PDB-2wbt: The Structure of a Double C2H2 Zinc Finger Protein from a Hyperth...

ID or keywords:

Entry

Database: PDB / ID: 2wbt

Title

The Structure of a Double C2H2 Zinc Finger Protein from a Hyperthermophilic Archaeal Virus in the Absence of DNA

Components

B-129

Keywords

DNA BINDING PROTEIN /

DNA-BINDING PROTEIN /

ZINC FINGER / METAL-BINDING / DNA-BINDING PROTEIN SSV

Function / homology

Function and homology information

metal ion binding
Similarity search - Function

Biological species

SULFOLOBUS VIRUS 1

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 2.7 Å

Authors

Eilers, B.J. / Menon, S. / Windham, A.B. / Kraft, P. / Dlakic, M. / Young, M.J. / Lawrence, C.M.

Citation

Journal: To be Published
Title: The Structure of a Double C2H2 Zinc Finger Protein from a Hyperthermophilic Archaeal Virus in the Absence of DNA
Authors: Eilers, B.J. / Menon, S. / Windham, A.B. / Kraft, P. / Dlakic, M. / Young, M.J. / Lawrence, C.M.

History

Deposition	Mar 3, 2009	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Mar 31, 2010	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: 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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PDBx/mmCIF format	2wbt.cif.gz	55.3 KB	Display	PDBx/mmCIF format
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PDBx/mmJSON format	2wbt.json.gz		Tree view	PDBx/mmJSON format
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Validation report

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

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Related structure data

Similar structure data	1qyu-d 5n5u-d 1zc3-2 5nkd-d 3r18-d 1zc3-1 6vnl-4 3ugp-d 1jbu-2 6lz2-2 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#87 - Mar 2007 Zinc Fingers similarity (6) #112 - Apr 2009 Oct and Sox Transcription Factors similarity (5) #257 - May 2021 Fetal Hemoglobin similarity (5) #122 - Feb 2010 Enhanceosome similarity (4) #245 - May 2020 Spliceosomes similarity (1)

Deposited unit

A: B-129

B: B-129

hetero molecules

29.9 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)	51.378, 120.464, 51.687
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	18
Space group name H-M	P2₁2₁2

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Refine code	Auth asym-ID	Auth seq-ID
1	1	1	1	A	77
2	1	1	1	B	77
1	2	1	1	A	80
2	2	1	1	B	80
1	3	1	1	A	93
2	3	1	1	B	93
1	4	1	1	A	103
2	4	1	1	B	103
1	5	1	1	A	106
2	5	1	1	B	106
1	6	1	1	A	119
2	6	1	1	B	119
1	7	1	1	A	124
2	7	1	1	B	124

#1: Protein	B-129 Mass: 14830.291 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: DISULFIDE BOND BETWEEN C 121 AND C 127 / Source: (gene. exp.) SULFOLOBUS VIRUS 1 / Plasmid: PEXP14-B129 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)RIL / References: UniProt: P20201
#2: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 17 / 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: 2.7 Å³/Da / Density % sol: 0.55 % / Description: NONE
Crystal grow	Method: vapor diffusion, sitting drop / pH: 5.3 Details: SITTING DROP VAPOR DIFFUSION, 20 MG/ML OF B129 IN 20 MM BIS-TRIS, PH 6.5, 60 MM NACL MIXED WITH 0.1 M AMMONIUM CITRATE DIBASIC, 10-14 % PEG 4000

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Data collection

Diffraction

Mean temperature: 110 K

Diffraction source

Source:

SYNCHROTRON / Site:

SSRL

/ Beamline: BL9-2 / Wavelength: 1.2833, 1.2830, 1.1696

Detector

Type: MARRESEARCH / Detector: CCD / Date: Mar 18, 2006
Details: FLAT COLLIMATING MIRROR, DOUBLE CRYSTAL MONOCHROMATOR, TOROID 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	1.2833	1
2	1.283	1
3	1.1696	1

Reflection

Resolution: 2.7→50 Å / Num. obs: 8209 / % possible obs: 78.7 % / Observed criterion σ(I): 5 / Redundancy: 2.9 % / R_merge(I) obs: 0.07 / Net I/σ(I): 17.2

Reflection shell

Resolution: 2.7→2.77 Å / Redundancy: 2.8 % / R_merge(I) obs: 0.24 / Mean I/σ(I) obs: 4.4 / % possible all: 78.8

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Processing

Software

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

Refinement

Method to determine structure:

MAD
Starting model: NONE

Resolution: 2.7→20 Å / Cor.coef. F_o:F_c: 0.905 / Cor.coef. F_o:F_c free: 0.874 / SU B: 28.596 / SU ML: 0.29 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.423 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.269	360	4.9 %	RANDOM
R_work	0.231	-	-	-
obs	0.233	6954	78.9 %	-

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: 23.08 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.01 Å²	0 Å²	0 Å²
2-	-	0.15 Å²	0 Å²
3-	-	-	-0.14 Å²

Refinement step

Cycle: LAST / Resolution: 2.7→20 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1905	0	4	17	1926

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.034	0.022	1967
X-RAY DIFFRACTION	r_bond_other_d	0.009	0.02	1377
X-RAY DIFFRACTION	r_angle_refined_deg	1.124	1.971	2658
X-RAY DIFFRACTION	r_angle_other_deg	1.005	3.004	3379
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.289	5	238
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	30.645	23.247	77
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.512	15	385
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	21.386	15	10
X-RAY DIFFRACTION	r_chiral_restr	0.054	0.2	311
X-RAY DIFFRACTION	r_gen_planes_refined	0.002	0.02	2085
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	373
X-RAY DIFFRACTION	r_nbd_refined	0.166	0.2	460
X-RAY DIFFRACTION	r_nbd_other	0.184	0.2	1332
X-RAY DIFFRACTION	r_nbtor_refined	0.169	0.2	953
X-RAY DIFFRACTION	r_nbtor_other	0.083	0.2	981
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.121	0.2	39
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined	0.02	0.2	1
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.426	0.2	12
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.237	0.2	46
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.151	0.2	3
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	0.346	1.5	1566
X-RAY DIFFRACTION	r_mcbond_other	0.031	1.5	469
X-RAY DIFFRACTION	r_mcangle_it	0.364	2	1965
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	0.317	3	879
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	0.541	4.5	692
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

Ens-ID: 1 / Number: 88 / Refine-ID: X-RAY DIFFRACTION

Dom-ID	Auth asym-ID	Type	Rms dev position (Å)	Weight position
1	A	tight positional	0.07	0.05
2	B	tight positional	0.07	0.05
1	A	tight thermal	0.3	0.5
2	B	tight thermal	0.3	0.5

LS refinement shell

Resolution: 2.7→2.77 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.373	24	-
R_work	0.278	502	-
obs	-	-	81.42 %

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	7.2818	-5.1293	2.1382	10.2946	-1.7713	0.6384	0.5273	0.4539	0.1648	-1.0402	-0.1168	-1.4762	-0.4778	0.337	-0.4105	0.1403	0.0013	0.1213	0.2345	-0.004	0.1678	36.495	66.036	2.415
2	11.6203	4.7896	2.8972	3.5461	2.4762	1.768	-0.2577	0.0519	2.5343	1.3582	-0.4855	-0.7853	-0.8305	0.3304	0.7432	0.2898	-0.0004	-0.1766	0.3204	-0.1662	0.4717	39.874	57.882	19.004
3	1.3633	0.5362	-0.3062	14.5105	-4.3929	8.5219	0.1746	0.4295	0.8841	-0.6357	0.2449	-1.1981	0.2917	1.2475	-0.4195	-0.0068	-0.0161	-0.1313	0.2508	0.0279	0.2037	43.423	47.406	11.881
4	1.8506	2.1583	-2.0827	4.5462	-3.317	4.17	0.0353	-0.2059	0.0491	-0.3111	-0.124	0.1149	0.4123	0.3343	0.0887	0.0284	0.0299	-0.0072	0.1639	-0.0002	-0.0642	27.795	36.412	15.856
5	1.5109	0.8462	-1.4033	1.6762	-2.3432	7.2456	-0.0152	0.1037	-0.3735	0.1911	-0.0164	-0.0238	0.432	-0.4179	0.0316	0.0839	-0.0378	-0.0345	0.1797	-0.0208	-0.0265	19.528	25.61	13.149
6	10.3555	-2.3594	-2.2954	12.2036	-0.5104	13.257	0.1054	0.7091	0.1348	-0.9877	-0.1343	-0.1557	-0.1437	0.0625	0.0289	-0.1042	0.0378	0.024	0.0099	0.0993	0.3235	37.818	55.544	1.621
7	11.6428	-3.9211	4.8947	6.4436	-5.7472	18.5801	-0.5535	-1.1262	0.9535	0.3784	0.197	-0.4884	-0.4097	-0.7089	0.3565	-0.1676	-0.0267	-0.0021	0.0235	-0.118	-0.0386	31.361	49.985	12.581
8	3.928	-3.5257	-1.21	3.4268	2.0964	4.2666	0.2134	0.0274	-0.0513	-0.2549	-0.0888	-0.1959	-0.1955	-0.056	-0.1246	-0.0059	-0.0231	0.0324	0.2061	0.0329	-0.1055	36.744	30.656	4.082
9	18.1447	-7.3666	-4.8246	10.9448	2.2154	6.4826	0.6444	0.3265	-0.8893	-0.1236	-0.486	0.3097	0.5456	0.2859	-0.1584	0.0288	-0.0177	-0.0131	0.0998	0.0397	-0.0775	45.458	19.943	3.035
10	8.1778	-0.4226	0.1454	2.9709	-0.5806	2.8822	0.2103	-0.3782	-0.5511	0.2128	0.2189	-0.093	0.3686	0.1333	-0.4292	0.086	0.0003	-0.0087	0.1683	0.0225	-0.0745	43.168	25.997	16.637

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	5 - 21
2	X-RAY DIFFRACTION	2	A	22 - 37
3	X-RAY DIFFRACTION	3	A	38 - 46
4	X-RAY DIFFRACTION	4	A	47 - 88
5	X-RAY DIFFRACTION	5	A	89 - 129
6	X-RAY DIFFRACTION	6	B	18 - 33
7	X-RAY DIFFRACTION	7	B	34 - 59
8	X-RAY DIFFRACTION	8	B	60 - 89
9	X-RAY DIFFRACTION	9	B	90 - 98
10	X-RAY DIFFRACTION	10	B	99 - 128

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