PDB-4il7: Crystal structure of A223 C-terminal domain, a structural protein...

ID or keywords:

Entry

Database: PDB / ID: 4il7

Title

Crystal structure of A223 C-terminal domain, a structural protein from sulfolobus turreted icosahedral virus (STIV)

Components

Putative uncharacterized protein

Keywords

VIRAL PROTEIN / partial jelly roll fold /

hypothetical protein / C381 and B345 /

Viral Capsid

Function / homology

Jelly Rolls - #1300 / Jelly Rolls /

Sandwich / Mainly Beta / Uncharacterized protein

Function and homology information

Biological species

Sulfolobus turreted icosahedral virus

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.4 Å

Authors

Sendamarai, A.K. / Lawrence, C.M.

Citation

Journal: Proc Natl Acad Sci U S A / Year: 2013
Title: Atomic structure of the 75 MDa extremophile Sulfolobus turreted icosahedral virus determined by CryoEM and X-ray crystallography.
Authors: David Veesler / Thiam-Seng Ng / Anoop K Sendamarai / Brian J Eilers / C Martin Lawrence / Shee-Mei Lok / Mark J Young / John E Johnson / Chi-yu Fu /

Abstract: Sulfolobus turreted icosahedral virus (STIV) was isolated in acidic hot springs where it infects the archeon Sulfolobus solfataricus. We determined the STIV structure using near-atomic resolution ...

History

Deposition	Dec 29, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 3, 2013	Provider: repository / Type: Initial release
Revision 1.1	May 1, 2013	Group: Database references
Revision 1.2	Feb 28, 2024	Group: Data collection / Database references Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	4il7.cif.gz	55.9 KB	Display	PDBx/mmCIF format
PDB format	pdb4il7.ent.gz	42.2 KB	Display	PDB format
PDBx/mmJSON format	4il7.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/il/4il7 ftp://data.pdbj.org/pub/pdb/validation_reports/il/4il7	HTTPS FTP

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Related structure data

Related structure data	5584C 3j31C C: citing same article (ref.)
Similar structure data	3jtn-1 3dm1-3 6gf1-2 3kat-d 2plt-d 6l1p-2 1u37-d 1y3k-d 4rjd-2 4rjd-1 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Putative uncharacterized protein

17.9 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)	65.853, 65.853, 43.673
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	154
Space group name H-M	P3₂21

#1: Protein	Putative uncharacterized protein / Hypothetical protein A223 Mass: 17935.160 Da / Num. of mol.: 1 / Mutation: L208M Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sulfolobus turreted icosahedral virus / Gene: A223 / Plasmid: pDEST14 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q6Q0L4
#2: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 102 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

Putative uncharacterized protein / Hypothetical protein A223

Mass: 17935.160 Da / Num. of mol.: 1 / Mutation: L208M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Sulfolobus turreted icosahedral virus / Gene: A223 / Plasmid: pDEST14 / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q6Q0L4

#2: Water

ChemComp-HOH / water /

Water

Mass: 18.015 Da / Num. of mol.: 102 / 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: 1.52 Å³/Da / Density % sol: 19.3 %
Crystal grow	Temperature: 298 K / pH: 5.6 Details: 10-15%v/v 2-Propanol, 5-10%w/v Polyethylene glycol 4,000, 0.1M Sodium citrate tribasic dihydrate 5.6 , VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.95369
Detector	Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 28, 2010
Radiation	Monochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.95369 Å / Relative weight: 1
Reflection	Resolution: 1.37→50 Å / Num. obs: 21677 / % possible obs: 93 % / Observed criterion σ(I): -3 / Redundancy: 5.9 % / R_sym value: 0.028 / Net I/σ(I): 23
Reflection shell	Resolution: 1.37→1.42 Å / Redundancy: 5.2 % / R_sym value: 0.255 / % possible all: 89.2

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Processing

Software

Name	Version	Classification
HKL-2000		data collection
SOLVE		phasing
REFMAC	5.7.0029	refinement
HKL-2000		data reduction
SCALEPACK		data scaling

Refinement

Method to determine structure:

SAD / Resolution: 1.4→19.34 Å / Cor.coef. F_o:F_c: 0.978 / Cor.coef. F_o:F_c free: 0.971 / SU B: 1.711 / SU ML: 0.031 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / ESU R: 0.054 / ESU R Free: 0.05 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.16506	1021	5 %	RANDOM
R_work	0.14017	-	-	-
obs	0.14136	19450	93.56 %	-
all	-	21677	-	-

Solvent computation

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

Displacement parameters

B_iso mean: 22.117 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.47 Å²	-0.47 Å²	0 Å²
2-	-	-0.47 Å²	0 Å²
3-	-	-	1.52 Å²

Refinement step

Cycle: LAST / Resolution: 1.4→19.34 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	631	0	0	102	733

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.02	0.02	759
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	700
X-RAY DIFFRACTION	r_angle_refined_deg	1.939	1.952	1058
X-RAY DIFFRACTION	r_angle_other_deg	1.758	3	1628
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.876	5	110
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	42.49	27.143	28
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	11.597	15	126
X-RAY DIFFRACTION	r_dihedral_angle_4_deg
X-RAY DIFFRACTION	r_chiral_restr	0.121	0.2	131
X-RAY DIFFRACTION	r_gen_planes_refined	0.01	0.02	934
X-RAY DIFFRACTION	r_gen_planes_other	0.009	0.02	170
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
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_rigid_bond_restr	3.785	3	1459
X-RAY DIFFRACTION	r_sphericity_free	36.541	5	30
X-RAY DIFFRACTION	r_sphericity_bonded	9.655	5	1507

LS refinement shell

Resolution: 1.4→1.436 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.239	91	-
R_work	0.178	1523	-
obs	-	-	99.32 %

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	4.798	-0.7077	-0.8028	11.0876	-4.9117	5.4353	-0.1257	0.0599	-0.5305	-0.1494	-0.0156	0.2331	0.2843	-0.1822	0.1413	0.0552	0.007	0.0332	0.0758	-0.0333	0.0858	6.6274	19.5991	-0.5892
2	1.7096	1.4212	-0.0739	7.7042	0.6937	1.1549	0.0713	0.0877	0.0796	-0.0619	-0.11	-0.1873	0.067	-0.0298	0.0387	0.0698	0.0159	0.0039	0.0856	0.0155	0.0266	8.778	32.5873	-1.9725
3	3.2016	4.122	-0.4376	8.4159	-2.1135	2.2023	-0.5402	0.4867	-0.5112	-0.5284	0.1746	-0.3792	-0.0742	-0.2774	0.3656	0.1805	-0.0225	0.0769	0.321	-0.2362	0.2775	-0.4593	23.4309	-3.3029
4	9.0732	6.0315	-0.0388	7.8952	-1.1287	1.6397	-0.0633	-0.4977	-0.5214	0.2256	-0.0279	0.1495	0.1014	-0.0187	0.0912	0.0794	0.0225	0.0683	0.103	0.0524	0.1477	2.6394	20.3458	8.0066
5	8.6654	5.1386	3.8349	3.0777	2.2885	1.7049	0.1322	-0.1409	0.1616	0.1383	-0.1169	0.0012	0.0842	-0.066	-0.0152	0.14	0.0202	-0.0786	0.194	-0.0283	0.308	14.4618	34.5883	9.1997
6	5.6072	-1.1126	1.9938	1.7074	0.226	3.8109	-0.0901	-0.1811	0.2733	0.1458	0.0139	-0.0041	-0.0457	-0.0007	0.0761	0.0757	-0.009	0.0161	0.1171	-0.0163	0.0411	3.6801	35.4311	9.4533
7	12.778	2.7392	0.0411	0.8016	-0.514	1.2984	-0.1794	0.1942	-0.209	-0.0886	0.1157	-0.0531	0.1011	-0.1243	0.0636	0.0942	-0.0245	-0.0017	0.1427	-0.0156	0.1316	-9.48	26.1243	3.4467
8	11.1177	3.3653	6.8605	2.1807	2.3273	4.2908	0.1373	-0.0674	-0.156	0.0176	-0.074	0.0655	0.0795	-0.0712	-0.0633	0.0719	-0.0167	0.0203	0.1107	-0.0048	0.068	-7.6347	29.2142	8.0838
9	10.5096	-2.5247	0.3022	0.9578	0.8276	3.658	-0.1717	-0.368	-0.1881	0.2509	0.1558	0.0387	0.2595	0.3017	0.0159	0.1831	0.0182	-0.0124	0.1291	-0.0066	0.0514	6.8656	30.8711	12.0472
10	7.4194	2.0672	3.1343	4.0963	1.7235	3.864	-0.0072	-0.5252	-0.5288	0.172	-0.1194	0.1864	0.1388	-0.2395	0.1267	0.053	0.0037	0.0636	0.1126	0.0196	0.1477	-2.1206	20.9985	7.9454
11	10.7937	4.2745	0.2155	9.965	-1.5253	2.6537	-0.1836	0.335	0.0286	-0.2364	0.1006	0.3311	-0.0041	-0.1538	0.083	0.035	0.0126	0.0019	0.0807	-0.0158	0.0278	-2.5338	29.4491	0.1722
12	3.9238	-1.4002	0.3199	3.5864	0.3609	2.9877	0.0504	-0.2415	0.3431	0.0805	-0.0283	-0.1556	-0.1658	0.033	-0.022	0.0434	-0.0021	-0.0047	0.0662	-0.0013	0.0481	8.698	37.3935	3.8037
13	4.707	2.0259	-0.7126	5.93	-0.3353	1.5006	-0.1831	-0.2323	-0.3783	0.2094	-0.0112	0.0631	0.0598	0.0068	0.1943	0.0394	0.0231	0.0388	0.0648	-0.0007	0.075	6.9117	21.6109	4.1949

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	139 - 143
2	X-RAY DIFFRACTION	2	A	144 - 150
3	X-RAY DIFFRACTION	3	A	151 - 158
4	X-RAY DIFFRACTION	4	A	159 - 165
5	X-RAY DIFFRACTION	5	A	166 - 171
6	X-RAY DIFFRACTION	6	A	172 - 177
7	X-RAY DIFFRACTION	7	A	178 - 183
8	X-RAY DIFFRACTION	8	A	184 - 188
9	X-RAY DIFFRACTION	9	A	189 - 194
10	X-RAY DIFFRACTION	10	A	195 - 203
11	X-RAY DIFFRACTION	11	A	204 - 208
12	X-RAY DIFFRACTION	12	A	209 - 215
13	X-RAY DIFFRACTION	13	A	216 - 221

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