PDB-2vqc: Structure of a DNA binding winged-helix protein, F-112, from Sulf...

ID or keywords:

Entry

Database: PDB / ID: 2vqc

Title

Structure of a DNA binding winged-helix protein, F-112, from Sulfolobus Spindle-shaped Virus 1.

Components

HYPOTHETICAL 13.2 KDA PROTEIN

Keywords

DNA BINDING PROTEIN / SSV / WINGED-HELIX / CRENARCHAEAL / DNA-BINDING PROTEIN / THERMOPHILIC PROTEIN / SULFOLOBUS SPINDLE VIRUS

Function / homology

F-112 protein-like / Sulfolobus spindle-shape virus 1 F-112 protein-like / Sulfolobus spindle-shape virus 1 F-112 protein-like superfamily / F-112 protein / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha / Protein F-112

Function and homology information

Biological species

SULFOLOBUS VIRUS-LIKE PARTICLE SSV1

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 2.3 Å

Authors

Menon, S.K. / Kraft, P. / Corn, G.J. / Wiedenheft, B. / Young, M.J. / Lawrence, C.M.

Citation

Journal: Virology / Year: 2008
Title: Cysteine Usage in Sulfolobus Spindle-Shaped Virus 1 and Extension to Hyperthermophilic Viruses in General.
Authors: Menon, S.K. / Maaty, W.S. / Corn, G.J. / Kwok, S.C. / Eilers, B.J. / Kraft, P. / Gillitzer, E. / Young, M.J. / Bothner, B. / Lawrence, C.M.

History

Deposition	Mar 12, 2008	Deposition site: PDBE / Processing site: PDBE
Supersession	May 6, 2008	ID: 2CMX
Revision 1.0	May 6, 2008	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 / Derived calculations ...Data collection / Derived calculations / 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 / struct_conn Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3	Nov 20, 2024	Group: Data collection / Database references / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	2vqc.cif.gz	30.2 KB	Display	PDBx/mmCIF format
PDB format	pdb2vqc.ent.gz	19.9 KB	Display	PDB format
PDBx/mmJSON format	2vqc.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	2vqc_validation.pdf.gz	423.7 KB	Display	wwPDB validaton report
Full document	2vqc_full_validation.pdf.gz	424.6 KB	Display
Data in XML	2vqc_validation.xml.gz	4.9 KB	Display
Data in CIF	2vqc_validation.cif.gz	6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/vq/2vqc ftp://data.pdbj.org/pub/pdb/validation_reports/vq/2vqc	HTTPS FTP

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Related structure data

Similar structure data	1pc0-d 6a8r-1 5v89-2 1m8m-d 5svx-d 3m1d-1 1baj-d 1uj8-d 5svi-2 4bd3-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: HYPOTHETICAL 13.2 KDA PROTEIN

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

1

Idetical with deposited unit
defined by software

Unit cell

Length a, b, c (Å)	87.716, 87.716, 34.491
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	146
Space group name H-M	H3

#1: Protein	HYPOTHETICAL 13.2 KDA PROTEIN / ORF F-112 / F-112 Mass: 14191.573 Da / Num. of mol.: 1 / Fragment: RESIDUES 2-112 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SULFOLOBUS VIRUS-LIKE PARTICLE SSV1 / Plasmid: PEXP14- SSV1 F112 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834 / References: UniProt: P20220
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 25 / 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: 1.8 Å³/Da / Density % sol: 31.9 % / Description: NONE
Crystal grow	Method: vapor diffusion, hanging drop / pH: 6 Details: HANGING DROP VAPOR DIFFUSION IN 0.1M MES (PH 6.0). QIUCK SOAK IN ML CONTAINING 25% GLYCEROL AS A CRYOPROTECTANT.

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

SSRL

/ Beamline: BL9-2 / Wavelength: 0.891940, 0.979180, 0.979320

Detector

Type: MARRESEARCH / Detector: CCD / Date: Apr 16, 2005 / Details: MIRROR

Radiation

Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.89194	1
2	0.97918	1
3	0.97932	1

Reflection

Resolution: 2.3→30 Å / Num. obs: 4411 / % possible obs: 99.9 % / Observed criterion σ(I): 3 / Redundancy: 7.7 % / R_merge(I) obs: 0.07 / Net I/σ(I): 20.6

Reflection shell

Resolution: 2.3→2.36 Å / Redundancy: 7.3 % / R_merge(I) obs: 0.11 / Mean I/σ(I) obs: 12.3 / % possible all: 100

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Processing

Software

Name	Version	Classification
MOSFLM		data reduction
SCALA		data scaling
SOLVE		phasing
RESOLVE		phasing
REFMAC	5.2.0005	refinement

Refinement

Method to determine structure:

MAD
Starting model: NONE

Resolution: 2.3→25.53 Å / Cor.coef. F_o:F_c: 0.948 / Cor.coef. F_o:F_c free: 0.943 / SU B: 10.361 / SU ML: 0.121 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.242 / ESU R Free: 0.179 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 1-3 AND 74-112 ARE DISORDERED

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.199	235	5.4 %	RANDOM
R_work	0.173	-	-	-
obs	0.175	4133	99.9 %	-

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: 23.47 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.01 Å²	0.01 Å²	0 Å²
2-	-	0.01 Å²	0 Å²
3-	-	-	-0.02 Å²

Refinement step

Cycle: LAST / Resolution: 2.3→25.53 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	582	0	0	25	607

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.022	593
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	548
X-RAY DIFFRACTION	r_angle_refined_deg	0.923	1.974	796
X-RAY DIFFRACTION	r_angle_other_deg	0.682	3	1287
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	4.165	5	69
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	30.633	24.815	27
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.02	15	123
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.348	15	3
X-RAY DIFFRACTION	r_chiral_restr	0.052	0.2	88
X-RAY DIFFRACTION	r_gen_planes_refined	0.002	0.02	626
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	112
X-RAY DIFFRACTION	r_nbd_refined	0.178	0.2	112
X-RAY DIFFRACTION	r_nbd_other	0.148	0.2	519
X-RAY DIFFRACTION	r_nbtor_refined	0.166	0.2	288
X-RAY DIFFRACTION	r_nbtor_other	0.08	0.2	315
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.121	0.2	20
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	0.625	0.2	1
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.129	0.2	24
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.115	0.2	4
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	0.306	1.5	460
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	0.387	2	568
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	0.667	3	288
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	0.986	4.5	228
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: 2.3→2.36 Å / Total num. of bins used: 20 /

	R_factor	Num. reflection
R_free	0.354	17
R_work	0.191	296

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	20.4345	7.862	8.3219	57.4117	8.2468	22.7477	0.318	0.0004	-0.3899	-0.4792	-0.4181	2.4629	1.1153	-0.6488	0.1001	0.018	-0.0331	-0.0629	0.0916	0.0351	0.0986	2.0594	27.6972	10.0265
2	42.6762	30.7014	19.1788	49.7622	19.8412	22.6668	-0.0935	-2.3763	-0.6202	0.7836	-0.0682	0.0833	0.7768	-1.3974	0.1617	-0.0087	0.0602	0.0943	0.1576	0.1364	0.0117	4.9289	31.1551	14.088
3	18.667	-9.9397	9.9288	42.4153	7.1081	9.4196	-0.1595	-0.8726	0.1352	1.4842	0.4268	0.1518	0.4233	0.28	-0.2673	0.1193	0.0207	0.0534	0.055	0.0492	-0.0365	9.9025	35.6217	16.0181
4	25.664	9.6917	5.2962	45.0534	13.6446	29.1903	-0.6705	-1.4059	-0.5206	2.2818	1.1624	-0.6554	-0.6024	0.7198	-0.4919	0.1289	0.111	-0.114	0.1427	0.0184	0.1977	14.7969	39.0837	17.8849
5	0.7557	2.0734	4.6449	12.3989	21.2602	39.3579	-0.2429	0.3183	0.3161	-0.3124	0.6423	-0.9061	-0.4986	2.1921	-0.3994	0.1127	-0.0321	0.0178	0.244	-0.02	0.2503	17.5521	40.5329	10.8135
6	12.5992	-1.7452	-1.2335	27.5463	-13.1586	6.6279	0.0625	0.57	0.7594	-0.5631	-0.1746	-0.3082	0.2189	0.1403	0.1121	0.0802	0.0126	0.0114	0.121	0.0136	-0.05	16.076	33.3608	5.1962
7	12.2454	3.099	2.7234	26.7784	9.7996	14.7917	0.2159	-0.4284	-0.3337	0.6233	0.1374	-0.9352	0.91	0.1413	-0.3533	-0.0226	0.0173	0.042	0.0234	-0.0005	-0.0983	15.2425	26.709	8.7057
8	14.7172	-19.6425	-9.0038	29.808	2.5934	30.2324	0.4127	-0.0665	-0.9424	0.0726	-0.6991	0.9689	-0.2028	-0.1293	0.2864	-0.0009	0.0007	-0.0503	-0.0072	-0.0159	-0.0375	10.241	27.8377	0.0199
9	27.921	-12.4986	1.5074	24.9401	6.2601	14.6935	-0.1603	0.9271	0.7008	-1.0581	-0.1315	0.1031	0.2106	0.0223	0.2918	0.0217	0.0169	-0.0065	-0.0108	0.0377	-0.0805	7.7063	32.3752	2.7628
10	36.2346	0.6387	-12.4086	28.351	-8.5056	34.4466	-0.0589	1.0795	-0.8374	-1.5818	-0.3227	0.5566	0.5266	-0.6922	0.3816	0.0086	0.0639	-0.0103	-0.0895	-0.007	-0.0381	5.5713	36.722	5.6537
11	21.2172	9.88	-5.036	33.49	27.885	32.8285	-0.9129	0.3685	0.236	-1.1077	0.7648	-0.7107	-1.5369	1.1084	0.1481	0.0343	0.0218	0.0039	0.0102	0.0294	0.0966	3.818	41.4088	9.8478
12	30.3591	18.6259	10.3914	45.7475	14.5771	18.423	0.4844	-0.5055	0.7896	0.7023	-0.9185	1.3741	0.4961	0.0473	0.4341	-0.0756	0.0713	0.0763	-0.1293	0.0107	0.0565	2.5465	45.9648	14.2541
13	17.8007	-7.0908	-7.1586	3.0456	-1.353	82.8492	0.5281	0.5713	-0.0682	0.6048	-0.2263	-1.0689	-0.6281	0.6828	-0.3018	0.1337	-0.0062	-0.0111	-0.0878	-0.0247	0.252	9.9821	47.361	10.5109
14	43.0197	-17.5736	30.1035	88.8264	21.3815	34.9574	-0.1969	3.3339	1.0185	-3.0548	-0.9842	0.607	-2.0445	2.3047	1.1811	0.9271	-0.0475	0.2399	0.6409	0.4089	0.3275	15.5234	44.4157	-1.7774
15	7.5185	-1.5928	-8.2568	16.0505	13.7661	42.6135	0.1094	0.1586	0.9628	-0.6429	0.0033	-0.4148	-0.553	1.0385	-0.1127	-0.1565	0.0205	-0.0144	-0.1949	-0.0072	0.0466	12.968	45.0751	10.8772

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	4 - 8
2	X-RAY DIFFRACTION	2	A	9 - 12
3	X-RAY DIFFRACTION	3	A	13 - 16
4	X-RAY DIFFRACTION	4	A	17 - 20
5	X-RAY DIFFRACTION	5	A	21 - 25
6	X-RAY DIFFRACTION	6	A	26 - 30
7	X-RAY DIFFRACTION	7	A	31 - 35
8	X-RAY DIFFRACTION	8	A	36 - 39
9	X-RAY DIFFRACTION	9	A	40 - 43
10	X-RAY DIFFRACTION	10	A	44 - 47
11	X-RAY DIFFRACTION	11	A	48 - 51
12	X-RAY DIFFRACTION	12	A	52 - 56
13	X-RAY DIFFRACTION	13	A	57 - 61
14	X-RAY DIFFRACTION	14	A	62 - 66
15	X-RAY DIFFRACTION	15	A	67 - 72

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