PDB-7zua: Crystal Structure of Ljungan virus 4 2A2 protein I222 crystal form

ID or keywords:

Entry

Database: PDB / ID: 7zua

Title

Crystal Structure of Ljungan virus 4 2A2 protein I222 crystal form

Components

Protein 2A

Keywords

VIRAL PROTEIN / 2A protein / unknown function / NlpC/P60 protein

Function / homology

Function and homology information

RNA-protein covalent cross-linking / : / host cell cytoplasmic vesicle membrane / cytoplasmic vesicle membrane / viral capsid / protein complex oligomerization / monoatomic ion channel activity / RNA helicase activity / symbiont entry into host cell / viral RNA genome replication ...
Similarity search - Function

Biological species

Ljungan virus 64-7855

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.68 Å

Authors

von Castelmur, E. / Perrakis, A.

Funding support

Netherlands, 1items

Citation

Journal: To Be Published
Title: Structural plasticity of Parechovirus family H-box 2A proteins
Authors: von Castelmur, E. / Perrakis, A.

History

Deposition	May 11, 2022	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	May 24, 2023	Provider: repository / Type: Initial release
Revision 1.1	Feb 7, 2024	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	7zua.cif.gz	78.9 KB	Display	PDBx/mmCIF format
PDB format	pdb7zua.ent.gz	45.1 KB	Display	PDB format
PDBx/mmJSON format	7zua.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	7zua_validation.pdf.gz	434.6 KB	Display	wwPDB validaton report
Full document	7zua_full_validation.pdf.gz	434.9 KB	Display
Data in XML	7zua_validation.xml.gz	7 KB	Display
Data in CIF	7zua_validation.cif.gz	8.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/zu/7zua ftp://data.pdbj.org/pub/pdb/validation_reports/zu/7zua	HTTPS FTP

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Related structure data

Related structure data	7ztwS S: Starting model for refinement
Similar structure data	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	#20 - Aug 2001 Poliovirus and Rhinovirus similarity (10)

Deposited unit

A: Protein 2A

hetero molecules

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

1

A: Protein 2A

hetero molecules

A: Protein 2A

hetero molecules

defined by author&software
Evidence: light scattering
27.6 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	58.513, 59.562, 72.827
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	23
Space group name H-M	I222

Components on special symmetry positions

ID	Model	Components
1	1	A-317- HOH

#1: Protein	Protein 2A Mass: 13741.598 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ljungan virus 64-7855 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: C0J6D4
#2: Chemical	ChemComp-ACT / ACETATE ION Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₃O₂
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 44 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.31 Å³/Da / Density % sol: 46.73 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.25 / Details: 0.1M Na acetate pH 5.25 10% PEG 6000

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.00003 Å
Detector	Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 7, 2014
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.00003 Å / Relative weight: 1
Reflection	Resolution: 1.68→46.11 Å / Num. obs: 14774 / % possible obs: 99.6 % / Redundancy: 3.3 % / CC_1/2: 0.999 / R_merge(I) obs: 0.041 / R_pim(I) all: 0.037 / Net I/σ(I): 11.4
Reflection shell	Resolution: 1.68→1.71 Å / R_merge(I) obs: 0.638 / Num. unique obs: 760 / CC_1/2: 0.642 / R_pim(I) all: 0.467

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0350	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 7ZTW

7ztw

Resolution: 1.68→46.106 Å / Cor.coef. F_o:F_c: 0.961 / Cor.coef. F_o:F_c free: 0.936 / WR_factor R_free: 0.256 / WR_factor R_work: 0.21 / SU B: 6.843 / SU ML: 0.097 / Average fsc free: 0.9441 / Average fsc work: 0.962 / Cross valid method: THROUGHOUT / ESU R: 0.112 / ESU R Free: 0.116
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2558	760	5.145 %
R_work	0.2092	14012	-
all	0.212	-	-
obs	-	14772	99.448 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 31.593 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.503 Å²	-0 Å²	0 Å²
2-	-	-0.45 Å²	-0 Å²
3-	-	-	-0.053 Å²

Refinement step

Cycle: LAST / Resolution: 1.68→46.106 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	927	0	4	44	975

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.012	955
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	873
X-RAY DIFFRACTION	r_angle_refined_deg	1.384	1.628	1293
X-RAY DIFFRACTION	r_angle_other_deg	0.483	1.59	2035
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.159	5	118
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	15.86	15.714	7
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	11.95	10.122	164
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	16.092	10	38
X-RAY DIFFRACTION	r_chiral_restr	0.064	0.2	148
X-RAY DIFFRACTION	r_chiral_restr_other	0.046	0.2	1
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	1065
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	187
X-RAY DIFFRACTION	r_nbd_refined	0.222	0.2	187
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.193	0.2	850
X-RAY DIFFRACTION	r_nbtor_refined	0.183	0.2	493
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.081	0.2	503
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.138	0.2	61
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.118	0.2	8
X-RAY DIFFRACTION	r_nbd_other	0.161	0.2	39
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.177	0.2	6
X-RAY DIFFRACTION	r_mcbond_it	5.407	1.999	473
X-RAY DIFFRACTION	r_mcbond_other	5.367	1.991	472
X-RAY DIFFRACTION	r_mcangle_it	6.781	2.957	587
X-RAY DIFFRACTION	r_mcangle_other	6.855	2.966	588
X-RAY DIFFRACTION	r_scbond_it	6.887	2.359	482
X-RAY DIFFRACTION	r_scbond_other	6.88	2.359	483
X-RAY DIFFRACTION	r_scangle_it	9.188	3.358	705
X-RAY DIFFRACTION	r_scangle_other	9.181	3.358	706
X-RAY DIFFRACTION	r_lrange_it	9.713	25.885	1105
X-RAY DIFFRACTION	r_lrange_other	9.731	25.659	1100

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
1.68-1.724	0.428	72	0.322	992	0.329	1065	0.877	0.931	99.9061	0.308
1.724-1.771	0.308	47	0.303	1009	0.303	1056	0.939	0.94	100	0.283
1.771-1.822	0.334	38	0.271	974	0.273	1012	0.922	0.95	100	0.245
1.822-1.878	0.343	51	0.246	948	0.251	1000	0.916	0.959	99.9	0.219
1.878-1.939	0.346	52	0.255	906	0.259	963	0.929	0.958	99.4808	0.227
1.939-2.007	0.305	26	0.249	904	0.251	931	0.931	0.957	99.8926	0.221
2.007-2.083	0.289	37	0.254	876	0.256	913	0.946	0.96	100	0.231
2.083-2.168	0.328	19	0.238	831	0.24	871	0.948	0.963	97.589	0.221
2.168-2.264	0.279	49	0.214	784	0.218	844	0.953	0.97	98.6967	0.2
2.264-2.374	0.251	57	0.199	731	0.203	799	0.968	0.976	98.6233	0.187
2.374-2.502	0.228	50	0.195	725	0.196	775	0.965	0.973	100	0.184
2.502-2.654	0.298	48	0.227	681	0.232	730	0.947	0.965	99.863	0.217
2.654-2.836	0.251	35	0.24	639	0.24	678	0.963	0.964	99.41	0.232
2.836-3.063	0.263	36	0.234	611	0.236	649	0.963	0.965	99.6918	0.231
3.063-3.353	0.204	38	0.213	548	0.212	590	0.976	0.976	99.322	0.219
3.353-3.747	0.238	22	0.196	519	0.198	541	0.971	0.98	100	0.205
3.747-4.322	0.191	31	0.159	449	0.161	484	0.982	0.986	99.1736	0.182
4.322-5.281	0.218	17	0.142	394	0.145	413	0.975	0.989	99.5157	0.164
5.281-7.42	0.303	23	0.198	302	0.204	328	0.948	0.979	99.0854	0.22
7.42-46.106	0.194	12	0.164	188	0.165	211	0.977	0.979	94.7867	0.203

Refinement TLS params.

Method: refined / Origin x: 15.6655 Å / Origin y: 22.0135 Å / Origin z: 25.4359 Å

	11	12	13	21	22	23	31	32	33
T	0.1191 Å²	-0.0274 Å²	0.0947 Å²	-	0.0931 Å²	-0.0184 Å²	-	-	0.0884 Å²
L	1.5117 °²	-0.1854 °²	-0.8328 °²	-	0.5467 °²	0.849 °²	-	-	1.5472 °²
S	-0.1042 Å °	-0.0182 Å °	0.0016 Å °	0.1177 Å °	-0.0226 Å °	0.0573 Å °	0.2512 Å °	-0.0647 Å °	0.1268 Å °

Refinement TLS group

Selection: ALL

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