PDB-3rkl: The crystal structure of A81 from Sulfolobus Turreted Icosahedral...

ID or keywords:

Entry

Database: PDB / ID: 3rkl

Title

The crystal structure of A81 from Sulfolobus Turreted Icosahedral Virus

Components

STIV-A81

Keywords

VIRAL PROTEIN / 4-helix bundle / Hyperthermophilic viral protein

Function / homology

Helix Hairpins - #1640 / Helix Hairpins / Helix non-globular / Special / ACETATE ION / Uncharacterized protein

Function and homology information

Biological species

Sulfolobus Turreted Icosahedral Virus

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 1.7 Å

Authors

Lintner, N.G. / Larson, E.T. / Young, M.J. / Lawrence, C.M.

Citation

Journal: To be Published
Title: The crystal structure of A81 from Sulfolobus Turreted Icosahedral Virus
Authors: Lintner, N.G. / Larson, E.T. / Young, M.J. / Lawrence, C.M.

History

Deposition	Apr 18, 2011	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 9, 2012	Provider: repository / Type: Initial release
Revision 1.1	Nov 8, 2017	Group: Refinement description / Category: software / Item: _software.name
Revision 1.2	Oct 16, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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_ref_seq_dif 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_ref_seq_dif.details

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3rkl.cif.gz	146.1 KB	Display	PDBx/mmCIF format
PDB format	pdb3rkl.ent.gz	119.4 KB	Display	PDB format
PDBx/mmJSON format	3rkl.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3rkl_validation.pdf.gz	442.3 KB	Display	wwPDB validaton report
Full document	3rkl_full_validation.pdf.gz	443.3 KB	Display
Data in XML	3rkl_validation.xml.gz	16.7 KB	Display
Data in CIF	3rkl_validation.cif.gz	22.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/rk/3rkl ftp://data.pdbj.org/pub/pdb/validation_reports/rk/3rkl	HTTPS FTP

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Related structure data

Similar structure data	3i7i-2 3i7g-2 5a88-d 1dbq-d 1vk9-2 1you-3 1ww6-d 1ww7-d 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

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: STIV-A81

B: STIV-A81

C: STIV-A81

D: STIV-A81

hetero molecules

41.6 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: STIV-A81

B: STIV-A81

C: STIV-A81

D: STIV-A81

hetero molecules

A: STIV-A81

B: STIV-A81

C: STIV-A81

D: STIV-A81

hetero molecules

defined by author&software
83.1 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	80.930, 88.962, 55.346
Angle α, β, γ (deg.)	90.00, 123.48, 90.00
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	A-88- ACT
2	1	A-88- ACT
3	1	D-88- ACT
4	1	D-88- ACT
5	1	A-91- HOH

#1: Protein	STIV-A81 Mass: 10363.312 Da / Num. of mol.: 4 / Mutation: L74M Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sulfolobus Turreted Icosahedral Virus / Gene: A81 / Plasmid: pDest14 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL / References: UniProt: Q6Q0J6
#2: Chemical	ChemComp-ACT / ACETATE ION Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₃O₂
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 157 / 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 Å³/Da / Density % sol: 38.63 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.8 Details: 18% MPD, 4% tertiary butanol, 0.1 M Na Citrate pH 5.8, 0.2 M ammonium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

SSRL

/ Beamline: BL9-2 / Wavelength: 0.97927, 0.97913, 0.91162

Detector

Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Dec 3, 2006 / Details: Rh coated flat mirror, toroidal focusing mirror

Radiation

Monochromator: Double crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.97927	1
2	0.97913	1
3	0.91162	1

Reflection

Resolution: 1.7→50 Å / Num. all: 36459 / Num. obs: 35400 / % possible obs: 97.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.6 % / R_sym value: 0.04 / Net I/σ(I): 31.4

Reflection shell

Resolution: 1.7→1.74 Å / % possible all: 86.2

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Processing

Software

Name	Version	Classification
Blu-Ice	Ice	data collection
SOLVE		phasing
REFMAC	5.5.0109	refinement
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

MAD / Resolution: 1.7→50 Å / Cor.coef. F_o:F_c: 0.969 / Cor.coef. F_o:F_c free: 0.959 / SU B: 3.481 / SU ML: 0.054 / Cross valid method: THROUGHOUT / ESU R Free: 0.099 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.19599	1770	5 %	RANDOM
R_work	0.16333	-	-	-
obs	0.16493	33623	98.48 %	-
all	-	34142	-	-

Solvent computation

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

Displacement parameters

B_iso mean: 31.944 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.18 Å²	0 Å²	0.92 Å²
2-	-	-0.71 Å²	0 Å²
3-	-	-	1.54 Å²

Refinement step

Cycle: LAST / Resolution: 1.7→50 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2620	0	8	157	2785

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.022	2694
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	1739
X-RAY DIFFRACTION	r_angle_refined_deg	1.014	1.975	3641
X-RAY DIFFRACTION	r_angle_other_deg	0.81	3	4329
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	4.415	5	326
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.994	27.143	140
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.247	15	525
X-RAY DIFFRACTION	r_dihedral_angle_4_deg
X-RAY DIFFRACTION	r_chiral_restr	0.067	0.2	421
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	2951
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	473
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	2.056	6	1609
X-RAY DIFFRACTION	r_mcbond_other	0.738	6	649
X-RAY DIFFRACTION	r_mcangle_it	3.423	8	2602
X-RAY DIFFRACTION	r_scbond_it	7.074	24	1085
X-RAY DIFFRACTION	r_scangle_it	10.626	36	1034
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.7→1.744 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.246	123	-
R_work	0.214	2394	-
obs	-	-	95.05 %

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	15.1839	8.2868	-3.9121	7.7969	-4.7215	5.7144	0.3512	-0.391	1.5787	0.273	0.0153	0.6741	-0.559	-0.1517	-0.3665	0.1328	0.023	0.1281	0.0318	-0.0313	0.3478	-11.0608	76.3219	69.1908
2	5.1323	-0.583	-1.3237	7.7225	-1.9043	0.8938	0.0165	0.4956	0.8546	-0.6573	0.4296	0.7933	0.1778	-0.2624	-0.4461	0.1363	-0.0054	-0.0252	0.1742	0.1334	0.2854	-16.1291	71.6495	64.3282
3	1.8786	-0.4804	-2.2167	1.9861	1.372	5.3427	-0.0676	0.094	-0.0766	0.0925	0.0284	0.0393	0.1044	-0.1228	0.0392	0.1039	-0.0068	-0.0115	0.0981	0.0073	0.0824	-7.8738	56.1714	64.8403
4	2.425	-1.4822	-3.0144	2.9652	2.6655	4.877	0.1832	0.2949	0.1903	-0.3851	-0.065	-0.0456	-0.4315	-0.3367	-0.1183	0.1502	0.0056	0.0104	0.118	0.0528	0.0826	-5.6071	63.1384	57.9221
5	3.0455	0.7283	-1.4454	8.0795	1.3984	12.2278	0.0543	-0.2148	0.1803	0.5329	0.1414	0.4563	-0.6922	-0.3331	-0.1956	0.21	0.0788	0.0855	0.1366	-0.012	0.1156	-13.2293	68.7225	82.5108
6	11.1348	1.5932	-6.3872	2.1399	0.1064	6.4831	-0.0829	0.6462	-0.1376	-0.201	0.0577	-0.0331	0.147	-0.3999	0.0252	0.057	0.0198	-0.0041	0.1621	0.0123	0.0424	-19.2253	40.9707	36.4794
7	3.7898	-0.488	-1.0058	0.2172	0.9604	4.7973	-0.1219	0.117	-0.1399	0.0924	-0.0534	0.0498	0.4767	-0.3179	0.1753	0.1191	-0.0257	0.0053	0.1372	-0.0055	0.0947	-21.2265	35.3703	41.6871
8	5.3504	-3.1714	2.0311	3.1035	-1.3445	2.5141	-0.0681	-0.1785	0.086	0.0703	0.01	-0.0376	0.0419	-0.0013	0.0581	0.1024	-0.0076	-0.0183	0.1073	0.0058	0.1039	-10.4251	38.7085	55.2579
9	23.8399	1.406	22.9967	3.5301	1.7571	22.2424	0.8405	1.4415	-0.6141	-0.3016	-0.2338	-0.0163	0.8538	1.3998	-0.6067	0.4227	0.2521	0.0122	0.3615	-0.0745	0.228	0.7191	25.2704	51.5196
10	1.973	-1.4439	0.3727	2.6651	-0.4802	2.3468	0.0046	0.0785	0.0602	-0.1615	0.0258	0.0221	-0.0708	-0.0907	-0.0304	0.0828	-0.0034	-0.0173	0.1382	0.0229	0.0994	-15.6837	42.9151	45.1137
11	8.5172	-1.4338	4.1818	3.0083	-1.7008	4.9208	0.0418	0.9804	0.1659	-0.2852	-0.0577	-0.1265	0.1244	0.4051	0.0159	0.0934	0.0209	0.0574	0.1905	0	0.0759	-6.2097	44.3701	33.6714
12	2.0884	0.0342	3.0982	1.3493	-1.2574	6.0937	-0.1933	0.228	0.201	0.0406	-0.2	-0.2832	-0.2757	0.4553	0.3933	0.1093	-0.0292	-0.0158	0.1572	0.0922	0.2267	-2.9234	50.5257	37.1008
13	3.7607	-2.7044	-1.8078	3.4681	2.4654	3.5815	-0.0702	-0.0799	-0.0036	0.0776	-0.0016	-0.0651	0.002	0.1162	0.0718	0.0955	-0.0081	0.003	0.1026	0.0073	0.1045	-6.0695	46.6565	54.0817
14	10.5431	-5.2235	-25.5719	3.8056	10.9948	64.3315	1.7269	0.9589	0.5379	-1.0159	-0.4338	-0.2828	-3.9927	-2.4204	-1.2932	0.4214	0.2449	0.0283	0.3225	0.0153	0.1147	-17.9744	60.2949	55.4676
15	2.0891	-1.6836	-0.2001	4.5374	1.5695	2.9879	-0.0275	0.0481	-0.0519	-0.2179	0.0876	-0.0709	0.0757	0.1395	-0.0602	0.0992	-0.0096	0.0246	0.1417	-0.006	0.094	-5.8258	42.51	42.9752
16	26.4941	10.3732	-0.5624	6.9812	0.2912	4.8074	-0.158	-0.2834	-1.713	-0.2227	-0.0503	-0.6992	0.4555	0.3684	0.2082	0.0795	0.0416	0.0043	0.0332	0.0243	0.4168	-0.1115	9.0055	66.8364
17	4.3271	0.3785	-0.51	5.6731	1.4733	0.4922	-0.3216	0.2095	-0.7485	-0.9907	0.2562	-0.3406	-0.2166	0.1003	0.0654	0.2471	-0.0315	0.0667	0.2717	-0.0323	0.3465	3.0224	14.2385	60.6367
18	5.522	-1.6167	3.67	1.7352	-1.5157	3.8265	-0.1204	0.1603	0.2032	0.0437	0.024	-0.0741	-0.1361	0.1085	0.0964	0.1181	-0.0078	-0.0185	0.1076	-0.0009	0.0895	-5.3005	29.4067	64.1854
19	10.2476	-5.8929	5.8074	4.7397	-3.6585	3.4795	0.3962	0.6968	-0.4005	-0.4716	-0.1829	0.2167	0.3373	0.333	-0.2133	0.1795	-0.0091	-0.0506	0.1467	-0.056	0.1048	-11.3469	22.7672	56.7615
20	5.9552	-2.0196	5.7119	3.5471	-2.4061	8.2328	0.132	-0.053	-0.3753	0.1194	0.02	-0.3437	0.2424	0.2549	-0.1521	0.1158	0.0174	-0.0644	0.1131	0.0091	0.1751	5.2944	17.2774	75.9547

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	2 - 11
2	X-RAY DIFFRACTION	2	A	12 - 22
3	X-RAY DIFFRACTION	3	A	23 - 48
4	X-RAY DIFFRACTION	4	A	49 - 72
5	X-RAY DIFFRACTION	5	A	73 - 81
6	X-RAY DIFFRACTION	6	B	2 - 13
7	X-RAY DIFFRACTION	7	B	14 - 23
8	X-RAY DIFFRACTION	8	B	24 - 48
9	X-RAY DIFFRACTION	9	B	49 - 56
10	X-RAY DIFFRACTION	10	B	57 - 81
11	X-RAY DIFFRACTION	11	C	2 - 13
12	X-RAY DIFFRACTION	12	C	14 - 22
13	X-RAY DIFFRACTION	13	C	23 - 48
14	X-RAY DIFFRACTION	14	C	49 - 56
15	X-RAY DIFFRACTION	15	C	57 - 81
16	X-RAY DIFFRACTION	16	D	2 - 11
17	X-RAY DIFFRACTION	17	D	12 - 23
18	X-RAY DIFFRACTION	18	D	24 - 48
19	X-RAY DIFFRACTION	19	D	49 - 67
20	X-RAY DIFFRACTION	20	D	68 - 81

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