d 4qgh-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) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

Related structure data

3hxuS

S: Starting model for refinement

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#16 - Apr 2001 Aminoacyl-tRNA Synthetases similarity (5)

Deposited unit

A: Alanine--tRNA ligase, cytoplasmic

B: Alanine--tRNA ligase, cytoplasmic

C: Alanine--tRNA ligase, cytoplasmic

D: Alanine--tRNA ligase, cytoplasmic

E: Alanine--tRNA ligase, cytoplasmic

F: Alanine--tRNA ligase, cytoplasmic

G: Alanine--tRNA ligase, cytoplasmic

H: Alanine--tRNA ligase, cytoplasmic

hetero molecules

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

1

A: Alanine--tRNA ligase, cytoplasmic

hetero molecules

defined by author&software
51 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Alanine--tRNA ligase, cytoplasmic

hetero molecules

defined by author&software
51 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: Alanine--tRNA ligase, cytoplasmic

hetero molecules

defined by author&software
51 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

D: Alanine--tRNA ligase, cytoplasmic

hetero molecules

defined by author&software
51 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

5

E: Alanine--tRNA ligase, cytoplasmic

hetero molecules

defined by author&software
51 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

6

F: Alanine--tRNA ligase, cytoplasmic

hetero molecules

defined by author&software
51 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

7

G: Alanine--tRNA ligase, cytoplasmic

hetero molecules

defined by author&software
51 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

8

H: Alanine--tRNA ligase, cytoplasmic

hetero molecules

defined by author&software
51 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	52.167, 98.260, 201.385
Angle α, β, γ (deg.)	90.070, 89.950, 90.110
Int Tables number	1
Space group name H-M	P1

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Component-ID: _ / Beg auth comp-ID: THR / Beg label comp-ID: THR / Refine code: _

Dom-ID	Ens-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	GLN	GLN	A	A	4 - 453	1 - 450
2	1	GLN	GLN	B	B	4 - 453	1 - 450
1	2	LYS	LYS	A	A	4 - 446	1 - 443
2	2	LYS	LYS	C	C	4 - 446	1 - 443
1	3	GLN	GLN	A	A	4 - 449	1 - 446
2	3	GLN	GLN	D	D	4 - 449	1 - 446
1	4	GLN	GLN	A	A	4 - 453	1 - 450
2	4	GLN	GLN	E	E	4 - 453	1 - 450
1	5	LYS	LYS	A	A	4 - 451	1 - 448
2	5	LYS	LYS	F	F	4 - 451	1 - 448
1	6	LYS	LYS	A	A	4 - 451	1 - 448
2	6	LYS	LYS	G	G	4 - 451	1 - 448
1	7	ALA	ALA	A	A	4 - 448	1 - 445
2	7	ALA	ALA	H	H	4 - 448	1 - 445
1	8	LYS	LYS	B	B	4 - 446	1 - 443
2	8	LYS	LYS	C	C	4 - 446	1 - 443
1	9	GLN	GLN	B	B	4 - 449	1 - 446
2	9	GLN	GLN	D	D	4 - 449	1 - 446
1	10	GLN	GLN	B	B	4 - 453	1 - 450
2	10	GLN	GLN	E	E	4 - 453	1 - 450
1	11	LYS	LYS	B	B	4 - 451	1 - 448
2	11	LYS	LYS	F	F	4 - 451	1 - 448
1	12	LYS	LYS	B	B	4 - 451	1 - 448
2	12	LYS	LYS	G	G	4 - 451	1 - 448
1	13	ALA	ALA	B	B	4 - 448	1 - 445
2	13	ALA	ALA	H	H	4 - 448	1 - 445
1	14	LYS	LYS	C	C	4 - 446	1 - 443
2	14	LYS	LYS	D	D	4 - 446	1 - 443
1	15	LYS	LYS	C	C	4 - 446	1 - 443
2	15	LYS	LYS	E	E	4 - 446	1 - 443
1	16	LYS	LYS	C	C	4 - 446	1 - 443
2	16	LYS	LYS	F	F	4 - 446	1 - 443
1	17	LYS	LYS	C	C	4 - 446	1 - 443
2	17	LYS	LYS	G	G	4 - 446	1 - 443
1	18	LYS	LYS	C	C	4 - 446	1 - 443
2	18	LYS	LYS	H	H	4 - 446	1 - 443
1	19	GLN	GLN	D	D	4 - 449	1 - 446
2	19	GLN	GLN	E	E	4 - 449	1 - 446
1	20	GLN	GLN	D	D	4 - 449	1 - 446
2	20	GLN	GLN	F	F	4 - 449	1 - 446
1	21	GLN	GLN	D	D	4 - 449	1 - 446
2	21	GLN	GLN	G	G	4 - 449	1 - 446
1	22	ALA	ALA	D	D	4 - 448	1 - 445
2	22	ALA	ALA	H	H	4 - 448	1 - 445
1	23	LYS	LYS	E	E	4 - 451	1 - 448
2	23	LYS	LYS	F	F	4 - 451	1 - 448
1	24	LYS	LYS	E	E	4 - 451	1 - 448
2	24	LYS	LYS	G	G	4 - 451	1 - 448
1	25	ALA	ALA	E	E	4 - 448	1 - 445
2	25	ALA	ALA	H	H	4 - 448	1 - 445
1	26	SER	SER	F	F	4 - 452	1 - 449
2	26	SER	SER	G	G	4 - 452	1 - 449
1	27	ALA	ALA	F	F	4 - 448	1 - 445
2	27	ALA	ALA	H	H	4 - 448	1 - 445
1	28	ALA	ALA	G	G	4 - 448	1 - 445
2	28	ALA	ALA	H	H	4 - 448	1 - 445

NCS ensembles :

#1: Protein	Alanine--tRNA ligase, cytoplasmic / Alanyl-tRNA synthetase / AlaRS / Renal carcinoma antigen NY-REN-42 Mass: 50623.250 Da / Num. of mol.: 8 / Fragment: residues 4-453 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: AARS Production host: Escherichia coli-Pichia pastoris shuttle vector pPpARG4 (others) References: UniProt: P49588, alanine-tRNA ligase
#2: Chemical	ChemComp-A5A / '5'-O-(N-(L-ALANYL)-SULFAMOYL)ADENOSINE Mass: 417.398 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₁₃H₁₉N₇O₇S

#1: Protein

Alanine--tRNA ligase, cytoplasmic / Alanyl-tRNA synthetase / AlaRS / Renal carcinoma antigen NY-REN-42

Mass: 50623.250 Da / Num. of mol.: 8 / Fragment: residues 4-453
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Homo sapiens (human) / Gene: AARS
Production host:

Escherichia coli-Pichia pastoris shuttle vector pPpARG4 (others)
References: UniProt: P49588, alanine-tRNA ligase

#2: Chemical

ChemComp-A5A / '5'-O-(N-(L-ALANYL)-SULFAMOYL)ADENOSINE

Mass: 417.398 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₁₃H₁₉N₇O₇S

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.55 Å³/Da / Density % sol: 51.74 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.1 M Hepes pH 7.5, 20% Polyethylene glycol 3350, 0.2 M MgCl2

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

SSRL

/ Beamline: BL11-1 / Wavelength: 1.1271 Å

Detector

Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 1, 2012

Radiation

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

Radiation wavelength

Wavelength: 1.1271 Å / Relative weight: 1

Reflection twin

Crystal-ID	ID	Operator	Domain-ID	Fraction
1	1	H, K, L	1	0.441
1	1	-h,-k,l	2	0.076
1	1	h,-k,-l	3	0.275
1	1	-H, K, -L	4	0.209

Reflection

Resolution: 2.68→50 Å / Num. obs: 100341 / % possible obs: 99.2 % / Redundancy: 6.9 % / R_merge(I) obs: 0.142 / Net I/av σ(I): 16.874 / Net I/σ(I): 5.5

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	CC_1/2	Diffraction-ID	% possible all
2.68-2.73	6.8	0.408	0.894	1	88.7
2.73-2.78	7.2	0.379	0.907	1	100
2.78-2.83	7.2	0.334	0.933	1	100
2.83-2.89	7.2	0.302	0.939	1	100
2.89-2.95	7.2	0.285	0.949	1	100
2.95-3.02	7.2	0.275	0.943	1	100
3.02-3.09	7.1	0.241	0.959	1	100
3.09-3.18	7.1	0.224	0.961	1	100
3.18-3.27	7.1	0.198	0.971	1	100
3.27-3.38	7.1	0.193	0.973	1	100
3.38-3.5	7	0.175	0.975	1	100
3.5-3.64	6.9	0.16	0.977	1	100
3.64-3.8	6.8	0.147	0.979	1	99.9
3.8-4	6.7	0.135	0.981	1	99.9
4-4.25	6.7	0.129	0.983	1	100
4.25-4.58	6.5	0.12	0.987	1	99.9
4.58-5.04	6.5	0.117	0.985	1	100
5.04-5.77	6.6	0.121	0.984	1	99.8
5.77-7.27	6.4	0.11	0.986	1	99.9
7.27-50	6	0.081	0.992	1	97

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Processing

Software

Name	Version	Classification
HKL-2000		data collection
HKL-2000		data scaling
REFMAC	5.8.0107	refinement
PDB_EXTRACT	3.2	data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3HXU

3hxu

Resolution: 2.68→49.13 Å / Cor.coef. F_o:F_c: 0.911 / Cor.coef. F_o:F_c free: 0.872 / SU B: 15.985 / SU ML: 0.359 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.08
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2542	5119	4.9 %	RANDOM
R_work	0.216	-	-	-
obs	0.2179	100341	93.42 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å

Displacement parameters

B_iso max: 141.16 Å² / B_iso mean: 55.755 Å² / B_iso min: 11.29 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-10.09 Å²	5.36 Å²	-19.53 Å²
2-	-	-1.42 Å²	-27.27 Å²
3-	-	-	11.52 Å²

Refinement step

Cycle: final / Resolution: 2.68→49.13 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	28360	0	224	0	28584
B_iso mean	-	-	42.79	-	-
Num. residues	-	-	-	-	3585

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.016	0.019	29200
X-RAY DIFFRACTION	r_bond_other_d	0.02	0.02	27610
X-RAY DIFFRACTION	r_angle_refined_deg	1.996	1.973	39522
X-RAY DIFFRACTION	r_angle_other_deg	3.151	3	63532
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.595	5	3577
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	32.608	24.165	1426
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	17.603	15	5001
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.377	15	208
X-RAY DIFFRACTION	r_chiral_restr	0.122	0.2	4295
X-RAY DIFFRACTION	r_gen_planes_refined	0.015	0.021	33203
X-RAY DIFFRACTION	r_gen_planes_other	0.016	0.02	6773
X-RAY DIFFRACTION	r_mcbond_it	4.478	5.517	14356
X-RAY DIFFRACTION	r_mcbond_other	4.478	5.517	14357
X-RAY DIFFRACTION	r_mcangle_it	6.913	8.272	17917

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	52708	0.14
1	2	B	52708	0.14
2	1	A	50504	0.16
2	2	C	50504	0.16
3	1	A	50956	0.16
3	2	D	50956	0.16
4	1	A	53048	0.13
4	2	E	53048	0.13
5	1	A	53282	0.13
5	2	F	53282	0.13
6	1	A	50608	0.16
6	2	G	50608	0.16
7	1	A	50152	0.16
7	2	H	50152	0.16
8	1	B	50168	0.16
8	2	C	50168	0.16
9	1	B	50474	0.16
9	2	D	50474	0.16
10	1	B	52336	0.13
10	2	E	52336	0.13
11	1	B	53564	0.12
11	2	F	53564	0.12
12	1	B	49704	0.16
12	2	G	49704	0.16
13	1	B	49908	0.16
13	2	H	49908	0.16
14	1	C	49676	0.17
14	2	D	49676	0.17
15	1	C	49890	0.16
15	2	E	49890	0.16
16	1	C	50486	0.16
16	2	F	50486	0.16
17	1	C	49046	0.17
17	2	G	49046	0.17
18	1	C	50356	0.16
18	2	H	50356	0.16
19	1	D	50518	0.16
19	2	E	50518	0.16
20	1	D	50508	0.16
20	2	F	50508	0.16
21	1	D	50454	0.16
21	2	G	50454	0.16
22	1	D	49900	0.17
22	2	H	49900	0.17
23	1	E	52912	0.13
23	2	F	52912	0.13
24	1	E	50422	0.17
24	2	G	50422	0.17
25	1	E	49898	0.16
25	2	H	49898	0.16
26	1	F	50148	0.17
26	2	G	50148	0.17
27	1	F	49950	0.16
27	2	H	49950	0.16
28	1	G	49484	0.17
28	2	H	49484	0.17

LS refinement shell

Resolution: 2.676→2.745 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.367	373	-
R_work	0.282	6919	-
all	-	7292	-
obs	-	-	86.71 %

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