PDB-2x48: ORF 55 from Sulfolobus islandicus rudivirus 1

ID or keywords:

Entry

Database: PDB / ID: 2x48

Title

ORF 55 from Sulfolobus islandicus rudivirus 1

Components

CAG38821

Keywords

VIRAL PROTEIN / ARCHEAL VIRUS

Function / homology

Homeodomain-like domain /

Homeodomain-like / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha /

PHOSPHATE ION / Uncharacterized protein 56

Function and homology information

Biological species

SULFOLOBUS ISLANDICUS ROD-SHAPED VIRUS 1

Method

X-RAY DIFFRACTION /

SYNCHROTRON / OTHER / Resolution: 2.6 Å

Authors

Oke, M. / Carter, L. / Johnson, K.A. / Liu, H. / Mcmahon, S. / Naismith, J.H. / White, M.F.

Citation

Journal: J.Struct.Funct.Genomics / Year: 2010
Title: The Scottish Structural Proteomics Facility: Targets, Methods and Outputs.
Authors: Oke, M. / Carter, L.G. / Johnson, K.A. / Liu, H. / Mcmahon, S.A. / Yan, X. / Kerou, M. / Weikart, N.D. / Kadi, N. / Sheikh, M.A. / Schmelz, S. / Dorward, M. / Zawadzki, M. / Cozens, C. / ...

History

Deposition	Jan 28, 2010	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jul 21, 2010	Provider: repository / Type: Initial release
Revision 1.1	May 7, 2011	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Version format compliance
Revision 1.3	Jan 24, 2018	Group: Source and taxonomy / Category: entity_src_gen Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name ..._entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	2x48.cif.gz	77 KB	Display	PDBx/mmCIF format
PDB format	pdb2x48.ent.gz	65.3 KB	Display	PDB format
PDBx/mmJSON format	2x48.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/x4/2x48 ftp://data.pdbj.org/pub/pdb/validation_reports/x4/2x48	HTTPS FTP

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Related structure data

Related structure data	2ivyC 2jg5C 2jg6C 2vw8C 2vxzC 2wj9C 2x0oC 2x3dC 2x3eC 2x3fC 2x3gC 2x3lC 2x3mC 2x3nC 2x3oC 2x4gC 2x4hC 2x4iC 2x4jC 2x4kC 2x4lC 2x5cC 2x5dC 2x5fC 2x5gC 2x5hC 2x5pC 2x5qC 2x5rC 2x5tC 2x7bC 2x7iC 2xu2C C: citing same article (ref.)
Similar structure data	5k28-2 4kju-2 4w4m-13 4w4m-7 4w4m-1 3q1j-d 1fgp-d 6a8r-1 4uz0-2 4w4m-5 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 - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: CAG38821

B: CAG38821

C: CAG38821

hetero molecules

19.1 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: CAG38821

hetero molecules

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

2

B: CAG38821

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

3

C: CAG38821

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

Unit cell

Length a, b, c (Å)	119.110, 119.110, 119.110
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	197
Space group name H-M	I23

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	B
2	1	A
3	1	C
1	2	B
2	2	A
3	2	C
1	3	B
2	3	A
3	3	C
1	4	B
2	4	C
3	4	A

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Refine code	Auth asym-ID	Auth seq-ID
1	1	1	6	B	5 - 10
2	1	1	6	A	5 - 10
3	1	1	6	C	5 - 10
1	1	2	6	B	11 - 19
2	1	2	6	A	11 - 19
3	1	2	6	C	11 - 19
1	1	3	6	B	20 - 35
2	1	3	6	A	20 - 35
3	1	3	6	C	20 - 35
1	1	4	6	B	36 - 50
2	1	4	6	C	36 - 50
3	1	4	6	A	36 - 50

NCS ensembles :

ID
1
2
3
4

#1: Protein	CAG38821 / UNCHARACTERIZED PROTEIN 56 / ORF55 Mass: 6328.236 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SULFOLOBUS ISLANDICUS ROD-SHAPED VIRUS 1 Variant: XX / Plasmid: PDEST14 / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): C43 / References: UniProt: Q8QHM9
#2: Chemical	ChemComp-PO4 / PHOSPHATE ION / Phosphate Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO₄
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 22 / 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: 3.75 Å³/Da / Density % sol: 67 % / Description: NONE
Crystal grow	pH: 8 / Details: PH 8

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.933
Detector	Type: ADSC CCD / Detector: CCD / Date: Sep 1, 2007 / Details: MIRRORS
Radiation	Monochromator: DIAMOND (111), GE(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.933 Å / Relative weight: 1
Reflection	Resolution: 2.6→84.22 Å / Num. obs: 8384 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 15.6 % / B_iso Wilson estimate: 0 Å² / R_merge(I) obs: 0.05 / Net I/σ(I): 36
Reflection shell	Resolution: 2.6→2.67 Å / Redundancy: 13.8 % / R_merge(I) obs: 0.49 / Mean I/σ(I) obs: 7 / % possible all: 100

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Processing

Software

Name	Version	Classification
REFMAC	5.2.0019	refinement
XDS		data reduction
SCALA		data scaling

Refinement

Method to determine structure: OTHER
Starting model: NONE

Resolution: 2.6→84.22 Å / Cor.coef. F_o:F_c: 0.934 / Cor.coef. F_o:F_c free: 0.925 / SU B: 25.848 / SU ML: 0.247 / Cross valid method: THROUGHOUT / ESU R: 0.396 / ESU R Free: 0.282 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.26657	419	4.8 %	RANDOM
R_work	0.22316	-	-	-
obs	0.22528	8384	99.8 %	-

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: 3.091 Å²

	B_aniso -1	B_aniso -2
1-	0 Å²	0 Å²
2-	-	0 Å²
3-	-	-

Refinement step

Cycle: LAST / Resolution: 2.6→84.22 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1305	0	5	22	1332

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.022	1339
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	924
X-RAY DIFFRACTION	r_angle_refined_deg	0.997	1.971	1797
X-RAY DIFFRACTION	r_angle_other_deg	0.792	3	2253
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	4.428	5	165
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	39.288	24.091	66
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	17.083	15	270
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	13.605	15	12
X-RAY DIFFRACTION	r_chiral_restr	0.057	0.2	201
X-RAY DIFFRACTION	r_gen_planes_refined	0.003	0.02	1464
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	264
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	0.224	1.5	807
X-RAY DIFFRACTION	r_mcbond_other	0.043	1.5	333
X-RAY DIFFRACTION	r_mcangle_it	0.449	2	1299
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	0.837	3	532
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	1.543	4.5	495
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

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	2	A	70	loose positional	0.41	5
1	1	B	70	loose positional	0.22	5
1	3	C	70	loose positional	0.44	5
2	2	A	138	loose positional	0.43	5
2	1	B	138	loose positional	0.34	5
2	3	C	138	loose positional	0.48	5
3	2	A	206	loose positional	0.28	5
3	1	B	206	loose positional	0.31	5
3	3	C	206	loose positional	0.39	5
4	3	A	210	loose positional	0.87	5
4	1	B	210	loose positional	0.88	5
4	2	C	210	loose positional	1.04	5
1	2	A	70	loose thermal	1.41	10
1	1	B	70	loose thermal	0.75	10
1	3	C	70	loose thermal	0.73	10
2	2	A	138	loose thermal	0.63	10
2	1	B	138	loose thermal	0.37	10
2	3	C	138	loose thermal	0.9	10
3	2	A	206	loose thermal	1.11	10
3	1	B	206	loose thermal	0.82	10
3	3	C	206	loose thermal	1.44	10
4	3	A	210	loose thermal	1.37	10
4	1	B	210	loose thermal	0.77	10
4	2	C	210	loose thermal	0.9	10

LS refinement shell

Resolution: 2.599→2.667 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.366	38	-
R_work	0.294	597	-
obs	-	-	100 %

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	48.3089	-21.1803	28.6413	32.2342	-27.2972	42.8888	-0.1621	0.4497	1.4666	0.2081	-0.202	-0.4303	-0.8597	0.1389	0.3641	0.6637	-0.0387	0.0431	0.1826	-0.0374	0.5826	-7.805	-8.153	47.102
2	37.0398	1.0212	18.9866	3.1288	-8.656	29.1832	-0.7877	0.809	1.9874	-0.392	0.0885	0.1615	-0.7831	0.0412	0.6993	0.7542	0.0216	-0.0089	0.4151	-0.0135	0.668	-8.444	-10.641	41.54
3	5.33	-2.3214	0.1639	10.4947	-5.456	14.7296	0.0131	0.3112	-0.2616	-0.3163	0.0427	-0.0404	0.0427	0.3222	-0.0558	0.3729	-0.0713	-0.0166	0.3451	-0.053	0.4854	-10.385	-20.272	49.192
4	13.5687	5.5038	1.2147	16.0594	-8.66	10.5916	-0.2655	1.0842	0.1869	-0.5383	0.7563	2.0195	0.0296	-1.4027	-0.4908	0.3947	0.0271	-0.0765	0.7929	-0.0808	0.9172	-19.443	-19.104	47.777
5	14.9396	1.7917	-4.9275	19.0748	-0.0505	13.0793	-0.0116	0.0737	0.7222	-0.0844	0.4094	0.5142	-0.4439	-1.7497	-0.3977	0.7113	0.0893	-0.0169	0.5444	0.1175	0.7	2.783	-10.431	46.948
6	6.877	0.4532	8.9251	26.8717	3.9925	41.2083	-0.3678	0.6844	0.7608	-0.4265	0.117	0.9687	-0.2631	-1.1748	0.2508	0.4746	-0.1062	-0.0327	0.6271	0.0734	0.687	4.966	-12.59	41.651
7	2.2384	-2.2387	5.9381	10.9505	-9.1469	25.671	0.1735	0.2936	0.086	-0.2656	0.0195	-0.1588	-0.0124	0.575	-0.193	0.4166	0.0116	0.0263	0.315	0.0227	0.5381	12.085	-19.064	49.483
8	14.6345	-3.1655	1.7744	11.5103	-0.2133	20.5204	0.3549	0.4967	-1.721	-0.6651	0.167	0.8437	1.6074	-1.591	-0.5219	0.5831	-0.187	-0.1328	0.4489	0.1339	0.78	5.934	-25.871	48.205
9	21.8438	10.1575	13.3966	36.4106	14.2865	15.045	-0.0347	-0.8923	-0.5253	-0.8956	-0.3697	1.0304	-0.4399	-0.6977	0.4043	0.3838	-0.0354	0.0983	0.5202	0.1195	0.7427	10.689	-2.393	47.278
10	18.7939	-5.293	-7.5396	23.1652	14.7527	30.0689	-0.7117	0.78	-0.7811	-0.734	-0.073	1.3068	0.6816	-0.1193	0.7847	0.5074	-0.028	0.0605	0.3395	0.0533	0.7071	13.215	-2.025	41.662
11	6.9967	-0.8682	7.3335	9.8466	5.3548	16.2767	-0.2772	-0.5062	-0.0484	-0.3891	-0.0592	-0.4589	-0.8357	0.11	0.3364	0.2296	-0.0332	0.1122	0.6563	0.0624	0.7529	22.464	0.863	49.231
12	24.8071	-1.8298	0.921	3.7942	2.892	8.3223	0.0775	0.5178	-0.4955	-0.2191	0.2919	-0.6924	1.0046	0.3591	-0.3694	0.5932	0.0331	0.0661	0.6564	0.0816	0.926	25.268	-7.685	47.581

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 10
2	X-RAY DIFFRACTION	2	A	11 - 19
3	X-RAY DIFFRACTION	3	A	20 - 35
4	X-RAY DIFFRACTION	4	A	36 - 54
5	X-RAY DIFFRACTION	5	B	1 - 10
6	X-RAY DIFFRACTION	6	B	11 - 19
7	X-RAY DIFFRACTION	7	B	20 - 35
8	X-RAY DIFFRACTION	8	B	36 - 54
9	X-RAY DIFFRACTION	9	C	1 - 10
10	X-RAY DIFFRACTION	10	C	11 - 19
11	X-RAY DIFFRACTION	11	C	20 - 35
12	X-RAY DIFFRACTION	12	C	36 - 54

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