PDB-3khw: Crystal structure of the large c-terminal domain of polymerase ba...

ID or keywords:

Entry

Database: PDB / ID: 3khw

Title

Crystal structure of the large c-terminal domain of polymerase basic protein 2 from influenza virus a/mexico/indre4487/2009(h1n1)

Components

Polymerase PB2

Keywords

VIRAL PROTEIN /

Structural Genomics / PB2 c-terminal domain /

Swine Flu /

H1N1 / NIAID / mRNA capping /

mRNA processing / Seattle Structural Genomics Center for Infectious Disease / SSGCID

Function / homology

Function and homology information

virion component => GO:0044423 /

cap snatching / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / host cell mitochondrion / 7-methylguanosine mRNA capping / viral RNA genome replication /

RNA-dependent RNA polymerase activity / DNA-templated transcription / host cell nucleus /

Biological species

Influenza A virus

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 2.1 Å

Authors

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Citation

Journal: Plos Pathog. / Year: 2010
Title: Biological and structural characterization of a host-adapting amino acid in influenza virus.
Authors: Yamada, S. / Hatta, M. / Staker, B.L. / Watanabe, S. / Imai, M. / Shinya, K. / Sakai-Tagawa, Y. / Ito, M. / Ozawa, M. / Watanabe, T. / Sakabe, S. / Li, C. / Kim, J.H. / Myler, P.J. / Phan, I. ...

History

Deposition	Oct 31, 2009	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 9, 2010	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	Aug 10, 2011	Group: Database references
Revision 1.3	May 23, 2012	Group: Database references
Revision 1.4	Sep 6, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3khw.cif.gz	96.1 KB	Display	PDBx/mmCIF format
PDB format	pdb3khw.ent.gz	74.1 KB	Display	PDB format
PDBx/mmJSON format	3khw.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/kh/3khw ftp://data.pdbj.org/pub/pdb/validation_reports/kh/3khw	HTTPS FTP

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Related structure data

Related structure data	3kc6SC 3l56C S: Starting model for refinement C: citing same article (ref.)
Similar structure data	3c7m-2 6vio-8 3r2v-d 1ni6-2 6scf-1 1cv7-d 6pfs-d 2qlk-d 3b45-d 6scf-2 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 - FunctionF&H Search Similarity search - HomologyF&H Search
Other databases	TargetDB: invaE.07055.a

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Polymerase PB2

B: Polymerase PB2

hetero molecules

45.8 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Polymerase PB2

hetero molecules

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

2

B: Polymerase PB2

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

Unit cell

Length a, b, c (Å)	53.859, 68.185, 107.352
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Details

UNKNOWN

#1: Protein	Polymerase PB2 Mass: 22864.252 Da / Num. of mol.: 2 / Fragment: C-terminal domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza A virus (A/Mexico/InDRE4487/2009(H1N1)) Strain: A/MEXICO/INDRE4487/2009(H1N1) / Gene: PB2 / Plasmid: PET28-SMT / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: C3W6M3
#2: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 234 / 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: 2.16 Å³/Da / Density % sol: 42.93 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 20% PEG 3350, 200MM AMMONIUM CITRATE, PROTEIN CONCENTRATION 24.4 MG/ML, VAPOR DIFFUSIONI, SITTING DROP, TEMPERATURE 293K, VAPOR DIFFUSION, SITTING DROP

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54178 / Wavelength: 1.54178 Å
Detector	Type: RIGAKU SATURN 944+ / Detector: CCD / Date: Oct 27, 2009 / Details: MIRRORS
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.54178 Å / Relative weight: 1
Reflection	Resolution: 2.1→50 Å / Num. obs: 23727 / % possible obs: 99.6 % / Redundancy: 6.7 % / R_merge(I) obs: 0.078 / Net I/σ(I): 11.5
Reflection shell	Resolution: 2.1→2.14 Å / Redundancy: 5.1 % / R_merge(I) obs: 0.194 / % possible all: 96.6

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Processing

Software

Name	Version	Classification
StructureStudio		data collection
PHASER		phasing
REFMAC	5.5.0104	refinement
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3KC6

3kc6

Resolution: 2.1→50 Å / Cor.coef. F_o:F_c: 0.952 / Cor.coef. F_o:F_c free: 0.932 / SU B: 10.904 / SU ML: 0.131 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.254 / ESU R Free: 0.197 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.238	1218	5.1 %	RANDOM
R_work	0.194	-	-	-
obs	0.197	23670	-	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 7.83 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.91 Å²	0 Å²	0 Å²
2-	-	-0.69 Å²	0 Å²
3-	-	-	-0.21 Å²

Refinement step

Cycle: LAST / Resolution: 2.1→50 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3095	0	6	234	3335

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.012	0.022	3188
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	2170
X-RAY DIFFRACTION	r_angle_refined_deg	1.316	1.973	4327
X-RAY DIFFRACTION	r_angle_other_deg	0.883	3	5300
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.033	5	406
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	33.73	24.265	136
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.15	15	544
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	19.266	15	22
X-RAY DIFFRACTION	r_chiral_restr	0.076	0.2	493
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.021	3562
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	634
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	0.552	1.5	2015
X-RAY DIFFRACTION	r_mcbond_other	0.136	1.5	820
X-RAY DIFFRACTION	r_mcangle_it	0.985	2	3250
X-RAY DIFFRACTION	r_scbond_it	1.619	3	1173
X-RAY DIFFRACTION	r_scangle_it	2.531	4.5	1077
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.1→2.15 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.251	88	-
R_work	0.185	1626	-
obs	-	-	97.78 %

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	5.6274	0.3314	-0.0089	2.2175	4.539	6.7868	0.1717	-0.7295	-0.4048	0.3919	-0.2651	0.0463	0.7193	-0.4304	0.0934	0.1653	-0.0709	-0.0304	0.2001	0.0676	0.2152	-23.2202	-11.4132	11.8512
2	6.0391	0.623	-0.0202	3.0931	-0.2019	4.5887	-0.0119	0.0873	0.2556	-0.1491	0.0429	0.2443	-0.1963	-0.1596	-0.0309	0.0852	0.0071	-0.0186	0.0634	-0.0035	0.0866	-18.6981	-1.6308	-0.4993
3	4.8834	0.1266	-0.7509	2.2507	-2.2033	8.8233	0.1303	-0.1332	0.3026	0.0445	0.1112	0.4013	0.0313	-0.822	-0.2415	0.0632	0.0054	0.0149	0.1117	-0.0377	0.1218	-22.2476	0.0492	12.6664
4	1.2998	0.5354	0.865	2.3072	-0.4977	3.0841	0.0958	-0.3178	0.0873	0.3817	0.0375	0.0707	-0.0238	-0.1537	-0.1334	0.0944	-0.0179	0.0206	0.1219	-0.0216	0.0916	-12.067	2.3543	18.0459
5	1.9582	-0.0649	-0.8238	1.4473	-0.0858	1.8565	0.1309	-0.1362	0.1145	0.0923	-0.0639	-0.0394	-0.0815	-0.0127	-0.067	0.0663	-0.0276	-0.0015	0.0553	-0.0154	0.0606	-9.2906	-0.9267	11.0002
6	6.6289	-4.7641	0.8495	7.2785	4.0001	2.7368	-0.356	-0.8735	-0.3875	0.9587	0.0392	0.4004	0.8758	-0.3189	0.3168	0.3582	-0.0389	0.0049	0.2587	0.0193	0.1713	-11.7822	-12.1369	19.9492
7	4.6371	4.1627	3.4203	12.9448	2.6884	1.3783	0.3935	-0.1359	-0.0534	0.2206	-0.4073	0.122	0.2583	-0.2198	0.0138	0.1691	-0.0316	-0.0431	0.1585	-0.0346	0.2159	-15.1239	-18.9008	8.2912
8	2.9692	0.8083	0.528	2.8141	1.4039	4.2838	-0.0462	0.0237	-0.0273	0.0142	-0.0278	0.0466	0.3781	0.2386	0.074	0.1081	0.0149	0.0421	0.0353	0.0102	0.0763	-1.5996	-6.1212	4.1746
9	2.129	-0.6034	0.4478	11.6108	-1.4909	12.8342	0.0565	0.135	0.3978	0.5575	-0.2279	-1.2256	-0.0217	1.1655	0.1714	0.0598	-0.0463	-0.0843	0.3704	0.0128	0.2151	11.5353	-2.3677	16.4712
10	8.2112	-2.0472	1.2488	8.1666	-1.9413	8.9363	0.0633	-0.2259	0.1241	0.1842	-0.3466	-0.1369	0.0628	0.9644	0.2833	0.0374	-0.0008	0.0079	0.1905	-0.0525	0.0746	6.7824	-2.2868	12.2973
11	3.2052	-0.1705	1.6565	1.6453	-0.3787	3.292	0.2195	0.3857	-0.2733	-0.0008	-0.0644	-0.1855	0.374	0.4676	-0.155	0.104	0.0804	-0.0448	0.1248	-0.0403	0.1187	21.117	-3.5568	44.555
12	1.6634	-3.4814	3.9081	5.6821	0.164	13.667	0.207	0.37	0.4169	-0.3298	0.1652	-0.7053	0.4856	1.193	-0.3722	0.166	0.0364	0.0163	0.464	-0.0509	0.1863	21.0615	-2.1886	31.0482
13	4.6898	2.7296	1.0897	4.2786	-0.9736	3.0196	0.0643	0.5118	-0.0714	-0.7253	0.0548	-0.4215	0.1117	0.195	-0.119	0.2321	0.0515	0.0783	0.1689	-0.003	0.1603	12.3322	2.7612	32.5439
14	3.0175	0.3652	0.0242	2.0645	0.2944	1.715	0.0377	0.0408	-0.0019	-0.0198	0.0072	-0.0283	0.1642	0.0621	-0.0449	0.0569	0.0179	-0.0172	0.056	0.0036	0.0335	9.7751	-0.1161	42.7358
15	9.1844	-2.8554	-1.604	8.7336	0.3842	4.951	0.3994	0.5843	0.0532	-0.6125	-0.3529	-0.4	0.1459	0.3098	-0.0465	0.2282	0.0291	-0.0297	0.2372	-0.0066	0.0307	10.1319	-4.2531	28.5703
16	0.1308	0.6043	-2.1662	7.0191	-0.7962	7.5926	-0.2294	0.027	-0.201	0.4621	-0.2976	0.2737	1.205	0.1942	0.527	0.3875	0.0147	0.0314	0.1126	-0.0192	0.2739	9.4527	-15.1667	40.0261
17	3.4505	-2.0929	0.7372	3.2679	0.5601	3.3365	0.0062	-0.1249	-0.3083	0.2907	0.0622	0.0595	0.6651	0.1435	-0.0685	0.1946	0.0111	-0.0238	0.0556	0.0243	0.1025	8.4695	-9.4208	45.5166
18	2.4997	0.2266	0.1124	4.7363	0.6525	14.4297	0.1526	0.194	-0.0459	-0.2852	-0.3191	0.5672	0.5552	-1.5581	0.1665	0.0841	-0.095	-0.0203	0.3824	-0.0647	0.1708	-10.7292	-3.7015	35.1458
19	11.8903	-3.0724	-4.5694	13.5196	4.4696	14.8339	-0.315	0.394	-0.4059	0.0947	-0.0697	-0.0391	1.2179	-1.0532	0.3847	0.1175	-0.1139	-0.0287	0.373	0.015	0.0658	-8.3382	-3.9184	35.8374
20	9.7175	2.1687	1.9315	5.9752	-1.073	6.0038	-0.1485	-0.0464	1.0355	0.2386	-0.1044	0.1099	0.0368	-0.6484	0.2529	0.0319	0.0018	-0.025	0.1502	0.0041	0.1222	-5.4309	2.4413	40.6764

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	541 - 554
2	X-RAY DIFFRACTION	2	A	555 - 567
3	X-RAY DIFFRACTION	3	A	568 - 585
4	X-RAY DIFFRACTION	4	A	586 - 599
5	X-RAY DIFFRACTION	5	A	600 - 638
6	X-RAY DIFFRACTION	6	A	639 - 654
7	X-RAY DIFFRACTION	7	A	655 - 674
8	X-RAY DIFFRACTION	8	A	675 - 699
9	X-RAY DIFFRACTION	9	A	700 - 718
10	X-RAY DIFFRACTION	10	A	719 - 741
11	X-RAY DIFFRACTION	11	B	541 - 576
12	X-RAY DIFFRACTION	12	B	577 - 588
13	X-RAY DIFFRACTION	13	B	589 - 597
14	X-RAY DIFFRACTION	14	B	598 - 627
15	X-RAY DIFFRACTION	15	B	628 - 646
16	X-RAY DIFFRACTION	16	B	647 - 663
17	X-RAY DIFFRACTION	17	B	664 - 695
18	X-RAY DIFFRACTION	18	B	696 - 716
19	X-RAY DIFFRACTION	19	B	717 - 730
20	X-RAY DIFFRACTION	20	B	731 - 741

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