PDB-3rlk: Crystal structure of the read-through domain from bacteriophage Q...

ID or keywords:

Entry

Database: PDB / ID: 3rlk

Title

Crystal structure of the read-through domain from bacteriophage Qbeta A1 protein, monoclinic crystal form

Components

A1 protein

Keywords

STRUCTURAL PROTEIN / Beta-barrel / polyproline helix

Function / homology

Read-through domain / Read-through domain / Levivirus coat protein / Levivirus coat protein / Bacteriophage RNA-type, capsid / viral capsid / structural molecule activity / Minor capsid protein A1

Function and homology information

Biological species

Enterobacteria phage Qbeta (virus)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MIRAS / Resolution: 1.76 Å

Authors

Rumnieks, J. / Tars, K.

Citation

Journal: Protein Sci. / Year: 2011
Title: Crystal structure of the read-through domain from bacteriophage Qbeta A1 protein
Authors: Rumnieks, J. / Tars, K.

History

Deposition	Apr 19, 2011	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 28, 2011	Provider: repository / Type: Initial release
Revision 1.1	Jun 26, 2013	Group: Database references
Revision 1.2	Feb 28, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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	3rlk.cif.gz	54.8 KB	Display	PDBx/mmCIF format
PDB format	pdb3rlk.ent.gz	37.2 KB	Display	PDB format
PDBx/mmJSON format	3rlk.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3rlk_validation.pdf.gz	418.3 KB	Display	wwPDB validaton report
Full document	3rlk_full_validation.pdf.gz	418.3 KB	Display
Data in XML	3rlk_validation.xml.gz	10.4 KB	Display
Data in CIF	3rlk_validation.cif.gz	14.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/rl/3rlk ftp://data.pdbj.org/pub/pdb/validation_reports/rl/3rlk	HTTPS FTP

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Related structure data

Related structure data	3rlcC C: citing same article (ref.)
Similar structure data	2g7h-d 4qu0-d 3nzi-d 5h5f-d 1n0w-d 2aio-d 5iag-d 4qua-d 5i9b-d 3k6y-d Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: A1 protein

hetero molecules

22 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	44.010, 49.120, 44.260
Angle α, β, γ (deg.)	90.00, 118.41, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	A1 protein / A1 read-through protein Mass: 21794.596 Da / Num. of mol.: 1 / Fragment: Read-through domain, UNP residues 145-329 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterobacteria phage Qbeta (virus) / Gene: A1 / Plasmid: pBAD / Production host: Escherichia coli (E. coli) / Strain (production host): TOP10 / References: UniProt: Q8LTE1
#2: Chemical	ChemComp-PG4 / TETRAETHYLENE GLYCOL Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₈H₁₈O₅ / Comment: precipitant*YM
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 155 / 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: 1.93 Å³/Da / Density % sol: 36.29 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.1 M Tris-HCl, 40% PEG 300, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

ESRF

/ Beamline: ID29 / Wavelength: 0.97618 Å

Detector

Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 5, 2009

Radiation

Monochromator: Si (311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.97618 Å / Relative weight: 1

Reflection

Redundancy: 4.3 % / Av σ(I) over netI: 8.5 / Number: 8965 / R_sym value: 0.077 / D res high: 3.5 Å / D res low: 38.65 Å / Num. obs: 2104 / % possible obs: 96.8

Diffraction reflection shell

Highest resolution (Å)	Lowest resolution (Å)	% possible obs (%)	ID	R_merge(I) obs	R_sym value	Redundancy
11.07	38.65	85.5	1	0.07	0.07	3
7.83	11.07	90.5	1	0.069	0.069	3.6
6.39	7.83	93.3	1	0.08	0.08	4
5.53	6.39	93.7	1	0.083	0.083	3.7
4.95	5.53	98.6	1	0.086	0.086	4.1
4.52	4.95	98.2	1	0.062	0.062	4.4
4.18	4.52	99.6	1	0.066	0.066	4.5
3.91	4.18	99.4	1	0.076	0.076	4.3
3.69	3.91	97.5	1	0.08	0.08	4.7
3.5	3.69	97.9	1	0.092	0.092	4.6

Reflection

Resolution: 1.76→38.93 Å / Num. obs: 16414 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / R_sym value: 0.078 / Net I/σ(I): 10

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured all	Num. unique all	R_sym value	% possible all
1.76-1.86	3.3	0.334	2.2	7776	2378	0.334	99.5
1.86-1.97	3.4	0.222	3.3	7810	2271	0.222	99.6
1.97-2.11	3.5	0.153	4.8	7376	2130	0.153	99.3
2.11-2.27	3.4	0.114	6.4	6780	1968	0.114	99.4
2.27-2.49	3.4	0.1	7	6243	1822	0.1	99.6
2.49-2.79	3.4	0.076	9	5634	1661	0.076	99.4
2.79-3.22	3.4	0.057	11.5	4902	1459	0.057	99.2
3.22-3.94	3.3	0.051	12.1	4037	1231	0.051	98.6
3.94-5.57	3.1	0.052	12	2889	947	0.052	96.6
5.57-38.93	3.4	0.046	13.4	1874	547	0.046	99.7

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Phasing

Phasing

Method:

MIRAS

Phasing set

ID
1
2
3
4
5

Phasing MIR

Resolution: 1.76→38.93 Å / FOM acentric: 0.34 / FOM centric: 0.4 / Reflection acentric: 15619 / Reflection centric: 853

Phasing MIR der

Native set-ID: 1 / Resolution: 1.76→38.93 Å

ID	Der set-ID	Power acentric	Power centric	Reflection acentric	Reflection centric
ISO_1	1	0	0	3810	306
ISO_2	2	0.46	0.32	3802	288
ISO_3	3	0.649	0.495	3694	306
ISO_4	4	2.247	1.54	3644	289
ISO_5	5	2.139	1.495	3368	282

Phasing MIR der shell

Highest resolution (Å)	Lowest resolution (Å)	Der-ID	Power acentric	Power centric	Reflection acentric	Reflection centric
7.73	38.93	ISO_1	0	0	154	32
5.52	7.73	ISO_1	0	0	292	34
4.52	5.52	ISO_1	0	0	406	40
3.92	4.52	ISO_1	0	0	486	46
3.51	3.92	ISO_1	0	0	531	35
3.21	3.51	ISO_1	0	0	614	40
2.97	3.21	ISO_1	0	0	662	40
2.78	2.97	ISO_1	0	0	663	38
2.62	2.78	ISO_1	0	0	2	1
2.49	2.62	ISO_1	0	0	0	0
2.37	2.49	ISO_1	0	0	0	0
2.27	2.37	ISO_1	0	0	0	0
2.18	2.27	ISO_1	0	0	0	0
2.11	2.18	ISO_1	0	0	0	0
2.03	2.11	ISO_1	0	0	0	0
1.97	2.03	ISO_1	0	0	0	0
1.91	1.97	ISO_1	0	0	0	0
1.86	1.91	ISO_1	0	0	0	0
1.81	1.86	ISO_1	0	0	0	0
1.76	1.81	ISO_1	0	0	0	0
7.73	38.93	ISO_2	0.648	0.507	153	27
5.52	7.73	ISO_2	0.638	0.492	287	33
4.52	5.52	ISO_2	0.57	0.397	406	40
3.92	4.52	ISO_2	0.527	0.346	486	41
3.51	3.92	ISO_2	0.503	0.261	530	32
3.21	3.51	ISO_2	0.418	0.278	614	38
2.97	3.21	ISO_2	0.39	0.232	662	38
2.78	2.97	ISO_2	0.353	0.261	662	38
2.62	2.78	ISO_2	0.191	0.128	2	1
2.49	2.62	ISO_2	0	0	0	0
2.37	2.49	ISO_2	0	0	0	0
2.27	2.37	ISO_2	0	0	0	0
2.18	2.27	ISO_2	0	0	0	0
2.11	2.18	ISO_2	0	0	0	0
2.03	2.11	ISO_2	0	0	0	0
1.97	2.03	ISO_2	0	0	0	0
1.91	1.97	ISO_2	0	0	0	0
1.86	1.91	ISO_2	0	0	0	0
1.81	1.86	ISO_2	0	0	0	0
1.76	1.81	ISO_2	0	0	0	0
7.73	38.93	ISO_3	0.79	0.885	142	32
5.52	7.73	ISO_3	0.9	0.777	273	34
4.52	5.52	ISO_3	0.797	0.569	390	40
3.92	4.52	ISO_3	0.725	0.503	477	46
3.51	3.92	ISO_3	0.706	0.43	511	35
3.21	3.51	ISO_3	0.611	0.4	603	40
2.97	3.21	ISO_3	0.569	0.398	646	40
2.78	2.97	ISO_3	0.497	0.375	650	38
2.62	2.78	ISO_3	0.299	0.149	2	1
2.49	2.62	ISO_3	0	0	0	0
2.37	2.49	ISO_3	0	0	0	0
2.27	2.37	ISO_3	0	0	0	0
2.18	2.27	ISO_3	0	0	0	0
2.11	2.18	ISO_3	0	0	0	0
2.03	2.11	ISO_3	0	0	0	0
1.97	2.03	ISO_3	0	0	0	0
1.91	1.97	ISO_3	0	0	0	0
1.86	1.91	ISO_3	0	0	0	0
1.81	1.86	ISO_3	0	0	0	0
1.76	1.81	ISO_3	0	0	0	0
7.73	38.93	ISO_4	1.507	1.49	141	31
5.52	7.73	ISO_4	1.925	1.616	273	34
4.52	5.52	ISO_4	1.878	1.35	381	34
3.92	4.52	ISO_4	1.618	0.894	464	36
3.51	3.92	ISO_4	1.577	1.032	500	35
3.21	3.51	ISO_4	1.629	0.947	598	40
2.97	3.21	ISO_4	1.794	1.303	642	40
2.78	2.97	ISO_4	1.833	1.237	643	38
2.62	2.78	ISO_4	1.555	0.73	2	1
2.49	2.62	ISO_4	0	0	0	0
2.37	2.49	ISO_4	0	0	0	0
2.27	2.37	ISO_4	0	0	0	0
2.18	2.27	ISO_4	0	0	0	0
2.11	2.18	ISO_4	0	0	0	0
2.03	2.11	ISO_4	0	0	0	0
1.97	2.03	ISO_4	0	0	0	0
1.91	1.97	ISO_4	0	0	0	0
1.86	1.91	ISO_4	0	0	0	0
1.81	1.86	ISO_4	0	0	0	0
1.76	1.81	ISO_4	0	0	0	0
7.73	38.93	ISO_5	2.128	1.661	154	31
5.52	7.73	ISO_5	2.661	2.215	292	34
4.52	5.52	ISO_5	2.335	1.493	406	40
3.92	4.52	ISO_5	2.023	1.302	485	46
3.51	3.92	ISO_5	2.001	1.223	531	35
3.21	3.51	ISO_5	1.984	1.337	614	40
2.97	3.21	ISO_5	2.156	1.476	662	40
2.78	2.97	ISO_5	2.016	1.753	224	16
2.62	2.78	ISO_5	0	0	0	0
2.49	2.62	ISO_5	0	0	0	0
2.37	2.49	ISO_5	0	0	0	0
2.27	2.37	ISO_5	0	0	0	0
2.18	2.27	ISO_5	0	0	0	0
2.11	2.18	ISO_5	0	0	0	0
2.03	2.11	ISO_5	0	0	0	0
1.97	2.03	ISO_5	0	0	0	0
1.91	1.97	ISO_5	0	0	0	0
1.86	1.91	ISO_5	0	0	0	0
1.81	1.86	ISO_5	0	0	0	0
1.76	1.81	ISO_5	0	0	0	0

Phasing MIR shell

Resolution (Å)	FOM acentric	FOM centric	Reflection acentric	Reflection centric
7.73-38.93	0.867	0.751	168	44
5.52-7.73	0.867	0.785	309	43
4.52-5.52	0.881	0.801	412	42
3.92-4.52	0.858	0.78	487	47
3.51-3.92	0.831	0.784	543	41
3.21-3.51	0.815	0.649	615	44
2.97-3.21	0.76	0.801	665	42
2.78-2.97	0.632	0.564	716	42
2.62-2.78	0.277	0.256	765	44
2.49-2.62	0.267	0.224	808	45
2.37-2.49	0.267	0.248	849	42
2.27-2.37	0.292	0.202	894	42
2.18-2.27	0.263	0.208	930	41
2.11-2.18	0.265	0.213	954	36
2.03-2.11	0.241	0.211	995	48
1.97-2.03	0.168	0.174	1040	42
1.91-1.97	0.128	0.101	1071	44
1.86-1.91	0.105	0.086	1105	43
1.81-1.86	0.067	0.065	1120	40
1.76-1.81	0.045	0.033	1173	41

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Processing

Software

Name	Version	Classification
MOSFLM		data reduction
SCALA	3.3.9	data scaling
SHARP		phasing
SOLOMON		phasing
REFMAC		refinement
PDB_EXTRACT	3.1	data extraction
ADSC	Quantum	data collection

Refinement

Method to determine structure:

MIRAS / Resolution: 1.76→38.93 Å / Cor.coef. F_o:F_c: 0.952 / Cor.coef. F_o:F_c free: 0.917 / WR_factor R_free: 0.2437 / WR_factor R_work: 0.1752 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8732 / SU B: 2.673 / SU ML: 0.087 / SU R Cruickshank DPI: 0.1325 / SU R_free: 0.1407 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.141 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2418	831	5.1 %	RANDOM
R_work	0.1736	-	-	-
obs	0.1768	15571	99.15 %	-

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 max: 43.6 Å² / B_iso mean: 17.1526 Å² / B_iso min: 7.07 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.95 Å²	0 Å²	0.3 Å²
2-	-	-0.23 Å²	0 Å²
3-	-	-	1.47 Å²

Refinement step

Cycle: LAST / Resolution: 1.76→38.93 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1463	0	13	155	1631

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.023	0.022	1523
X-RAY DIFFRACTION	r_angle_refined_deg	1.925	1.969	2074
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.778	5	182
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	27.126	23.286	70
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.795	15	229
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	24.561	15	11
X-RAY DIFFRACTION	r_chiral_restr	0.14	0.2	213
X-RAY DIFFRACTION	r_gen_planes_refined	0.011	0.022	1194
X-RAY DIFFRACTION	r_mcbond_it	1.271	1.5	921
X-RAY DIFFRACTION	r_mcangle_it	1.997	2	1499
X-RAY DIFFRACTION	r_scbond_it	3.225	3	602
X-RAY DIFFRACTION	r_scangle_it	4.805	4.5	575

LS refinement shell

Resolution: 1.76→1.808 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.313	63	-
R_work	0.245	1151	-
all	-	1214	-
obs	-	-	99.35 %

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