PDB-2co5: F93 FROM STIV, a winged-helix DNA-binding protein

ID or keywords:

Entry

Database: PDB / ID: 2co5

Title

F93 FROM STIV, a winged-helix DNA-binding protein

Components

VIRAL PROTEIN F93

Keywords

VIRAL PROTEIN/WINGED HELIX / VIRAL PROTEIN-WINGED HELIX COMPLEX / WINGED HELIX / DNA-BINDING / HTH / WHTH / F93 / DISULFIDE BOND / STIV / SULFOLOBUS TURRETED ICOSAHEDRAL VIRUS / VIRAL PROTEIN / VIRUS / ARCHAEA / CRENARCHAEA / ARCHAEAL VIRUS / CRENARCHAEAL VIRUS / THERMOPHILIC PROTEIN / THERMOPHILIC VIRUS / SULFOLOBUS / YELLOWSTONE

Function / homology

Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha / Uncharacterized protein

Function and homology information

Biological species

SULFOLOBUS TURRETED ICOSAHEDRAL VIRUS

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.2 Å

Authors

Larson, E.T. / Reiter, D. / Lawrence, C.M.

Citation

Journal: Virology / Year: 2007
Title: A Winged-Helix Protein from Sulfolobus Turreted Icosahedral Virus Points Toward Stabilizing Disulfide Bonds in the Intracellular Proteins of a Hyperthermophilic Virus.
Authors: Larson, E.T. / Eilers, B. / Menon, S. / Reiter, D. / Ortmann, A. / Young, M.J. / Lawrence, C.M.

History

Deposition	May 25, 2006	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	May 31, 2006	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	May 8, 2019	Group: Data collection / Experimental preparation / Other Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	2co5.cif.gz	50.5 KB	Display	PDBx/mmCIF format
PDB format	pdb2co5.ent.gz	42.3 KB	Display	PDB format
PDBx/mmJSON format	2co5.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	2co5_validation.pdf.gz	432.5 KB	Display	wwPDB validaton report
Full document	2co5_full_validation.pdf.gz	434.6 KB	Display
Data in XML	2co5_validation.xml.gz	9.4 KB	Display
Data in CIF	2co5_validation.cif.gz	12.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/co/2co5 ftp://data.pdbj.org/pub/pdb/validation_reports/co/2co5	HTTPS FTP

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Related structure data

Similar structure data	3cuo-1 4k2e-1 3coj-2 2v70-2 1t29-d 4ooi-1 5v89-1 2v9s-3 3coj-1 2l6g-d 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: VIRAL PROTEIN F93

B: VIRAL PROTEIN F93

24 kDa, 2 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)	42.050, 102.594, 92.398
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	20
Space group name H-M	C222₁

Components on special symmetry positions

ID	Model	Components
1	1	B-2009- HOH

#1: Protein	VIRAL PROTEIN F93 Mass: 12000.183 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SULFOLOBUS TURRETED ICOSAHEDRAL VIRUS / Strain: ISOLATE YNPRC179 Description: STIV WAS ISOLATED FROM SULFOLOBUS SPECIES IN ACIDIC HOT SPRINGS (PH 2.9-3.9, 72-92 DEGREES C)IN THE RABBIT CREEK THERMAL AREA WITHIN MIDWAY GEYSER BASIN IN YELLOWSTONE NATIONAL PARK, USA. Plasmid: PEXP14-STIVF93 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)-CODON PLUS (RIL) / References: UniProt: Q6Q0J9
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 69 / Source method: isolated from a natural source / Formula: H₂O
Sequence details	C-TERMINAL 6XHIS TAG WAS ADDED DURING CLONING TO FACILITATE PURIFICATION

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.1 Å³/Da / Density % sol: 41 % / Description: NONE
Crystal grow	Method: vapor diffusion, hanging drop / pH: 4.75 Details: HANGING DROP VAPOR DIFFUSION, 9.0-10.5 MG/ML F93 IN 10 MM TRIS-HCL, PH 8.0, 50 MM NACL, 0.5 MM TCEP MIXED WITH BUFFER CONTAINING 0.1 M SODIUM ACETATE, PH 4.75-5.0, 0.1 M MAGNESIUM NITRATE ...Details: HANGING DROP VAPOR DIFFUSION, 9.0-10.5 MG/ML F93 IN 10 MM TRIS-HCL, PH 8.0, 50 MM NACL, 0.5 MM TCEP MIXED WITH BUFFER CONTAINING 0.1 M SODIUM ACETATE, PH 4.75-5.0, 0.1 M MAGNESIUM NITRATE HEXAHYDRATE, 16-20% PEG 20,000.

Crystal

Density Matthews: 2.1 Å³/Da / Density % sol: 41 % / Description: NONE

Crystal grow

Method: vapor diffusion, hanging drop / pH: 4.75
Details: HANGING DROP VAPOR DIFFUSION, 9.0-10.5 MG/ML F93 IN 10 MM TRIS-HCL, PH 8.0, 50 MM NACL, 0.5 MM TCEP MIXED WITH BUFFER CONTAINING 0.1 M SODIUM ACETATE, PH 4.75-5.0, 0.1 M MAGNESIUM NITRATE ...

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.98789
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 17, 2006 Details: VERTICAL FOCUSING MIRROR, SINGLE CRYSTAL SI(311) BENT MONOCHROMATOR (HORIZONTAL FOCUSING)
Radiation	Monochromator: SIDE-SCATTERING CUBEROOT I- BEAM BENT SINGLE CRYSTAL, ASYMETRIC CUT 12.2 DEGS. Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.98789 Å / Relative weight: 1
Reflection	Resolution: 2.2→50 Å / Num. obs: 10466 / % possible obs: 99.8 % / Observed criterion σ(I): 3 / Redundancy: 7.1 % / R_merge(I) obs: 0.06 / Net I/σ(I): 33
Reflection shell	Resolution: 2.2→2.28 Å / Redundancy: 7.3 % / R_merge(I) obs: 0.34 / Mean I/σ(I) obs: 4.2 / % possible all: 100

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Processing

Software

Name	Version	Classification
HKL-2000		data reduction
HKL-2000		data scaling
SOLVE		phasing
RESOLVE		phasing
REFMAC	5.2.0019	refinement

Refinement

Method to determine structure:

SAD
Starting model: NONE

Resolution: 2.2→46.37 Å / Cor.coef. F_o:F_c: 0.957 / Cor.coef. F_o:F_c free: 0.941 / SU B: 13.322 / SU ML: 0.17 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.304 / ESU R Free: 0.213 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. TLS MOTION DETERMINATION SERVER (J PAINTER & E A MERRITT (2006) J. APPL. CRYST. 39, 109-111) WAS USED FOR SELECTION OF OPTIMAL TLS GROUPS USED IN REFINEMENT.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.232	508	4.9 %	RANDOM
R_work	0.19	-	-	-
obs	0.192	9938	99.7 %	-

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: 42.8 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.71 Å²	0 Å²	0 Å²
2-	-	-1.37 Å²	0 Å²
3-	-	-	-0.34 Å²

Refinement step

Cycle: LAST / Resolution: 2.2→46.37 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1570	0	0	69	1639

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.022	1629
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	1216
X-RAY DIFFRACTION	r_angle_refined_deg	0.991	1.999	2179
X-RAY DIFFRACTION	r_angle_other_deg	0.789	3.001	2957
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.135	5	192
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.991	23.077	78
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.796	15	356
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	15.73	15	15
X-RAY DIFFRACTION	r_chiral_restr	0.061	0.2	241
X-RAY DIFFRACTION	r_gen_planes_refined	0.003	0.02	1721
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	338
X-RAY DIFFRACTION	r_nbd_refined	0.202	0.2	338
X-RAY DIFFRACTION	r_nbd_other	0.172	0.2	1162
X-RAY DIFFRACTION	r_nbtor_refined	0.178	0.2	781
X-RAY DIFFRACTION	r_nbtor_other	0.082	0.2	842
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.113	0.2	74
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	0.104	0.2	11
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.168	0.2	38
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.155	0.2	12
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	1.994	6	1277
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	2.509	8	1527
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	9.21	36	813
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	11.446	54	648
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

LS refinement shell

Resolution: 2.2→2.26 Å / Total num. of bins used: 20 /

	R_factor	Num. reflection
R_free	0.285	41
R_work	0.225	699

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	14.1314	-5.1238	5.6652	12.5129	11.7842	26.2171	-0.0557	-0.8368	-0.925	0.7418	-0.0546	0.4257	0.1188	-0.9239	0.1103	-0.2078	-0.0632	0.0231	-0.1059	0.0422	-0.1051	7.2277	32.7695	63.0293
2	3.4378	2.5352	1.125	6.2177	4.1665	7.3208	0.2537	0.6993	-1.054	-0.2018	0.3587	-0.4954	0.4757	0.664	-0.6125	-0.144	-0.0014	-0.0178	0.0616	-0.2077	0.0675	16.264	24.4186	54.7554
3	15.1947	-4.5439	11.2707	24.9437	-10.3665	24.9963	0.317	1.198	-0.6809	-1.0047	-0.2259	-1.2138	0.8876	1.3095	-0.0911	-0.251	-0.0045	0.1133	0.1272	-0.1144	-0.0685	21.0726	31.852	54.2215
4	7.7068	2.5481	-0.021	6.6473	0.0082	5.4161	0.1409	-0.3828	-1.1696	0.5543	-0.0103	-0.2378	0.566	0.5097	-0.1306	-0.1737	0.0398	-0.0344	-0.0117	0.0093	0.0142	15.0257	25.906	64.9281
5	34.4101	8.6967	9.8981	10.7585	-1.9289	5.1402	1.0711	0.1719	-3.322	-0.0084	-0.0021	-2.0474	0.9618	0.7577	-1.069	0.1372	0.1052	-0.114	0.039	-0.1674	0.5646	18.0317	17.361	59.9388
6	87.7111	-30.7529	33.6062	60.6344	3.4841	17.5515	0.1156	-0.4213	-0.6555	0.3257	-0.1217	0.01	1.9412	-1.6999	0.0061	-0.0625	-0.06	-0.0529	-0.2007	-0.0286	0.125	2.6562	22.1842	55.3271
7	21.1497	-8.1168	4.0798	27.6285	-7.191	19.702	0.5315	1.0834	-0.3423	-1.2201	-0.4094	0.6193	0.063	0.0405	-0.1221	-0.1972	-0.0282	-0.0005	-0.1013	-0.1078	-0.1009	-1.7414	33.2388	49.6889
8	10.2321	-2.7439	4.295	4.5065	1.3876	4.8534	-0.2274	0.4847	0.2948	-0.0927	0.1546	-0.45	-0.4656	0.3906	0.0728	-0.1006	-0.0533	0.0109	-0.2008	0.0071	-0.2355	3.4863	43.5004	58.7386
9	3.7741	3.4158	0.2404	18.1392	-1.8161	3.9872	-0.2423	0.459	0.2217	-0.7893	0.0278	1.1858	-1.2183	-1.3333	0.2146	0.0035	0.2041	-0.0998	0.1047	0.0104	-0.1317	-13.6969	47.5879	55.679
10	6.7804	2.5643	0.4066	5.0827	5.1796	12.0734	0.0159	0.188	-0.4772	-0.2962	-0.0994	0.3291	-0.0862	-1.067	0.0836	-0.1824	0.0427	-0.0707	-0.097	0.0477	-0.1287	-10.0089	40.9324	61.3935
11	7.7424	2.7508	2.1949	9.1056	-0.9686	16.5269	-0.222	-0.3555	0.5149	-0.2901	0.3518	0.3891	-1.7956	-0.4329	-0.1298	0.297	0.0663	-0.0392	-0.2538	0.0223	-0.1416	-3.5354	54.8971	63.3442
12	22.7338	2.6957	-1.6843	8.1711	-0.6102	6.8963	0.0832	0.2282	1.8742	-0.2929	0.1332	0.8421	-1.2162	-1.0032	-0.2165	0.3816	0.1909	-0.0699	-0.1858	0.0621	-0.0452	-9.6487	57.2819	58.8362
13	15.7438	-24.454	-2.4347	41.7272	2.8024	8.9476	0.2798	1.1935	1.002	-0.4225	0.0504	-1.3491	-1.6648	0.7797	-0.3302	0.0462	-0.1372	0.0874	-0.0443	0.0643	-0.1876	4.9682	47.3508	51.7156
14	20.5325	-5.0045	-0.8309	32.976	0.8932	0.0486	-0.0591	1.8088	-0.2049	-1.4839	-0.5085	-0.4769	-0.0315	0.8266	0.5676	-0.1126	-0.0479	0.0705	0.0396	0.0103	-0.2366	6.7937	36.7523	48.1151

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	5 - 12
2	X-RAY DIFFRACTION	2	A	13 - 27
3	X-RAY DIFFRACTION	3	A	28 - 39
4	X-RAY DIFFRACTION	4	A	40 - 62
5	X-RAY DIFFRACTION	5	A	63 - 78
6	X-RAY DIFFRACTION	6	A	79 - 83
7	X-RAY DIFFRACTION	7	A	84 - 96
8	X-RAY DIFFRACTION	8	B	1 - 16
9	X-RAY DIFFRACTION	9	B	17 - 36
10	X-RAY DIFFRACTION	10	B	37 - 51
11	X-RAY DIFFRACTION	11	B	52 - 62
12	X-RAY DIFFRACTION	12	B	63 - 78
13	X-RAY DIFFRACTION	13	B	79 - 87
14	X-RAY DIFFRACTION	14	B	88 - 94

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