PDB-5tvl: Crystal structure of foldase protein PrsA from Streptococcus pneu...

ID or keywords:

Entry

Database: PDB / ID: 5tvl

Title

Crystal structure of foldase protein PrsA from Streptococcus pneumoniae str. Canada MDR_19A

Components

Foldase protein PrsA

Keywords

ISOMERASE / foldase prsA surface-exposed protein / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID

Function / homology

Function and homology information

peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / protein folding / plasma membrane
Similarity search - Function

Biological species

Streptococcus pneumoniae (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.55 Å

Authors

Borek, D. / Yim, V. / Kudritska, M. / Wawrzak, Z. / Stogios, P.J. / Otwinowski, Z. / Savchenko, A. / Anderson, W. / Center for Structural Genomics of Infectious Diseases (CSGID)

Citation

Journal: To Be Published
Title: Crystal structure of foldase protein PrsA from Streptococcus pneumoniae str. Canada MDR_19A
Authors: Center for Structural Genomics of Infectious Diseases (CSGID)

History

Deposition	Nov 9, 2016	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 23, 2016	Provider: repository / Type: Initial release
Revision 1.1	Nov 30, 2016	Group: Structure summary
Revision 2.0	Feb 17, 2021	Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_residues / pdbx_validate_torsion / struct_conf / struct_ref_seq / struct_sheet_range / struct_site / struct_site_gen Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_seq_id / _atom_site_anisotrop.pdbx_auth_seq_id / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_nonpoly_scheme.pdb_seq_num / _pdbx_poly_seq_scheme.pdb_seq_num / _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_unobs_or_zero_occ_residues.auth_seq_id / _pdbx_validate_torsion.auth_seq_id / _struct_conf.beg_auth_seq_id / _struct_conf.end_auth_seq_id / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_sheet_range.beg_auth_seq_id / _struct_sheet_range.end_auth_seq_id / _struct_site.details / _struct_site.pdbx_auth_seq_id / _struct_site_gen.auth_seq_id
Revision 2.1	Mar 6, 2024	Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	5tvl.cif.gz	441.7 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	5tvl_validation.pdf.gz	476.9 KB	Display	wwPDB validaton report
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Related structure data

Similar structure data	3b2d-d 11887 3rg1-1 2c0m-d 3rg1-2 3t6q-d 3rg1-4 5xm8-d 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	TargetTrack: CSGID-IDP95642

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#261 - Sep 2021 DNA-Sequencing Nanopores similarity (1) #163 - Jul 2013 HIV Capsid similarity (1) #245 - May 2020 Spliceosomes similarity (1) #22 - Oct 2001 Photosystem I similarity (1) #262 - Oct 2021 Fifty Years of Open Access to PDB Structures similarity (1) #29 - May 2002 Penicillin-binding Proteins similarity (1) #95 - Nov 2007 Multidrug Resistance Transporters similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#261 - Sep 2021
DNA-Sequencing Nanopores
similarity (1)
#163 - Jul 2013
HIV Capsid
similarity (1)
#245 - May 2020
Spliceosomes
similarity (1)
#22 - Oct 2001
Photosystem I
similarity (1)
#262 - Oct 2021
Fifty Years of Open Access to PDB Structures
similarity (1)
#29 - May 2002
Penicillin-binding Proteins
similarity (1)
#95 - Nov 2007
Multidrug Resistance Transporters
similarity (1)

Deposited unit

A: Foldase protein PrsA

B: Foldase protein PrsA

C: Foldase protein PrsA

D: Foldase protein PrsA

hetero molecules

129 kDa, 4 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)	72.315, 70.940, 116.626
Angle α, β, γ (deg.)	90.00, 91.49, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Foldase protein PrsA Mass: 31890.312 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Strain: Canada MDR_19A / Gene: prsA, SPH_1082 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / Variant (production host): CodonPlus(DE3)-RIL / References: UniProt: B1IBE1, peptidylprolyl isomerase
#2: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO₄
#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C₃H₈O₃
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 91 / 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: 2.34 Å³/Da / Density % sol: 47.53 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 11 / Details: 2M Ammonium Sulfate, 0.05 M CAPSO pH 11

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
Detector	Type: RAYONIX MX-225 / Detector: CCD / Date: Oct 7, 2012
Radiation	Monochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97872 Å / Relative weight: 1
Reflection	Resolution: 2.45→50 Å / Num. obs: 43458 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 9.8 % / CC_1/2: 1 / R_merge(I) obs: 0.09 / R_sym value: 0.09 / Net I/σ(I): 20.04
Reflection shell	Resolution: 2.45→2.49 Å / Redundancy: 6.2 % / R_merge(I) obs: 0 / Mean I/σ(I) obs: 0.9 / CC_1/2: 0.58 / % possible all: 90.9

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0135	refinement
HKL-3000		data reduction
HKL-3000		data scaling
HKL-3000		phasing

Refinement

Method to determine structure:

SAD / Resolution: 2.55→50 Å / Cor.coef. F_o:F_c: 0.922 / Cor.coef. F_o:F_c free: 0.854 / SU B: 31.841 / SU ML: 0.331 / Cross valid method: THROUGHOUT / ESU R Free: 0.439 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.29708	1646	5.2 %	RANDOM
R_work	0.22527	-	-	-
obs	0.22879	30311	82.35 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å

Displacement parameters

B_iso mean: 56.404 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.11 Å²	0 Å²	0.11 Å²
2-	-	0.19 Å²	-0 Å²
3-	-	-	-0.3 Å²

Refinement step

Cycle: 1 / Resolution: 2.55→50 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8456	0	64	91	8611

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.02	8635
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	8367
X-RAY DIFFRACTION	r_angle_refined_deg	0.985	1.967	11612
X-RAY DIFFRACTION	r_angle_other_deg	0.797	3	19374
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.089	5	1066
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	39.267	27.19	420
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.998	15	1697
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	12.724	15	16
X-RAY DIFFRACTION	r_chiral_restr	0.052	0.2	1345
X-RAY DIFFRACTION	r_gen_planes_refined	0.002	0.02	9744
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1764
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	2.87	2.56	4282
X-RAY DIFFRACTION	r_mcbond_other	2.869	2.559	4281
X-RAY DIFFRACTION	r_mcangle_it	4.66	3.823	5342
X-RAY DIFFRACTION	r_mcangle_other	4.659	3.824	5343
X-RAY DIFFRACTION	r_scbond_it	3.413	2.848	4353
X-RAY DIFFRACTION	r_scbond_other	3.413	2.848	4353
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	5.421	4.131	6271
X-RAY DIFFRACTION	r_long_range_B_refined	7.527	19.341	9349
X-RAY DIFFRACTION	r_long_range_B_other	7.526	19.343	9348
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.55→2.616 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.397	67	-
R_work	0.322	1021	-
obs	-	-	38.19 %

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	8.0008	1.9304	6.0259	3.0093	6.5424	18.5039	-0.4258	1.4164	0.1591	-0.1854	0.324	0.5052	-0.8412	1.3766	0.1019	0.1487	-0.149	-0.0329	0.5996	0.0083	0.4755	69.531	7.051	-43.953
2	2.6921	1.5198	-0.9568	1.2858	-0.53	7.4631	-0.1371	0.2447	0.2064	-0.0415	0.0086	0.1295	-0.3119	-0.0193	0.1284	0.2051	-0.0281	-0.0566	0.2314	0.0129	0.1532	63.062	11.105	-28.632
3	7.5169	1.2988	9.1564	2.1632	-1.1183	14.9323	0.0079	0.4004	0.1419	0.1359	-0.154	-0.0002	-0.2272	0.8054	0.146	0.2515	-0.0186	0.0807	0.266	-0.05	0.2931	73.002	10.987	-6.25
4	13.8414	3.7468	7.7668	19.4528	7.0516	7.0294	-0.0962	-0.3024	0.2321	0.695	0.3343	-0.8519	0.1586	0.2538	-0.2381	0.2016	0.0429	-0.0519	0.2328	0.0385	0.2241	75.553	-6.435	-6.87
5	13.8159	0.9012	2.9667	8.3889	1.8949	6.4172	-0.2367	0.5244	-0.292	-0.2425	0.0766	-0.722	0.1048	0.6865	0.1602	0.1366	-0.0177	-0.004	0.2438	-0.0319	0.2206	69.101	-13.049	-16.891
6	0.0374	0.0384	0.2819	3.8928	3.5201	9.1792	-0.0056	0.0331	0.0789	-0.2161	-0.0272	0.0171	0.0351	0.4058	0.0327	0.1671	-0.0729	-0.0107	0.296	0.0031	0.236	70.342	0.11	-13.336
7	2.1659	0.7074	-4.7991	0.7379	-1.7177	10.7066	0.2268	-0.091	-0.0422	-0.0542	-0.2387	0.1901	-0.5216	0.2157	0.012	0.2377	-0.0001	-0.0176	0.5468	-0.1228	0.17	60.789	8.733	11.26
8	2.9761	1.0288	-3.0711	2.9034	0.9452	5.3856	-0.1936	-0.5934	0.2282	0.2647	0.2118	0.4897	0.7962	0.9229	-0.0182	0.3272	0.2461	-0.0285	0.4613	0.0079	0.1054	52.377	-17.04	15.746
9	4.4896	6.1147	6.2494	8.9936	5.3037	24.2807	0.3352	-0.1527	-0.3576	0.3208	-0.0869	-0.5248	0.9551	-0.702	-0.2483	0.7072	0.0438	0.157	0.2153	0.131	0.3272	43.988	-32.792	14.311
10	8.6278	14.7843	7.6238	25.3368	13.0645	6.7374	0.3333	0.4715	-1.2623	0.5249	0.7894	-2.1726	0.2844	0.398	-1.1228	0.7853	0.3221	0.1141	0.4659	0.1195	0.2778	50.066	-32.53	21.84
11	1.0517	-3.8462	0.0827	32.8148	-5.9636	1.722	0.0005	0.3156	-0.2267	0.0432	-0.4716	-0.909	-0.0405	-0.2282	0.471	0.4013	0.4066	0.0003	0.6804	0.0913	0.5541	57.046	-33.836	16.416
12	2.5162	2.1586	-1.6993	2.0091	-1.577	1.2385	-0.3306	0.116	-0.563	-0.132	-0.002	-0.4304	0.1159	0.0094	0.3326	0.5172	0.4053	0.0527	0.909	-0.1476	0.2777	59.993	-26.231	12.385
13	4.1005	-1.0824	0.3959	2.7957	1.4338	1.0126	-0.3794	-0.0097	0.2827	0.1569	0.3094	-0.007	0.0908	0.251	0.07	0.371	0.128	0.0227	0.3779	-0.0102	0.0537	49.808	-16.299	15.398
14	4.4906	1.0518	-1.3009	0.7402	2.6941	18.7282	-0.2149	0.565	0.1776	-0.1255	0.2979	0.0489	-0.5632	0.732	-0.083	0.3161	0.0278	0.0412	0.2622	0.0409	0.2585	48.15	-21.65	3.62
15	52.3625	4.8389	6.7275	0.5065	0.6484	0.9192	0.6825	-1.6672	-1.2272	-0.0564	-0.3801	-0.1417	0.1718	-0.2921	-0.3024	0.8669	0.5692	-0.4155	0.9396	0.0618	0.4482	54.392	-21.103	23.661
16	0.628	2.3406	1.4393	10.8793	4.6363	3.546	0.0048	0.0676	0.0202	0.629	-0.1541	-0.2066	-0.19	0.3081	0.1493	0.2568	0.0156	-0.0157	0.5407	0.0417	0.1907	60.23	-2.151	25.855
17	5.8573	-3.4917	6.6263	3.9746	-9.4873	23.7071	-0.2775	-0.2733	0.3716	-0.2334	0.0828	-0.1333	0.8557	-0.1009	0.1946	0.2339	-0.095	-0.0008	0.4077	0.0197	0.1605	60.309	1.883	10.503
18	5.2226	7.7142	-4.5431	14.4379	-2.4223	9.9976	-0.0038	-0.0918	0.2353	-0.0738	-0.1237	0.5838	-0.0697	0.0923	0.1276	0.1672	0.0061	-0.0238	0.2774	-0.0243	0.1958	57.751	8.772	-1.899
19	0.8019	-1.9908	-1.193	5.9442	4.1046	3.0842	-0.0903	-0.0795	0.2972	-0.3248	-0.0561	-0.2093	-0.5249	-0.1426	0.1464	0.5317	0.0154	-0.1869	0.2763	-0.1624	0.5281	63.329	21.064	-13.007
20	12.1885	0.4056	-1.5838	1.2133	-1.4667	1.8722	-0.2165	-0.2015	0.321	0.5913	0.2952	0.0408	-0.6763	-0.3317	-0.0786	0.4046	0.0295	0.0023	0.2973	-0.0868	0.373	57.034	16.562	-15.983
21	12.7129	1.2882	-1.7735	0.1586	-0.0755	22.6872	-0.125	-0.4362	-0.3157	0.0755	-0.0314	-0.0843	-0.4013	0.0539	0.1563	0.3546	0.0601	-0.0946	0.2303	0.0254	0.2289	33.15	3.106	45.662
22	1.1836	-0.5632	0.3488	1.4785	0.0833	3.7533	-0.0048	-0.0858	0.3384	-0.0242	0.0176	-0.0692	-0.1528	0.1966	-0.0127	0.199	0.0344	-0.0217	0.2979	-0.0285	0.1681	39.919	8.245	29.085
23	11.2219	3.219	3.9252	4.967	5.7258	10.025	0.1218	-0.2305	0.1837	-0.149	-0.0767	0.2435	0.0539	-0.5195	-0.0451	0.2352	0.0111	-0.0305	0.1861	0.032	0.1145	31.337	8.051	7.012
24	24.8022	-1.1156	11.5631	0.0566	-0.5129	5.4735	-0.3294	-0.2574	0.086	-0.0045	0.0786	0.0007	-0.2935	-0.0998	0.2509	0.4404	-0.1103	-0.2708	0.7352	-0.104	0.5948	28.606	-4.804	2.705
25	8.3119	-5.516	5.5022	10.1749	-2.2267	4.0611	0.6005	0.0521	-0.1609	-0.7762	-0.6171	0.3449	0.4711	-0.0618	0.0167	0.3664	0.027	0.0255	0.3157	-0.0905	0.1743	36.443	-13.836	8.889
26	6.95	4.4036	1.71	4.3557	3.6147	6.9078	0.0812	-1.2604	-0.0316	0.4011	-0.5154	0.1318	0.0716	-0.5868	0.4343	0.2899	0.1622	0.0425	0.5286	-0.0342	0.1061	39.411	-14.043	20.545
27	5.4832	-2.6023	-2.2303	12.3503	-10.0339	13.7074	-0.2556	-0.154	0.0395	0.1455	0.1685	0.1767	0.193	-0.1656	0.0871	0.1484	-0.0059	0.0119	0.1787	-0.0685	0.1581	33.756	-3.786	13.425
28	3.2162	3.165	-8.7218	5.2262	-10.51	25.4699	-0.0179	0.3658	-0.2655	-0.1554	-0.4494	-0.0873	0.0948	-0.2613	0.4672	0.2534	-0.0061	0.0559	0.384	-0.0576	0.2119	39.937	7.102	-3.664
29	3.4963	-6.6244	1.5218	12.6333	-2.899	1.0725	0.8251	0.4178	0.2812	-1.5994	-0.8887	-0.5891	-0.1219	0.1102	0.0636	0.8257	0.1836	0.1323	0.3573	0.076	0.261	50.91	3.853	-18.12
30	4.0454	-1.8098	-0.2739	3.9243	-0.2885	1.1277	-0.1957	-0.1739	-0.2202	0.041	0.1835	-0.1248	0.157	0.0848	0.0123	0.1444	0.0318	0.0011	0.2877	0.0287	0.1758	60.383	-23.978	-13.12
31	5.981	2.8297	-4.2444	2.3964	-3.4817	7.5897	-0.1711	-0.2248	-1.1634	-0.3529	-0.1578	-0.1405	0.4391	0.3953	0.3289	0.2662	0.0395	-0.0195	0.1548	-0.0104	0.419	59.593	-31.439	-16.654
32	10.6915	-4.5632	-0.6031	9.3979	-7.2275	7.5644	-0.2916	-0.2486	-0.5745	-0.6279	0.2115	0.2072	0.741	-0.147	0.08	0.3227	-0.0408	-0.0766	0.5574	0.0218	0.2773	49.503	-27.19	-12.143
33	5.0722	-1.3904	0.0614	2.0669	0.6743	1.852	-0.1357	0.1003	0.1522	-0.0148	0.0736	-0.0557	0.1827	-0.1112	0.0622	0.2296	-0.0023	0.0021	0.2422	0.0233	0.1314	57.822	-15.445	-16.338
34	6.4498	-3.1983	4.8411	2.381	-0.9738	9.1009	-0.1393	-0.062	-0.178	-0.0608	0.2153	-0.107	-0.278	0.0725	-0.0761	0.1949	-0.0212	0.0264	0.1765	0.0231	0.1937	58.288	-18.968	-14.088
35	2.0123	3.8659	-1.5592	7.4321	-2.9966	1.2084	-0.3824	0.2391	0.0866	-0.7821	0.4548	0.1882	0.3047	-0.1889	-0.0723	0.6774	0.3755	-0.1194	0.8399	0.2173	0.1886	45.382	-0.96	-25.189
36	4.6098	-1.0519	8.5252	19.2047	3.8076	17.5521	-0.2422	-0.3597	-0.106	-0.0751	0.3681	0.2553	-0.4297	-0.7108	-0.1258	0.177	-0.096	0.0527	0.5309	0.0462	0.1822	43.768	-0.198	-13.845
37	5.6755	3.4832	8.183	12.5783	11.3852	21.0225	0.3018	0.2876	-0.5012	-0.0296	0.1033	-0.6245	0.5505	-0.0428	-0.4051	0.2163	0.0324	0.0986	0.278	-0.0223	0.2198	47.931	2.836	-1.742
38	4.4179	-6.2738	-5.1939	11.9153	7.83	6.248	0.1161	-0.1202	0.3669	-0.1975	0.1328	-0.0506	-0.2472	0.2535	-0.249	0.2981	-0.0946	-0.1405	0.3066	0.1029	0.3452	43.787	11.119	4.702
39	2.3712	-0.5266	-1.4183	2.49	-2.2999	11.9691	0.1916	0.0459	0.4685	0.321	-0.1044	-0.1254	-1.1073	0.0999	-0.0872	0.2351	-0.0156	-0.0051	0.1636	-0.0376	0.3675	39.173	18.945	17.439
40	4.8054	2.8852	-3.6355	6.6918	1.3877	8.8395	0.1528	-0.1591	0.195	-0.066	-0.0087	-0.4438	-0.7252	1.1577	-0.1441	0.1636	-0.0867	-0.1152	0.3859	0.0504	0.5413	45.795	14.774	17.371
41	1.5124	-2.0743	2.2657	3.2458	-3.5211	6.0639	0.0018	0.0746	-0.0339	0.0289	0.0635	0.0486	0.0034	-0.2037	-0.0652	0.1863	0.0198	-0.0153	0.2832	-0.0101	0.1488	35.401	6.684	27.298
42	5.9892	2.8698	3.9934	3.4192	1.518	7.2359	0.169	-0.1834	0.0851	-0.0337	-0.092	-0.0778	-0.4934	-0.4162	-0.0769	0.1912	0.0287	-0.0084	0.1893	-0.004	0.1514	46.166	2.671	51.418
43	13.4299	5.9383	-8.4325	3.4818	0.3128	25.0178	0.6073	-0.5642	0.2775	0.4347	-0.1857	0.0074	0.0605	0.9265	-0.4216	0.3231	-0.0857	-0.1905	0.2194	0.0429	0.2815	60.689	9.925	47.322
44	21.8066	0.0622	15.7896	0.4628	-3.194	34.1274	0.1776	0.5798	-1.0664	0.3203	-0.1216	-0.114	-2.1318	1.2983	-0.0559	0.2669	-0.1065	0.0025	0.3688	-0.1041	0.319	66.892	11.463	35.294
45	5.7821	1.8938	-5.3194	3.8478	-5.9121	17.1744	0.279	0.7393	0.0894	0.1722	0.0904	0.3198	-0.7304	0.1855	-0.3693	0.1855	0.002	-0.0379	0.3103	0.0011	0.1747	56.243	9.886	34.067
46	1.0996	0.6539	1.5382	2.663	0.0457	2.6136	0.0724	-0.0119	-0.0555	0.033	0.0931	0.0713	-0.0407	0.0853	-0.1655	0.2334	-0.0204	0.0394	0.4351	-0.0482	0.1592	54.374	-3.52	54.066
47	1.3606	-0.5069	-1.83	0.3882	-0.396	8.4517	-0.4029	-0.1569	-0.5594	0.2452	0.1367	0.2539	0.1824	-0.1255	0.2663	0.3527	0.0754	-0.0708	0.2914	0.0355	0.6294	64.734	-19.192	61.92
48	2.825	1.9346	-2.5176	4.9842	-4.6501	4.6472	-0.0756	-0.3421	-0.2721	0.1716	0.0239	0.1159	-0.2448	-0.0094	0.0517	0.3021	0.2178	-0.0656	0.4086	-0.0308	0.2714	80.688	-8.831	49.752
49	2.7638	1.9661	-3.6791	2.0678	-5.0703	13.9528	0.076	0.6243	0.1471	-0.1763	0.1052	0.1168	0.589	0.4803	-0.1812	0.6589	0.12	-0.1587	0.5235	0.0692	0.0725	85.94	-5.902	30.559
50	8.7202	0.0443	5.4395	10.4485	3.1819	4.3537	2.5625	-0.1516	-0.8887	-2.8284	-1.9116	-0.5156	0.7353	-0.628	-0.6509	1.5354	0.403	-0.1436	0.9193	0.3582	0.5881	96.374	-11.553	36.327
51	1.795	-2.4802	-3.1155	11.2913	2.2323	6.1338	0.2428	-0.3443	0.2249	-0.6259	-0.0776	-0.3626	-0.5204	0.6995	-0.1651	0.2601	-0.0037	-0.0768	0.2318	-0.1182	0.4834	90.583	-0.341	40.831
52	1.1037	-2.6076	3.8808	6.7558	-9.262	13.7507	-0.275	0.1294	0.0596	0.993	0.0148	0.0425	-1.1768	0.5057	0.2603	0.537	-0.0241	-0.0283	0.3339	0.0648	0.6673	85.445	-0.155	48.93
53	7.3046	4.2449	4.8384	9.3879	1.046	25.9229	0.4274	-0.2568	0.4298	-0.1425	0.0151	1.2858	-0.5643	-1.4789	-0.4426	0.1379	0.1339	-0.0394	0.4046	0.0698	0.4694	73.629	-6.557	50.599
54	0.0298	0.1667	0.3028	2.9559	5.6125	10.8209	0.0908	-0.0301	-0.0371	0.0096	-0.248	0.0166	-0.0334	-0.7581	0.1572	0.3971	-0.0845	-0.1567	0.7355	0.0362	0.4371	76.135	-12.304	45.406
55	0.5571	-0.0043	1.4086	0.0505	-0.4103	7.2344	0.2139	-0.0449	-0.1778	-0.0335	0.0949	0.0031	0.6378	-0.6877	-0.3088	0.364	0.0449	-0.3586	0.3752	-0.126	0.3783	82.69	-13.437	42.561
56	0.8114	-0.7548	-1.1584	1.9516	-0.5463	4.0089	0.0613	0.1326	-0.1222	-0.296	-0.1528	0.0792	0.1844	-0.3654	0.0916	0.2173	-0.0284	-0.1246	0.386	0.0556	0.2672	82.138	-10.988	49.213
57	0.418	0.358	2.1865	2.9027	2.9093	12.2887	-0.0806	-0.0634	0.1218	0.02	-0.1115	-0.573	-0.2305	-0.0601	0.1921	0.1322	0.2406	-0.0548	0.5071	-0.0551	0.3724	68.064	-11.039	62.182
58	13.9477	-2.902	-0.9933	1.3499	-1.2704	3.0045	0.0131	0.2728	-0.1424	-0.0876	-0.0924	-0.0137	0.1883	0.0915	0.0793	0.2175	0.0008	-0.0054	0.2381	-0.0493	0.2175	50.217	-10.044	49.388
59	4.8189	1.8139	3.5672	1.9439	-5.2955	37.6006	0.2167	-0.3907	0.6996	-0.265	0.1525	0.4387	2.0264	-1.8086	-0.3693	0.2928	-0.0109	0.0703	0.3259	0.0434	0.2718	31.639	-3.931	41.383
60	0.4729	1.7298	1.1075	6.3744	4.0807	2.6128	0.046	-0.0255	-0.02	0.1556	-0.1064	0.1007	0.1127	-0.079	0.0603	0.505	-0.1983	-0.0935	0.4223	-0.0113	0.6407	38.848	-8.82	39.242
61	3.2495	0.1981	2.4431	1.6042	3.3281	8.3126	-0.585	0.4396	0.2335	-0.0905	0.3831	0.0791	-0.5986	1.1965	0.2019	0.3443	-0.2716	-0.0471	0.4148	-0.0111	0.1672	71.175	15.952	-22.613
62	2.3367	-1.0209	1.8253	0.7706	-2.2437	7.9611	0.0687	-0.1064	-0.044	-0.1032	0.006	0.0133	0.3071	0.1796	-0.0746	0.2281	-0.0301	-0.0685	0.251	-0.0162	0.1734	62.987	2.636	-31.242
63	4.8149	-3.3368	4.8094	3.0998	-4.0187	7.0155	0.006	0.0823	0.2428	0.2822	-0.1281	-0.1006	-0.3486	0.4193	0.122	0.1912	-0.0085	-0.0288	0.2003	-0.0031	0.1771	54.632	6.259	-49.929
64	1.2851	-0.052	-3.9899	0.0041	0.1706	13.5523	-0.1494	-0.0002	-0.0979	-0.0134	0.0004	0.014	0.1297	-0.8371	0.149	0.2624	0.1646	-0.016	0.6889	0.0476	0.2739	39.122	12.663	-41.2
65	18.5726	1.1761	15.2436	0.0763	0.9668	12.5127	-0.0287	0.3034	0.0189	0.0175	0.0058	0.013	-0.0053	0.2428	0.023	0.2858	0.0726	0.0942	0.8164	-0.0348	0.2105	39.354	14.69	-27.762
66	1.8281	-0.3545	0.0264	4.1903	5.8493	8.3186	-0.0114	-0.4721	-0.1071	-0.1033	0.132	-0.0731	-0.1395	0.0429	-0.1206	0.3749	0.0079	-0.0012	0.4169	-0.0452	0.1121	48.32	8.979	-36.915
67	2.3887	2.1449	-0.1571	2.0322	-0.2432	0.3545	0.0813	-0.1011	-0.2463	0.0317	-0.0096	-0.1186	-0.0097	0.0236	-0.0717	0.1862	0.0057	-0.0306	0.2593	-0.0158	0.2252	38.941	-12.566	-54.95
68	1.6945	-3.9833	-3.0539	14.2122	11.8182	9.9502	-0.1563	-0.1023	-0.2688	-0.9022	0.6525	-0.3656	-0.9275	0.6192	-0.4961	0.3937	-0.1581	0.2148	0.4739	-0.1007	0.4075	16.883	-5.039	-39.789
69	0.1485	-0.6453	2.952	2.8663	-13.2498	61.566	0.104	-0.0381	-0.0125	-0.2247	0.0968	0.0446	0.4657	-0.2111	-0.2008	1.2232	-0.3974	0.1025	0.8964	0.0418	0.0795	16.029	-6.492	-25.243
70	2.6981	2.7317	1.9137	2.7819	1.9542	1.3829	0.4672	-0.4453	0.0405	0.4066	-0.4994	0.003	0.2852	-0.4079	0.0323	0.4451	0.039	0.3302	0.4644	-0.0579	0.396	6.839	-9.013	-33.387
71	0.5745	-0.2046	-0.596	0.0767	0.2123	0.6316	0.7291	0.0419	0.5956	-0.2654	-0.0295	-0.2011	-0.7361	-0.0226	-0.6996	1.0942	0.1107	0.4431	0.0851	-0.1297	1.3706	9.054	0.314	-35.485
72	0.1038	-0.054	-0.0191	4.3988	8.0258	14.7075	0.2738	0.0208	0.0644	-0.0419	-0.1607	-0.1014	0.1419	-0.3065	-0.113	0.7508	-0.0444	0.1934	0.3505	-0.061	0.4961	17.448	3.184	-38.057
73	3.1391	3.4585	-0.9297	4.9992	2.2561	10.3432	0.8377	-0.2824	0.5688	0.4553	0.2982	0.3301	-1.3781	1.5901	-1.1359	0.4621	-0.308	0.1463	0.3573	-0.2067	0.388	25.01	-6.662	-44.671
74	21.7596	4.715	-2.4046	9.8194	2.8766	1.6237	-0.2237	-0.5877	0.0021	0.3749	0.4807	-0.3308	0.1371	0.3583	-0.257	0.2582	0.0124	0.1047	0.3437	-0.1366	0.3933	21.494	-15.255	-42.072
75	5.8065	3.874	4.2499	13.9973	-2.8689	6.0188	1.456	0.0128	-0.6851	2.3354	-0.2714	0.8853	0.3875	0.05	-1.1846	0.5397	-0.0128	-0.0127	0.4113	-0.121	0.2914	17.739	-13.044	-35.397
76	3.3013	3.8614	1.1342	14.4383	7.6079	4.4005	0.1998	-0.4383	0.1358	0.5032	-0.2886	0.4187	0.177	0.0414	0.0888	0.1966	-0.0412	0.2458	0.4787	-0.0565	0.51	17.057	-9.049	-38.288
77	5.0828	0.85	0.8779	3.3259	0.3574	0.1666	0.03	0.1297	0.01	0.026	-0.0396	0.2522	0.0084	0.028	0.0095	0.2033	0.0013	-0.0286	0.2905	0.046	0.1896	30.351	-12.762	-57.586
78	16.3191	4.1002	-2.3169	1.8354	0.4749	4.1661	0.1619	-0.2104	-0.0637	0.0716	-0.1778	0.022	0.3389	0.1617	0.0159	0.2381	0.0743	-0.0598	0.2153	-0.016	0.1477	52.731	-7.68	-46.745
79	8.5474	-6.0267	1.476	8.1781	5.0432	9.7035	-0.0417	0.3988	0.5898	0.863	0.4874	-0.7698	1.2877	1.3382	-0.4458	0.1871	0.1068	-0.0847	0.8086	0.0147	0.0796	70.958	0.143	-39.141
80	37.1875	-18.3512	9.3576	26.0664	6.0245	9.0145	0.3277	0.7067	-0.5687	1.1506	0.1142	-0.2034	0.9288	0.4783	-0.442	0.6113	0.0916	0.1195	0.2776	0.0278	0.2167	64.341	-6.405	-37.804

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	2 - 11
2	X-RAY DIFFRACTION	2	A	12 - 35
3	X-RAY DIFFRACTION	3	A	36 - 50
4	X-RAY DIFFRACTION	4	A	51 - 62
5	X-RAY DIFFRACTION	5	A	63 - 73
6	X-RAY DIFFRACTION	6	A	74 - 93
7	X-RAY DIFFRACTION	7	A	94 - 113
8	X-RAY DIFFRACTION	8	A	114 - 132
9	X-RAY DIFFRACTION	9	A	133 - 139
10	X-RAY DIFFRACTION	10	A	140 - 148
11	X-RAY DIFFRACTION	11	A	149 - 154
12	X-RAY DIFFRACTION	12	A	155 - 169
13	X-RAY DIFFRACTION	13	A	170 - 202
14	X-RAY DIFFRACTION	14	A	203 - 211
15	X-RAY DIFFRACTION	15	A	212 - 216
16	X-RAY DIFFRACTION	16	A	217 - 229
17	X-RAY DIFFRACTION	17	A	230 - 240
18	X-RAY DIFFRACTION	18	A	241 - 251
19	X-RAY DIFFRACTION	19	A	252 - 264
20	X-RAY DIFFRACTION	20	A	265 - 274
21	X-RAY DIFFRACTION	21	B	3 - 12
22	X-RAY DIFFRACTION	22	B	13 - 36
23	X-RAY DIFFRACTION	23	B	37 - 49
24	X-RAY DIFFRACTION	24	B	50 - 54
25	X-RAY DIFFRACTION	25	B	55 - 66
26	X-RAY DIFFRACTION	26	B	67 - 77
27	X-RAY DIFFRACTION	27	B	78 - 91
28	X-RAY DIFFRACTION	28	B	92 - 106
29	X-RAY DIFFRACTION	29	B	107 - 117
30	X-RAY DIFFRACTION	30	B	118 - 137
31	X-RAY DIFFRACTION	31	B	138 - 158
32	X-RAY DIFFRACTION	32	B	159 - 168
33	X-RAY DIFFRACTION	33	B	169 - 198
34	X-RAY DIFFRACTION	34	B	199 - 219
35	X-RAY DIFFRACTION	35	B	220 - 227
36	X-RAY DIFFRACTION	36	B	228 - 235
37	X-RAY DIFFRACTION	37	B	236 - 244
38	X-RAY DIFFRACTION	38	B	245 - 253
39	X-RAY DIFFRACTION	39	B	254 - 265
40	X-RAY DIFFRACTION	40	B	266 - 274
41	X-RAY DIFFRACTION	41	C	3 - 35
42	X-RAY DIFFRACTION	42	C	36 - 49
43	X-RAY DIFFRACTION	43	C	50 - 61
44	X-RAY DIFFRACTION	44	C	62 - 67
45	X-RAY DIFFRACTION	45	C	68 - 87
46	X-RAY DIFFRACTION	46	C	88 - 105
47	X-RAY DIFFRACTION	47	C	106 - 115
48	X-RAY DIFFRACTION	48	C	116 - 128
49	X-RAY DIFFRACTION	49	C	129 - 139
50	X-RAY DIFFRACTION	50	C	140 - 145
51	X-RAY DIFFRACTION	51	C	146 - 159
52	X-RAY DIFFRACTION	52	C	160 - 170
53	X-RAY DIFFRACTION	53	C	171 - 179
54	X-RAY DIFFRACTION	54	C	180 - 185
55	X-RAY DIFFRACTION	55	C	186 - 206
56	X-RAY DIFFRACTION	56	C	207 - 222
57	X-RAY DIFFRACTION	57	C	223 - 237
58	X-RAY DIFFRACTION	58	C	238 - 257
59	X-RAY DIFFRACTION	59	C	258 - 265
60	X-RAY DIFFRACTION	60	C	266 - 274
61	X-RAY DIFFRACTION	61	D	2 - 20
62	X-RAY DIFFRACTION	62	D	21 - 36
63	X-RAY DIFFRACTION	63	D	37 - 50
64	X-RAY DIFFRACTION	64	D	51 - 64
65	X-RAY DIFFRACTION	65	D	65 - 71
66	X-RAY DIFFRACTION	66	D	72 - 93
67	X-RAY DIFFRACTION	67	D	94 - 121
68	X-RAY DIFFRACTION	68	D	122 - 127
69	X-RAY DIFFRACTION	69	D	128 - 134
70	X-RAY DIFFRACTION	70	D	135 - 149
71	X-RAY DIFFRACTION	71	D	150 - 155
72	X-RAY DIFFRACTION	72	D	156 - 165
73	X-RAY DIFFRACTION	73	D	166 - 179
74	X-RAY DIFFRACTION	74	D	180 - 189
75	X-RAY DIFFRACTION	75	D	190 - 207
76	X-RAY DIFFRACTION	76	D	208 - 216
77	X-RAY DIFFRACTION	77	D	217 - 237
78	X-RAY DIFFRACTION	78	D	238 - 257
79	X-RAY DIFFRACTION	79	D	258 - 266
80	X-RAY DIFFRACTION	80	D	267 - 274

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News

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Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

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Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

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