PDB-3wrw: Crystal structure of the N-terminal domain of resistance protein

ID or keywords:

Entry

Database: PDB / ID: 3wrw

Title

Crystal structure of the N-terminal domain of resistance protein

Components

Tm-1 protein

Keywords

TRANSFERASE / alpha/beta domain / resistance factor

Function / homology

Function and homology information

host-mediated perturbation of viral RNA genome replication / catalytic activity / defense response to virus / protein homodimerization activity / ATP binding
Similarity search - Function

Biological species

Solanum lycopersicum (tomato)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 2.71 Å

Authors

Katoh, E. / Kezuka, Y.

Citation

Journal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Structural basis for the recognition-evasion arms race between Tomato mosaic virus and the resistance gene Tm-1
Authors: Ishibashi, K. / Kezuka, Y. / Kobayashi, C. / Kato, M. / Inoue, T. / Nonaka, T. / Ishikawa, M. / Matsumura, H. / Katoh, E.

History

Deposition	Feb 27, 2014	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Aug 13, 2014	Provider: repository / Type: Initial release
Revision 1.1	Nov 16, 2016	Group: Database references
Revision 1.2	Oct 16, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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_leaving_atom_flag / _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	3wrw.cif.gz	445.8 KB	Display	PDBx/mmCIF format
PDB format	pdb3wrw.ent.gz	367.9 KB	Display	PDB format
PDBx/mmJSON format	3wrw.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	3wrw_validation.pdf.gz	512 KB	Display	wwPDB validaton report
Full document	3wrw_full_validation.pdf.gz	617.1 KB	Display
Data in XML	3wrw_validation.xml.gz	101.3 KB	Display
Data in CIF	3wrw_validation.cif.gz	131.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/wr/3wrw ftp://data.pdbj.org/pub/pdb/validation_reports/wr/3wrw	HTTPS FTP

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Related structure data

Related structure data	3wrvC 3wrxC 3wryC 3vkw C: citing same article (ref.)
Similar structure data	4hn1-d 5cr7-d 5tdh-1 3dzu-d 6q6i-d 3ogm-8 4y30-d 4k6m-1 7aaj-d 3ufh-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) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

Related structure data

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	#50 - Feb 2004 Glycolytic Enzymes similarity (1) #228 - Dec 2018 Directed Evolution of Enzymes similarity (1)

Deposited unit

A: Tm-1 protein

B: Tm-1 protein

C: Tm-1 protein

D: Tm-1 protein

E: Tm-1 protein

F: Tm-1 protein

hetero molecules

280 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Tm-1 protein

B: Tm-1 protein

hetero molecules

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

2

C: Tm-1 protein

D: Tm-1 protein

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

3

E: Tm-1 protein

F: Tm-1 protein

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

Unit cell

Length a, b, c (Å)	77.970, 105.280, 110.620
Angle α, β, γ (deg.)	94.56, 109.27, 107.99
Int Tables number	1
Space group name H-M	P1

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Component-ID: 1 / Refine code: 5

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	PRO	PRO	PHE	PHE	A	A	9 - 38	9 - 38
2	1	PRO	PRO	PHE	PHE	B	B	9 - 38	9 - 38
3	1	PRO	PRO	PHE	PHE	C	C	9 - 38	9 - 38
4	1	PRO	PRO	PHE	PHE	D	D	9 - 38	9 - 38
5	1	PRO	PRO	PHE	PHE	E	E	9 - 38	9 - 38
6	1	PRO	PRO	PHE	PHE	F	F	9 - 38	9 - 38
1	2	GLY	GLY	LEU	LEU	A	A	47 - 75	47 - 75
2	2	GLY	GLY	LEU	LEU	B	B	47 - 75	47 - 75
3	2	GLY	GLY	LEU	LEU	C	C	47 - 75	47 - 75
4	2	GLY	GLY	LEU	LEU	D	D	47 - 75	47 - 75
5	2	GLY	GLY	LEU	LEU	E	E	47 - 75	47 - 75
6	2	GLY	GLY	LEU	LEU	F	F	47 - 75	47 - 75
1	3	ALA	ALA	GLU	GLU	A	A	97 - 200	97 - 200
2	3	ALA	ALA	GLU	GLU	B	B	97 - 200	97 - 200
3	3	ALA	ALA	GLU	GLU	C	C	97 - 200	97 - 200
4	3	ALA	ALA	GLU	GLU	D	D	97 - 200	97 - 200
5	3	ALA	ALA	GLU	GLU	E	E	97 - 200	97 - 200
6	3	ALA	ALA	GLU	GLU	F	F	97 - 200	97 - 200
1	4	VAL	VAL	VAL	VAL	A	A	214 - 309	214 - 309
2	4	VAL	VAL	VAL	VAL	B	B	214 - 309	214 - 309
3	4	VAL	VAL	VAL	VAL	C	C	214 - 309	214 - 309
4	4	VAL	VAL	VAL	VAL	D	D	214 - 309	214 - 309
5	4	VAL	VAL	VAL	VAL	E	E	214 - 309	214 - 309
6	4	VAL	VAL	VAL	VAL	F	F	214 - 309	214 - 309
1	5	LEU	LEU	LEU	LEU	A	A	335 - 397	335 - 397
2	5	LEU	LEU	LEU	LEU	B	B	335 - 397	335 - 397
3	5	LEU	LEU	LEU	LEU	C	C	335 - 397	335 - 397
4	5	LEU	LEU	LEU	LEU	D	D	335 - 397	335 - 397
5	5	LEU	LEU	LEU	LEU	E	E	335 - 397	335 - 397
6	5	LEU	LEU	LEU	LEU	F	F	335 - 397	335 - 397
1	6	CYS	CYS	PRO	PRO	A	A	403 - 430	403 - 430
2	6	CYS	CYS	PRO	PRO	B	B	403 - 430	403 - 430
3	6	CYS	CYS	PRO	PRO	C	C	403 - 430	403 - 430
4	6	CYS	CYS	PRO	PRO	D	D	403 - 430	403 - 430
5	6	CYS	CYS	PRO	PRO	E	E	403 - 430	403 - 430
6	6	CYS	CYS	PRO	PRO	F	F	403 - 430	403 - 430

NCS ensembles :

ID
1
2
3
4
5
6

NCS oper:

ID	Code	Matrix	Vector
1	given	(1), (1), (1)
2	given	(0.238933, -0.646319, -0.724694), (-0.650005, -0.660896, 0.375113), (-0.721391, 0.381428, -0.578021)	77.48631, 18.33951, 116.31963
3	given	(-0.437499, -0.542928, -0.716815), (0.595621, 0.422236, -0.683339), (0.673669, -0.72591, 0.138652)	23.84267, 23.5826, 75.56933
4	given	(-0.978278, 0.116822, 0.171245), (0.149524, -0.174502, 0.973238), (0.143578, 0.977702, 0.153244)	13.21903, 14.77442, 65.29681
5	given	(0.57122, 0.496071, 0.653927), (0.500401, -0.84199, 0.201625), (0.65062, 0.212054, -0.729196)	-74.7751, 88.76293, 111.73338
6	given	(-0.669203, 0.509036, 0.541341), (-0.449039, 0.303423, -0.840416), (-0.592057, -0.805492, 0.025525)	-78.32125, 51.306, 139.94305

#1: Protein	Tm-1 protein / Resistance protein Mass: 46626.445 Da / Num. of mol.: 6 / Fragment: N-terminal domain, UNP residues 1-431 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Solanum lycopersicum (tomato) / Gene: Tm-1 / Production host: Escherichia coli (E. coli) / References: UniProt: A7M6E7
#2: Chemical	ChemComp-TLA / L(+)-TARTARIC ACID Mass: 150.087 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₄H₆O₆
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 44 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.85 Å³/Da / Density % sol: 56.9 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 8.0% (W/v) PEG 8000, 0.4M ammonium tartrate dibasic, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

SPring-8

/ Beamline: BL38B1 / Wavelength: 0.9788, 0.9792, 0.9639

Detector

Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 21, 2011

Radiation

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

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.9788	1
2	0.9792	1
3	0.9639	1

Reflection

Resolution: 2.71→49.64 Å / Num. all: 79784 / Num. obs: 79784 / % possible obs: 95 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3

Reflection shell

Resolution: 2.71→2.86 Å / Redundancy: 2 % / R_merge(I) obs: 0.237 / Mean I/σ(I) obs: 3.1 / % possible all: 95.5

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Processing

Software

Name	Version	Classification
ADSC	Quantum	data collection
AutoSol		phasing
REFMAC	5.6.0117	refinement
MOSFLM		data reduction
SCALA		data scaling

Refinement

Method to determine structure:

MAD / Resolution: 2.71→49.64 Å / Cor.coef. F_o:F_c: 0.948 / Cor.coef. F_o:F_c free: 0.905 / SU B: 14.497 / SU ML: 0.294 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.176 / ESU R Free: 0.378 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.27781	3975	5 %	RANDOM
R_work	0.20707	-	-	-
all	0.21059	75809	-	-
obs	0.21059	75809	94.97 %	-

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: 56.944 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.82 Å²	-0.27 Å²	-0.25 Å²
2-	-	-1.06 Å²	0.98 Å²
3-	-	-	-0.93 Å²

Refinement step

Cycle: LAST / Resolution: 2.71→49.64 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	17782	0	20	44	17846

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.012	0.019	18091
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	11978
X-RAY DIFFRACTION	r_angle_refined_deg	1.543	1.879	24491
X-RAY DIFFRACTION	r_angle_other_deg	0.958	3	29462
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.853	5	2358
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	40.505	24.842	696
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	20.73	15	2944
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	19.662	15	78
X-RAY DIFFRACTION	r_chiral_restr	0.083	0.2	2946
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.021	20074
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	3480

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	178	MEDIUM POSITIONAL	0.19	0.5
1	2	B	178	MEDIUM POSITIONAL	0.23	0.5
1	3	C	178	MEDIUM POSITIONAL	0.23	0.5
1	4	D	178	MEDIUM POSITIONAL	0.23	0.5
1	5	E	178	MEDIUM POSITIONAL	0.18	0.5
1	6	F	178	MEDIUM POSITIONAL	0.26	0.5
1	1	A	245	LOOSE POSITIONAL	0.48	5
1	2	B	245	LOOSE POSITIONAL	0.82	5
1	3	C	245	LOOSE POSITIONAL	0.73	5
1	4	D	245	LOOSE POSITIONAL	0.68	5
1	5	E	245	LOOSE POSITIONAL	0.52	5
1	6	F	245	LOOSE POSITIONAL	0.62	5
1	1	A	178	MEDIUM THERMAL	9.4	2
1	2	B	178	MEDIUM THERMAL	5.03	2
1	3	C	178	MEDIUM THERMAL	6.51	2
1	4	D	178	MEDIUM THERMAL	3.79	2
1	5	E	178	MEDIUM THERMAL	11.33	2
1	6	F	178	MEDIUM THERMAL	18.91	2
1	1	A	245	LOOSE THERMAL	9.13	10
1	2	B	245	LOOSE THERMAL	7.29	10
1	3	C	245	LOOSE THERMAL	8.89	10
1	4	D	245	LOOSE THERMAL	5.49	10
1	5	E	245	LOOSE THERMAL	12.69	10
1	6	F	245	LOOSE THERMAL	17.13	10
2	1	A	172	MEDIUM POSITIONAL	0.23	0.5
2	2	B	172	MEDIUM POSITIONAL	0.29	0.5
2	3	C	172	MEDIUM POSITIONAL	0.29	0.5
2	4	D	172	MEDIUM POSITIONAL	0.32	0.5
2	5	E	172	MEDIUM POSITIONAL	0.23	0.5
2	6	F	172	MEDIUM POSITIONAL	0.32	0.5
2	1	A	186	LOOSE POSITIONAL	0.49	5
2	2	B	186	LOOSE POSITIONAL	0.56	5
2	3	C	186	LOOSE POSITIONAL	0.57	5
2	4	D	186	LOOSE POSITIONAL	0.55	5
2	5	E	186	LOOSE POSITIONAL	0.58	5
2	6	F	186	LOOSE POSITIONAL	1.12	5
2	1	A	172	MEDIUM THERMAL	12.89	2
2	2	B	172	MEDIUM THERMAL	7.96	2
2	3	C	172	MEDIUM THERMAL	5.28	2
2	4	D	172	MEDIUM THERMAL	7.63	2
2	5	E	172	MEDIUM THERMAL	14.42	2
2	6	F	172	MEDIUM THERMAL	17.74	2
2	1	A	186	LOOSE THERMAL	11.93	10
2	2	B	186	LOOSE THERMAL	8.18	10
2	3	C	186	LOOSE THERMAL	6.01	10
2	4	D	186	LOOSE THERMAL	8.06	10
2	5	E	186	LOOSE THERMAL	14.33	10
2	6	F	186	LOOSE THERMAL	17.53	10
3	1	A	608	MEDIUM POSITIONAL	0.24	0.5
3	2	B	608	MEDIUM POSITIONAL	0.22	0.5
3	3	C	608	MEDIUM POSITIONAL	0.26	0.5
3	4	D	608	MEDIUM POSITIONAL	0.22	0.5
3	5	E	608	MEDIUM POSITIONAL	0.23	0.5
3	6	F	608	MEDIUM POSITIONAL	0.32	0.5
3	1	A	600	LOOSE POSITIONAL	0.45	5
3	2	B	600	LOOSE POSITIONAL	0.64	5
3	3	C	600	LOOSE POSITIONAL	0.59	5
3	4	D	600	LOOSE POSITIONAL	0.48	5
3	5	E	600	LOOSE POSITIONAL	0.46	5
3	6	F	600	LOOSE POSITIONAL	0.59	5
3	1	A	608	MEDIUM THERMAL	8.08	2
3	2	B	608	MEDIUM THERMAL	5.92	2
3	3	C	608	MEDIUM THERMAL	6.52	2
3	4	D	608	MEDIUM THERMAL	6.05	2
3	5	E	608	MEDIUM THERMAL	7.17	2
3	6	F	608	MEDIUM THERMAL	14.18	2
3	1	A	600	LOOSE THERMAL	8.31	10
3	2	B	600	LOOSE THERMAL	6.38	10
3	3	C	600	LOOSE THERMAL	6.34	10
3	4	D	600	LOOSE THERMAL	6.74	10
3	5	E	600	LOOSE THERMAL	8.13	10
3	6	F	600	LOOSE THERMAL	14.43	10
4	1	A	560	MEDIUM POSITIONAL	0.22	0.5
4	2	B	560	MEDIUM POSITIONAL	0.27	0.5
4	3	C	560	MEDIUM POSITIONAL	0.28	0.5
4	4	D	560	MEDIUM POSITIONAL	0.23	0.5
4	5	E	560	MEDIUM POSITIONAL	0.29	0.5
4	6	F	560	MEDIUM POSITIONAL	0.25	0.5
4	1	A	599	LOOSE POSITIONAL	0.45	5
4	2	B	599	LOOSE POSITIONAL	0.58	5
4	3	C	599	LOOSE POSITIONAL	0.48	5
4	4	D	599	LOOSE POSITIONAL	0.51	5
4	5	E	599	LOOSE POSITIONAL	0.56	5
4	6	F	599	LOOSE POSITIONAL	0.7	5
4	1	A	560	MEDIUM THERMAL	10.6	2
4	2	B	560	MEDIUM THERMAL	7.18	2
4	3	C	560	MEDIUM THERMAL	11.45	2
4	4	D	560	MEDIUM THERMAL	16.73	2
4	5	E	560	MEDIUM THERMAL	19.77	2
4	6	F	560	MEDIUM THERMAL	18.74	2
4	1	A	599	LOOSE THERMAL	10.32	10
4	2	B	599	LOOSE THERMAL	9.32	10
4	3	C	599	LOOSE THERMAL	14.23	10
4	4	D	599	LOOSE THERMAL	16.85	10
4	5	E	599	LOOSE THERMAL	21.42	10
4	6	F	599	LOOSE THERMAL	18.5	10
5	1	A	366	MEDIUM POSITIONAL	0.23	0.5
5	2	B	366	MEDIUM POSITIONAL	0.34	0.5
5	3	C	366	MEDIUM POSITIONAL	0.34	0.5
5	4	D	366	MEDIUM POSITIONAL	0.27	0.5
5	5	E	366	MEDIUM POSITIONAL	0.31	0.5
5	6	F	366	MEDIUM POSITIONAL	0.28	0.5
5	1	A	429	LOOSE POSITIONAL	0.48	5
5	2	B	429	LOOSE POSITIONAL	0.56	5
5	3	C	429	LOOSE POSITIONAL	0.64	5
5	4	D	429	LOOSE POSITIONAL	0.65	5
5	5	E	429	LOOSE POSITIONAL	0.57	5
5	6	F	429	LOOSE POSITIONAL	0.59	5
5	1	A	366	MEDIUM THERMAL	19.18	2
5	2	B	366	MEDIUM THERMAL	13.28	2
5	3	C	366	MEDIUM THERMAL	13.09	2
5	4	D	366	MEDIUM THERMAL	16.53	2
5	5	E	366	MEDIUM THERMAL	15.22	2
5	6	F	366	MEDIUM THERMAL	25.33	2
5	1	A	429	LOOSE THERMAL	19.46	10
5	2	B	429	LOOSE THERMAL	15.38	10
5	3	C	429	LOOSE THERMAL	12.76	10
5	4	D	429	LOOSE THERMAL	14.88	10
5	5	E	429	LOOSE THERMAL	13.87	10
5	6	F	429	LOOSE THERMAL	23.29	10
6	1	A	166	MEDIUM POSITIONAL	0.26	0.5
6	2	B	166	MEDIUM POSITIONAL	0.33	0.5
6	3	C	166	MEDIUM POSITIONAL	0.25	0.5
6	4	D	166	MEDIUM POSITIONAL	0.29	0.5
6	5	E	166	MEDIUM POSITIONAL	0.38	0.5
6	6	F	166	MEDIUM POSITIONAL	0.36	0.5
6	1	A	196	LOOSE POSITIONAL	0.5	5
6	2	B	196	LOOSE POSITIONAL	0.68	5
6	3	C	196	LOOSE POSITIONAL	0.75	5
6	4	D	196	LOOSE POSITIONAL	0.6	5
6	5	E	196	LOOSE POSITIONAL	0.54	5
6	6	F	196	LOOSE POSITIONAL	0.68	5
6	1	A	166	MEDIUM THERMAL	8.27	2
6	2	B	166	MEDIUM THERMAL	17.53	2
6	3	C	166	MEDIUM THERMAL	21.59	2
6	4	D	166	MEDIUM THERMAL	26.41	2
6	5	E	166	MEDIUM THERMAL	27.6	2
6	6	F	166	MEDIUM THERMAL	18.15	2
6	1	A	196	LOOSE THERMAL	10.2	10
6	2	B	196	LOOSE THERMAL	20.01	10
6	3	C	196	LOOSE THERMAL	21.37	10
6	4	D	196	LOOSE THERMAL	25.93	10
6	5	E	196	LOOSE THERMAL	29.16	10
6	6	F	196	LOOSE THERMAL	19.49	10

LS refinement shell

Resolution: 2.71→2.78 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.378	298	-
R_work	0.302	5633	-
obs	-	-	95.52 %

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