PDB-3isr: The Crystal Structure of a Putative Cysteine Protease from Cytoph...

ID or keywords:

Entry

Database: PDB / ID: 3isr

Title

The Crystal Structure of a Putative Cysteine Protease from Cytophaga hutchinsonii to 1.9A

Components

Transglutaminase-like enzymes, putative cysteine protease

Keywords

HYDROLASE /

Transglutaminase /

cysteine /

protease /

cytophaga / hutchinsonii / PSI / MCSG /

Structural Genomics / Midwest Center for Structural Genomics /

Protein Structure Initiative

Function / homology

Function and homology information

peptidase activity
Similarity search - Function

Biological species

Cytophaga hutchinsonii (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON / Resolution: 1.9 Å

Authors

Stein, A.J. / Bigelow, L. / Trevino, D. / Buck, K. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)

Citation

Journal: To be Published
Title: The Crystal Structure of a Putative Cysteine Protease from Cytophaga hutchinsonii to 1.9A
Authors: Stein, A.J. / Bigelow, L. / Trevino, D. / Buck, K. / Joachimiak, A.

History

Deposition	Aug 27, 2009	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 8, 2009	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.2	Nov 1, 2017	Group: Refinement description / Category: software

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3isr.cif.gz	244.4 KB	Display	PDBx/mmCIF format
PDB format	pdb3isr.ent.gz	209 KB	Display	PDB format
PDBx/mmJSON format	3isr.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/is/3isr ftp://data.pdbj.org/pub/pdb/validation_reports/is/3isr	HTTPS FTP

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Related structure data

Similar structure data	4bub-d 2yw3-d 3vpd-1 4epl-2 6ii0-d 4hdh-d 4h5f-d 1nj2-1 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: APC62855

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#209 - May 2017 Tissue Transglutaminase and Celiac Disease similarity (3)

Deposited unit

A: Transglutaminase-like enzymes, putative cysteine protease

B: Transglutaminase-like enzymes, putative cysteine protease

C: Transglutaminase-like enzymes, putative cysteine protease

D: Transglutaminase-like enzymes, putative cysteine protease

133 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author

2

A: Transglutaminase-like enzymes, putative cysteine protease

B: Transglutaminase-like enzymes, putative cysteine protease

defined by author&software
66.3 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: Transglutaminase-like enzymes, putative cysteine protease

D: Transglutaminase-like enzymes, putative cysteine protease

defined by author&software
66.3 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	90.716, 115.240, 131.262
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Details

authors state that biological unit is the same as asymmetric unit.

#1: Protein	Transglutaminase-like enzymes, putative cysteine protease Mass: 33159.617 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: pMCSG19 / Source: (gene. exp.) Cytophaga hutchinsonii (bacteria) / Strain: ATCC 33406 / Gene: CHU_2601, CHU_261 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q11RW0, UniProt: A0A6N4STR6*PLUS
#2: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 565 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

Transglutaminase-like enzymes, putative cysteine protease

Mass: 33159.617 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: pMCSG19 / Source: (gene. exp.)

Cytophaga hutchinsonii (bacteria) / Strain: ATCC 33406 / Gene: CHU_2601, CHU_261 / Production host:

Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q11RW0, UniProt: A0A6N4STR6*PLUS

#2: Water

ChemComp-HOH / water /

Water

Mass: 18.015 Da / Num. of mol.: 565 / 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: 54.5 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion / pH: 6.9 Details: 20% PEG 3350, 0.2M Sodium thiocyanate, pH 6.9, vapor diffusion, temperature 289K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 19-ID / Wavelength: 0.9794 Å

Detector

Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 7, 2009

Radiation

Monochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.9794 Å / Relative weight: 1

Reflection

Resolution: 1.9→50 Å / Num. obs: 108506 / % possible obs: 99.5 % / Redundancy: 4.9 % / R_merge(I) obs: 0.073 / Χ²: 1.54 / Net I/σ(I): 8.7

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique all	Χ²	Diffraction-ID	% possible all
1.9-1.97	4.9	0.689	10752	0.873	1	100
1.97-2.05	5	0.445	10786	0.863	1	100
2.05-2.14	5	0.294	10783	0.875	1	100
2.14-2.25	5	0.209	10795	0.918	1	100
2.25-2.39	5	0.154	10829	0.963	1	99.9
2.39-2.58	5	0.114	10840	1.04	1	99.9
2.58-2.84	5	0.087	10845	1.291	1	99.7
2.84-3.25	4.9	0.073	10866	2.08	1	99.6
3.25-4.09	4.8	0.056	10945	2.891	1	99.3
4.09-50	4.8	0.049	11065	3.675	1	97.2

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
REFMAC	refmac_5.5.0102	refinement
PDB_EXTRACT	3.004	data extraction
SBC-Collect		data collection
HKL-3000		data reduction
HKL-3000		data scaling
SHELX		phasing
MLPHARE		phasing
DM		phasing
ARP/wARP		model building
Coot		model building

Refinement

Resolution: 1.9→48.28 Å / Cor.coef. F_o:F_c: 0.962 / Cor.coef. F_o:F_c free: 0.949 / WR_factor R_free: 0.22 / WR_factor R_work: 0.187 / SU B: 6.816 / SU ML: 0.09 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.139 / ESU R Free: 0.129 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.22	5394	5 %	RANDOM
R_work	0.187	-	-	-
obs	0.189	108299	99.26 %	-

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: 16.899 Å²

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

Refinement step

Cycle: LAST / Resolution: 1.9→48.28 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8923	0	0	565	9488

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.022	9177
X-RAY DIFFRACTION	r_angle_refined_deg	1.207	1.935	12526
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.905	5	1157
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	37.168	23.661	407
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.823	15	1379
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	13.169	15	43
X-RAY DIFFRACTION	r_chiral_restr	0.084	0.2	1439
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.021	7033
X-RAY DIFFRACTION	r_mcbond_it	0.562	1.5	5751
X-RAY DIFFRACTION	r_mcangle_it	1.033	2	9299
X-RAY DIFFRACTION	r_scbond_it	1.808	3	3426
X-RAY DIFFRACTION	r_scangle_it	2.74	4.5	3221

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	Num. reflection all	% reflection obs (%)
1.898-1.947	0.295	401	0.267	7310	7951	96.982
1.947-2	0.254	406	0.239	7321	7761	99.562
2-2.058	0.27	352	0.209	7222	7601	99.645
2.058-2.122	0.244	333	0.196	6990	7329	99.918
2.122-2.191	0.234	352	0.189	6803	7164	99.874
2.191-2.268	0.237	331	0.183	6556	6896	99.869
2.268-2.353	0.215	349	0.186	6290	6648	99.865
2.353-2.449	0.225	328	0.184	6109	6445	99.876
2.449-2.558	0.234	304	0.189	5835	6152	99.789
2.558-2.682	0.262	321	0.192	5571	5906	99.763
2.682-2.827	0.239	271	0.197	5352	5633	99.822
2.827-2.997	0.241	258	0.191	5061	5338	99.644
2.997-3.204	0.209	256	0.191	4757	5036	99.543
3.204-3.459	0.217	217	0.178	4455	4699	99.425
3.459-3.787	0.204	193	0.178	4097	4332	99.03
3.787-4.231	0.208	207	0.165	3688	3927	99.185
4.231-4.879	0.169	174	0.152	3281	3520	98.153
4.879-5.961	0.189	158	0.183	2784	2987	98.493
5.961-8.366	0.21	102	0.216	2203	2363	97.545
8.366-48.282	0.247	81	0.214	1220	1419	91.684

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	7.7658	-0.9747	-7.0757	0.1261	0.8551	6.7572	0.3545	-0.0182	0.5137	-0.0131	0.0438	-0.0611	-0.6152	-0.2725	-0.3983	0.5387	0.0536	-0.0218	0.4883	-0.0498	0.5041	-16.6892	-7.0525	19.7812
2	11.7896	-8.9132	-1.9856	8.4655	1.3392	2.7399	0.2341	0.645	0.2288	-0.2516	-0.3645	-0.3584	0.0069	0.3036	0.1305	0.226	-0.0303	0.0085	0.2155	0.0388	0.1033	3.7866	-18.9145	10.4681
3	7.052	-3.4713	0.064	4.717	0.4401	3.2088	0.0764	0.181	-0.1103	-0.1397	-0.1041	0.055	0.1895	0.0497	0.0277	0.18	-0.0502	-0.0176	0.1117	0.0029	0.0417	-0.0529	-22.5246	20.1337
4	4.2614	-1.4335	-1.1298	1.4824	0.613	2.5467	0.1205	0.3942	-0.1901	-0.2174	-0.1672	0.1327	0.294	0.051	0.0467	0.2615	-0.0291	-0.0354	0.212	-0.0403	0.1709	-2.612	-27.4691	12.0223
5	2.7233	-0.7175	-0.3983	3.0737	0.8031	2.9216	-0.017	0.1158	-0.19	-0.0869	0.0123	-0.0999	0.349	0.2954	0.0047	0.1843	0	-0.0297	0.1747	-0.0013	0.1277	3.9366	-27.4542	20.0812
6	1.8494	-1.7395	-1.8117	4.1025	3.7748	5.1273	-0.0724	0.1445	-0.0483	-0.0941	-0.1786	0.4026	0.0828	-0.2541	0.2511	0.1206	-0.0207	-0.014	0.1858	0.0251	0.1475	-11.807	-10.9043	21.5136
7	1.5058	-1.8897	0.9358	6.2695	-2.6877	1.2065	-0.1765	-0.2417	0.084	0.5151	0.2694	0.3755	-0.2138	-0.2351	-0.093	0.2558	0.0328	0.0424	0.365	-0.029	0.2507	-10.5883	-5.8646	46.0596
8	1.9888	-0.2714	-0.9767	2.1083	-0.1131	1.2817	-0.0162	-0.1642	0.0456	0.1578	-0.0365	-0.157	0.0514	0.013	0.0527	0.092	-0.009	-0.0204	0.1047	0.02	0.0338	6.4258	-10.2634	41.1733
9	15.8149	-4.6321	4.6085	4.8801	0.2265	2.054	-0.5312	-0.8542	0.6459	-0.0081	0.2018	0.0346	-0.2799	-0.2873	0.3294	0.4214	0.0155	-0.0413	0.192	-0.074	0.2019	3.9437	5.6541	44.4475
10	4.1783	-0.4274	-1.3852	1.8334	-0.1537	2.9547	0.0175	0.0778	0.406	-0.0296	-0.0057	-0.114	-0.252	0.0156	-0.0119	0.1119	-0.0206	-0.0489	0.0633	0.0213	0.1101	4.0263	2.8115	30.8901
11	2.2621	2.8061	2.2818	5.4773	0.4036	5.2738	0.02	0.1147	-0.1451	-0.0575	0.0941	-0.2535	0.1435	0.1639	-0.114	0.0671	-0.009	-0.0204	0.1267	0.0408	0.1567	15.0361	-5.3458	32.6977
12	2.3751	0.9671	-0.0736	2.7036	0.128	2.215	-0.0596	0.0394	0.1194	0.0168	0.0081	-0.1121	-0.0074	0.0383	0.0514	0.0438	0.0065	-0.0279	0.039	0.019	0.0521	5.2523	-4.917	33.629
13	1.4233	-0.5254	0.3441	2.5363	0.8914	2.41	-0.0555	0.1412	0.1152	-0.2236	0.0187	0.0168	-0.0612	-0.0487	0.0368	0.0581	-0.0095	-0.0177	0.0983	0.0126	0.0614	-3.6536	-6.4178	25.632
14	1.4827	-0.6073	1.1557	3.5837	0.0283	2.0302	-0.0117	0.0043	0.2664	-0.1455	-0.0555	0.2119	-0.0769	-0.0006	0.0672	0.0956	0.0051	-0.0019	0.1148	-0.0002	0.113	-4.5777	-4.8327	22.1987
15	9.2651	-0.1982	2.2514	4.6199	0.357	6.1521	0.0501	-0.3448	-0.2207	0.1089	-0.0237	-0.0794	0.379	0.1434	-0.0264	0.1002	-0.0072	0.0042	0.0668	0.0243	0.0289	3.3894	-15.4709	32.6153
16	3.6752	-3.2035	-0.8083	7.1068	1.994	4.2668	0.0164	0.1355	0.366	-0.0776	0.0142	-0.5732	-0.001	0.3168	-0.0307	0.1507	-0.0219	0.0044	0.2012	0.0192	0.1064	10.4621	-22.2063	22.5754
17	28.5147	-19.8451	10.9338	13.8889	-7.448	4.5892	0.184	0.3381	1.2276	-0.1668	-0.2619	-1.0334	-0.0931	0.2471	0.0779	0.4162	-0.1092	0.0778	0.4398	0.0226	0.4671	10.7231	-16.8552	10.4341
18	0.2418	-0.0388	-0.8571	1.8811	1.9107	4.7584	-0.0189	0.1008	0.0687	-0.3963	-0.1146	0.3281	-0.3952	-0.4284	0.1335	0.2868	0.0259	-0.088	0.2835	0.0137	0.3183	-10.8411	-2.1595	16.2405
19	0.0031	0.0009	0.0008	0.0006	-0.0005	0.0017	-0.0052	-0.0112	0.0445	0.011	-0.0086	0.0123	-0.0286	0.0148	0.0138	0.7549	-0.0463	-0.006	0.4817	-0.0505	0.6912	-10.1654	9.2487	32.6922
20	7.905	-1.9804	-4.2483	11.5038	6.3386	13.5972	0.0099	-0.1527	-0.0868	-0.3555	-0.2732	0.6715	0.0989	-0.6475	0.2633	0.04	0.0267	-0.0312	0.1942	-0.0002	0.1337	-13.3221	-4.5854	29.8936
21	2.6824	0.6412	1.1282	2.2971	5.2876	13.6252	0.0171	-0.3798	-0.344	0.3506	0.1075	-0.0038	0.3663	-0.0105	-0.1246	0.4603	-0.0091	0.0037	0.2329	0.0662	0.385	9.6792	-49.0493	48.3299
22	1.2316	-0.7537	-0.5781	9.3178	1.9737	0.9544	-0.0914	-0.3413	0.0362	0.1507	0.13	-0.0214	0.0676	-0.0808	-0.0386	0.2971	-0.0143	-0.0049	0.2831	0.0334	0.1317	5.7698	-24.1301	63.6029
23	2.943	-1.6527	-0.6431	10.901	1.4315	2.1947	0.0071	-0.1518	-0.1183	0.1995	-0.0491	0.1332	-0.0335	-0.2593	0.042	0.1685	-0.0196	0.0174	0.2167	0.0474	0.0364	0.3955	-23.4946	54.913
24	1.8925	0.5538	-0.6406	2.7868	2.0211	2.2076	-0.0101	-0.164	-0.1409	0.1512	-0.145	0.1265	0.1381	-0.2741	0.1551	0.3353	-0.0384	0.0426	0.4639	0.0628	0.1527	-5.0482	-24.1909	63.1141
25	2.853	-1.1621	-1.1351	3.1768	1.2634	2.4807	0.0314	0.0497	-0.0574	-0.0601	-0.1162	0.2563	-0.1155	-0.3762	0.0848	0.2018	-0.0107	0.0172	0.2589	0.0356	0.1094	-3.609	-20.6733	51.2613
26	4.661	0.1857	0.6261	22.1883	1.2682	4.7649	0.1479	-0.0514	0.3344	-0.2835	-0.164	-0.0283	-0.3628	-0.2795	0.0162	0.2687	0.0121	0.0292	0.3644	0.0098	0.103	0.1615	-10.3472	66.2376
27	3.4551	-4.2827	-4.6993	5.9966	6.536	7.616	-0.1519	-0.1713	-0.36	0.2577	-0.008	0.1815	0.2894	-0.0336	0.1598	0.2932	-0.0319	0.0035	0.22	0.0744	0.2074	5.1141	-38.0683	56.2088
28	0.0169	-0.0735	0.0323	0.5738	-0.7638	1.8597	0.0001	0.0593	0.0259	-0.1169	-0.2711	-0.281	0.3051	0.3418	0.2711	0.4808	0.0475	0.0082	0.4206	0.0562	0.4597	16.62	-41.5964	31.6534
29	3.3998	1.5123	1.2244	5.8746	1.9965	3.025	-0.0197	0.1648	-0.1486	-0.16	-0.0339	0.1237	0.1886	-0.1405	0.0536	0.1028	-0.0108	0.0084	0.0904	0.0305	0.0463	9.8791	-24.9991	33.3557
30	7.2171	-2.1734	-0.5573	13.7797	-1.0121	10.3504	-0.0301	0.5756	-0.2115	-0.7287	-0.0575	-0.31	0.2706	0.6123	0.0877	0.1255	-0.0318	0.0151	0.1757	0.0069	0.128	26.081	-22.5422	30.3444
31	11.3682	9.8733	-6.4529	8.9764	-5.7773	3.7394	-0.7294	0.6251	-1.013	-1.036	0.1536	-0.9966	0.5935	-0.1976	0.5758	0.5886	0.2706	0.0934	0.5251	-0.031	0.448	25.7223	-34.9255	31.6349
32	3.5965	-0.1818	-0.2264	5.3036	2.4174	3.201	-0.0145	-0.1303	-0.1375	0.1303	0.03	-0.3008	0.0402	0.1707	-0.0155	0.1151	0.0157	-0.0258	0.0939	0.081	0.1464	26.1186	-27.7422	45.2871
33	2.4875	0.5219	0.2946	1.722	0.3798	1.6752	0.0186	-0.0768	0.1326	0.0598	-0.0066	-0.1625	-0.058	0.0065	-0.012	0.0718	-0.002	-0.0135	0.0498	0.0396	0.0725	19.67	-21.2922	42.147
34	1.268	-0.3776	-1.2368	1.7032	0.5865	2.1164	-0.0405	-0.555	0.0428	0.4608	0.1821	-0.312	0.061	0.2351	-0.1417	0.3081	0.0032	-0.0527	0.3617	0.0173	0.2053	13.6754	-29.29	56.8985
35	1.517	-0.0449	0.9291	2.5596	0.3089	2.9569	0.0918	-0.1099	-0.2381	0.1493	-0.0382	-0.1508	0.1824	-0.0755	-0.0536	0.1446	-0.0246	0.0017	0.0625	0.0438	0.0905	15.9116	-33.6784	44.4073
36	3.3387	-1.661	0.0706	1.5259	-0.5941	0.6644	-0.1321	-0.2451	-0.2464	0.0631	0.1322	-0.0255	0.1255	-0.1501	-0.0001	0.2467	-0.0401	-0.0155	0.124	0.0801	0.126	10.4629	-33.8691	51.5293
37	2.4381	-2.8529	-2.9439	4.5351	4.2119	5.3508	0.1562	-0.1063	0.1556	-0.0446	-0.0269	-0.0933	-0.3692	-0.221	-0.1292	0.1947	-0.0042	-0.0027	0.2309	0.0098	0.1252	5.743	-15.8448	49.3537
38	2.6326	-6.435	4.6342	16.2982	-9.6576	13.193	-0.0664	-0.034	0.2028	0.0273	0.1014	-0.6432	-0.2387	0.0392	-0.035	0.32	-0.0435	0.0422	0.4222	-0.0101	0.3111	9.4006	-14.1222	64.6151
39	2.6516	-1.4279	-0.9524	2.2672	0.1742	0.9957	-0.2224	-0.3863	-0.3681	0.5121	0.086	0.1832	0.3986	-0.0206	0.1364	0.4716	-0.0407	-0.0136	0.3166	0.0991	0.2478	13.2222	-39.6878	61.149
40	4.2068	2.0672	1.1075	4.8322	-1.0678	7.7875	-0.3027	0.1242	-0.4247	-0.0758	0.1178	-0.451	0.3863	0.4762	0.1848	0.2548	0.0029	0.0097	0.0897	0.0406	0.223	18.6782	-41.7051	45.3621
41	26.472	-14.6426	28.5518	8.1239	-15.6892	31.3313	0.36	-0.0905	-0.5788	-0.1243	0.1192	0.3	0.7053	0.1008	-0.4792	0.3971	0.0285	0.1047	0.4802	-0.0159	0.5788	62.4039	-6.5544	20.9711
42	18.2395	-3.8802	1.3882	1.2667	0.5277	1.774	0.0301	0.485	-0.1971	-0.1904	-0.107	0.06	-0.1909	-0.1151	0.0769	0.3581	-0.0371	0.0373	0.3056	-0.0007	0.1577	42.1323	5.9009	12.1644
43	5.8354	-2.8149	-0.1689	4.9293	-0.5105	2.3985	-0.102	0.2721	-0.1017	-0.1655	0.053	-0.1732	-0.3116	-0.0284	0.049	0.2015	-0.044	0.0442	0.1559	0.0009	0.0927	46.4078	8.8304	22.3182
44	2.8743	-0.6254	1.6925	1.4524	-1.8442	3.1377	0.1518	0.3215	0.0409	-0.1925	-0.0843	-0.1176	-0.1434	0.1189	-0.0674	0.4498	0.0025	0.1094	0.2927	0.0529	0.2537	49.3746	13.8308	13.5567
45	3.0584	-0.7608	0.0206	4.0711	-0.9115	1.8328	-0.0469	0.0006	0.2377	0.0703	0.0462	-0.1896	-0.4367	-0.0891	0.0007	0.2175	-0.0199	0.044	0.1783	0.0037	0.1341	44.6478	13.7958	25.7058
46	29.5332	-12.5918	2.592	11.1631	-0.6202	2.6884	0.2192	0.3207	0.315	-0.3846	-0.0336	0.2757	-0.3817	-0.3231	-0.1857	0.4232	-0.0179	0.0406	0.3355	0.067	0.1381	36.2758	13.9279	10.4551
47	1.4755	-0.9339	0.6162	4.0747	-2.6336	3.5038	-0.0198	0.0415	-0.2766	-0.0517	-0.1238	-0.4898	-0.0531	0.4845	0.1436	0.1213	0.0052	0.0327	0.24	-0.007	0.3028	59.0865	-4.6779	24.8505
48	1.3727	-3.3202	-0.3983	9.1716	0.8743	0.1882	-0.1977	-0.3363	-0.0585	0.2774	0.2728	-0.2673	0.0564	0.2401	-0.075	0.3311	0.0552	-0.0534	0.4993	0.0573	0.4431	54.7852	-8.7199	46.998
49	3.3068	-0.2087	0.598	1.8293	-0.3098	2.8397	-0.0208	-0.2692	-0.1623	0.1281	-0.0488	-0.122	-0.0157	0.0593	0.0695	0.0805	0.0023	-0.0228	0.0993	0.0287	0.1197	38.6874	-3.1476	41.1549
50	9.6143	0.0263	-2.5579	0.5886	0.691	2.8843	-0.1544	-0.5932	-0.6111	0.2815	-0.0317	-0.1004	0.4447	0.2381	0.1861	0.2009	0.0385	-0.0334	0.1524	0.1066	0.315	43.2432	-18.8849	43.3938
51	4.494	0.5851	3.7221	1.684	1.6213	6.2041	-0.0454	-0.0884	-0.4019	-0.0643	-0.0395	-0.0374	0.2835	0.03	0.0849	0.1325	0.018	0.0345	0.107	-0.0019	0.3384	41.4745	-19.7819	31.7872
52	3.3659	-1.4283	0.0986	7.4574	1.9519	3.0597	0.0488	0.3846	-0.2966	-0.5662	-0.1681	0.1229	-0.0289	-0.1669	0.1193	0.1384	-0.0232	0.0062	0.1808	-0.0357	0.1809	31.4533	-9.8409	24.0722
53	2.1307	0.7484	0.2389	2.1071	0.2484	1.6611	-0.0178	0.0428	-0.3005	0.0222	0.0135	-0.1264	0.0669	-0.0172	0.0043	0.0529	0.0155	0.0063	0.0664	0.0113	0.1459	37.7222	-9.5848	34.1413
54	2.6613	-0.7267	-0.9574	2.95	-0.9399	3.5603	-0.0002	0.4508	-0.4215	-0.6155	0.0085	0.1058	0.3407	-0.1077	-0.0083	0.274	-0.0141	0.0414	0.2467	-0.069	0.2753	47.2539	-6.0731	17.7201
55	1.252	-0.3385	-0.9696	1.3938	-0.2181	1.7033	-0.0405	-0.0064	-0.1879	-0.0092	-0.0032	-0.2461	0.0386	0.2277	0.0437	0.102	0.0138	0.0236	0.1542	0.0066	0.2785	50.3624	-9.7503	29.6782
56	8.0497	-0.1516	-2.7859	2.5042	-0.6314	4.3434	0.0816	-0.1825	-0.0425	-0.0042	-0.0748	-0.197	-0.1599	0.0598	-0.0068	0.0959	-0.0033	0.0035	0.069	0.0001	0.1094	44.7274	1.2938	30.9465
57	3.8613	-3.8806	1.9776	9.4909	-2.9298	4.048	-0.0808	0.1476	-0.2428	-0.2057	0.1949	0.2898	-0.1727	-0.369	-0.1141	0.159	-0.0077	0.0098	0.2064	0.022	0.1179	36.5519	8.0252	24.581
58	12.2728	-9.003	-6.3899	12.7922	8.8312	7.5183	0.146	0.0413	-0.8644	-0.5372	-0.1638	0.462	-0.017	-0.2966	0.0177	0.3895	-0.0357	-0.047	0.4076	0.0465	0.2789	32.3394	6.5139	12.9922
59	6.3966	-5.075	-3.1692	7.731	2.2548	1.6314	0.1609	0.6354	-0.0007	-0.3053	-0.2102	-0.6004	-0.0627	-0.1727	0.0493	0.371	0.0443	0.0953	0.7043	-0.0369	0.3877	55.6243	-6.0945	12.6198
60	2.1596	1.7336	0.4044	2.2412	0.6663	5.1757	0.0194	-0.0609	-0.2452	-0.0914	-0.0866	-0.2291	0.4644	0.3309	0.0672	0.1384	0.0937	0.042	0.2102	0.0246	0.367	56.1095	-16.6152	29.0294
61	7.4763	-4.669	6.646	3.374	-5.0919	7.9142	0.0224	-0.3682	0.3432	0.1613	0.268	0.0556	-0.1827	-0.3124	-0.2904	0.5195	-0.0541	0.0144	0.3844	-0.1055	0.5133	33.4942	34.6792	48.5563
62	2.1608	-2.5085	1.0338	9.8487	-0.8259	0.5654	0.0187	-0.558	-0.0989	0.5401	0.0577	0.1293	0.0683	-0.151	-0.0764	0.4883	-0.027	-0.0172	0.6441	-0.0031	0.1449	38.5027	9.403	65.0797
63	2.3541	-1.4942	-0.4253	4.2082	-0.6014	1.8189	0.0101	-0.4822	-0.0113	0.3804	-0.0086	-0.333	0.1431	0.2791	-0.0016	0.2293	-0.0151	-0.1018	0.4143	0.0115	0.1365	44.2164	8.3132	56.266
64	2.2617	-0.7132	0.4881	3.635	-2.4163	1.7159	0.0516	-0.6058	-0.0833	0.4265	-0.1817	-0.2174	-0.0918	0.2592	0.1302	0.5261	-0.0026	-0.1195	0.6398	0.0173	0.3015	49.4219	7.9789	62.505
65	2.6296	-1.2826	1.3762	3.669	-1.1124	2.6521	0.0849	-0.3047	-0.0694	-0.0587	0.0826	-0.4443	0.2593	0.2918	-0.1675	0.2616	0.012	-0.0532	0.4336	0.0161	0.2669	47.5537	5.8301	52.004
66	4.6376	-4.6571	-3.0268	18.3452	2.9298	2.9779	-0.0219	-0.2971	-0.4535	0.5863	-0.0425	0.3799	-0.0281	0.3411	0.0643	0.4922	-0.0037	-0.1711	0.6414	0.1011	0.2853	44.3433	-6.2768	66.7148
67	5.5243	-3.4129	4.2189	5.8368	-5.0226	7.2841	-0.0233	-0.3986	0.5959	0.5138	-0.1071	-0.1479	-0.1934	0.3926	0.1304	0.2159	-0.0729	0.0295	0.2854	-0.1414	0.174	36.9929	24.6485	54.6406
68	15.9753	-16.0095	-10.071	16.1379	10.1196	6.373	0.4026	0.276	0.346	-0.4717	-0.2365	-0.1307	-0.2833	-0.0949	-0.1661	0.4405	-0.009	-0.018	0.3052	0.0846	0.547	28.5685	27.1913	31.6215
69	3.7226	0.6079	-1.1621	3.5061	-1.1094	3.3806	0.0328	0.1449	0.1285	-0.1945	-0.0353	-0.1286	-0.1193	0.192	0.0025	0.1049	0.0051	-0.0214	0.088	0.0036	0.0276	34.0512	10.2664	34.6801
70	4.5751	-0.0333	-0.4489	20.2	5.0875	7.0648	-0.1402	0.319	0.5249	-0.8151	0.0145	0.4636	-0.3921	-0.6667	0.1258	0.1403	0.0047	-0.0835	0.2385	0.0754	0.2031	17.5847	13.088	31.4288
71	3.3944	0.7354	-0.5132	4.6249	-0.8798	2.4265	0.1509	-0.1149	0.397	0.0724	-0.0445	0.5327	-0.1251	-0.1411	-0.1063	0.0737	0.0053	-0.009	0.1094	-0.0453	0.2014	18.587	16.0722	44.0641
72	3.3237	0.6916	-0.2483	2.0907	0.0313	1.6907	0.0494	-0.2981	-0.0986	0.128	-0.0925	0.1504	0.1298	-0.0136	0.0431	0.0695	-0.0036	-0.0101	0.0856	-0.0082	0.0449	25.5881	6.8833	44.4563
73	12.5682	-2.0693	-0.0252	9.4646	0.666	3.7129	-0.0316	-1.4199	-0.2654	0.6123	0.2661	0.8206	0.1542	-0.2995	-0.2344	0.3571	-0.0666	0.0456	0.5472	-0.0183	0.1296	29.5875	14.0297	61.6124
74	1.4585	-0.178	-0.4188	2.8741	-0.3108	2.7397	0.1034	-0.3012	0.3415	0.1331	-0.0734	0.1279	-0.0498	0.1064	-0.03	0.1191	-0.0285	-0.0081	0.1361	-0.0581	0.1339	28.9477	18.9747	45.7689
75	5.7358	-3.1047	-1.0872	5.2005	1.3496	2.4239	-0.0083	-0.3478	0.3255	0.2813	0.0384	0.0909	-0.0464	0.2515	-0.0301	0.1774	-0.0654	-0.0118	0.2458	-0.0863	0.0677	32.5819	19.5641	54.9573
76	7.3279	2.3271	0.5185	9.3333	0.6535	5.0027	-0.0294	-0.1037	-0.3281	-0.3576	0.1101	-0.4702	0.3048	0.2557	-0.0807	0.1365	0.0123	-0.0185	0.2001	-0.016	0.0849	36.6217	7.8328	43.8538
77	4.1201	-4.1577	2.1616	9.2246	-4.2491	5.3288	0.0573	-0.6111	-0.371	0.2615	0.0513	0.0952	0.351	0.2384	-0.1086	0.2399	0.0023	-0.1075	0.3597	0.0931	0.2118	40.0135	-1.5964	53.3551
78	0.887	-5.0235	-2.2655	30.571	11.7456	6.3491	-0.0495	-0.0189	-0.097	0.6041	0.0611	1.1096	-0.1051	0.0165	-0.0115	0.5386	-0.01	-0.0451	0.7392	0.0516	0.5608	34.3408	0.0542	65.8339
79	3.8793	-3.4709	-0.5081	6.2996	4.5665	5.4028	-0.3267	-0.3099	0.1801	0.1966	0.1035	0.1222	-0.1162	0.0076	0.2232	0.5023	-0.1168	0.0241	0.6775	-0.2517	0.3587	32.6236	25.0646	64.939
80	3.3503	0.4346	-0.9635	2.2206	-0.3698	3.8965	-0.0831	-0.2494	0.5162	0.1637	0.1023	0.1958	-0.3426	-0.173	-0.0193	0.211	-0.0293	0.034	0.1529	-0.0864	0.2671	25.3004	27.5749	49.2712

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	-3 - 3
2	X-RAY DIFFRACTION	2	A	4 - 13
3	X-RAY DIFFRACTION	3	A	14 - 32
4	X-RAY DIFFRACTION	4	A	33 - 47
5	X-RAY DIFFRACTION	5	A	48 - 70
6	X-RAY DIFFRACTION	6	A	71 - 86
7	X-RAY DIFFRACTION	7	A	87 - 101
8	X-RAY DIFFRACTION	8	A	102 - 119
9	X-RAY DIFFRACTION	9	A	120 - 128
10	X-RAY DIFFRACTION	10	A	129 - 154
11	X-RAY DIFFRACTION	11	A	155 - 164
12	X-RAY DIFFRACTION	12	A	165 - 190
13	X-RAY DIFFRACTION	13	A	191 - 220
14	X-RAY DIFFRACTION	14	A	221 - 233
15	X-RAY DIFFRACTION	15	A	234 - 239
16	X-RAY DIFFRACTION	16	A	240 - 249
17	X-RAY DIFFRACTION	17	A	250 - 256
18	X-RAY DIFFRACTION	18	A	257 - 271
19	X-RAY DIFFRACTION	19	A	272 - 276
20	X-RAY DIFFRACTION	20	A	277 - 282
21	X-RAY DIFFRACTION	21	B	-6 - 1
22	X-RAY DIFFRACTION	22	B	2 - 13
23	X-RAY DIFFRACTION	23	B	14 - 32
24	X-RAY DIFFRACTION	24	B	33 - 47
25	X-RAY DIFFRACTION	25	B	48 - 64
26	X-RAY DIFFRACTION	26	B	65 - 71
27	X-RAY DIFFRACTION	27	B	72 - 83
28	X-RAY DIFFRACTION	28	B	84 - 95
29	X-RAY DIFFRACTION	29	B	96 - 115
30	X-RAY DIFFRACTION	30	B	116 - 124
31	X-RAY DIFFRACTION	31	B	125 - 131
32	X-RAY DIFFRACTION	32	B	132 - 153
33	X-RAY DIFFRACTION	33	B	154 - 189
34	X-RAY DIFFRACTION	34	B	190 - 203
35	X-RAY DIFFRACTION	35	B	204 - 224
36	X-RAY DIFFRACTION	36	B	225 - 235
37	X-RAY DIFFRACTION	37	B	236 - 249
38	X-RAY DIFFRACTION	38	B	250 - 255
39	X-RAY DIFFRACTION	39	B	256 - 269
40	X-RAY DIFFRACTION	40	B	270 - 282
41	X-RAY DIFFRACTION	41	C	-2 - 3
42	X-RAY DIFFRACTION	42	C	4 - 13
43	X-RAY DIFFRACTION	43	C	14 - 32
44	X-RAY DIFFRACTION	44	C	33 - 46
45	X-RAY DIFFRACTION	45	C	47 - 64
46	X-RAY DIFFRACTION	46	C	65 - 72
47	X-RAY DIFFRACTION	47	C	73 - 86
48	X-RAY DIFFRACTION	48	C	87 - 101
49	X-RAY DIFFRACTION	49	C	102 - 117
50	X-RAY DIFFRACTION	50	C	118 - 135
51	X-RAY DIFFRACTION	51	C	136 - 145
52	X-RAY DIFFRACTION	52	C	146 - 157
53	X-RAY DIFFRACTION	53	C	158 - 190
54	X-RAY DIFFRACTION	54	C	191 - 203
55	X-RAY DIFFRACTION	55	C	204 - 230
56	X-RAY DIFFRACTION	56	C	231 - 239
57	X-RAY DIFFRACTION	57	C	240 - 248
58	X-RAY DIFFRACTION	58	C	249 - 255
59	X-RAY DIFFRACTION	59	C	256 - 266
60	X-RAY DIFFRACTION	60	C	267 - 282
61	X-RAY DIFFRACTION	61	D	-6 - 1
62	X-RAY DIFFRACTION	62	D	2 - 13
63	X-RAY DIFFRACTION	63	D	14 - 32
64	X-RAY DIFFRACTION	64	D	33 - 50
65	X-RAY DIFFRACTION	65	D	51 - 63
66	X-RAY DIFFRACTION	66	D	64 - 71
67	X-RAY DIFFRACTION	67	D	72 - 86
68	X-RAY DIFFRACTION	68	D	87 - 95
69	X-RAY DIFFRACTION	69	D	96 - 117
70	X-RAY DIFFRACTION	70	D	118 - 128
71	X-RAY DIFFRACTION	71	D	129 - 149
72	X-RAY DIFFRACTION	72	D	150 - 192
73	X-RAY DIFFRACTION	73	D	193 - 203
74	X-RAY DIFFRACTION	74	D	204 - 223
75	X-RAY DIFFRACTION	75	D	224 - 233
76	X-RAY DIFFRACTION	76	D	234 - 239
77	X-RAY DIFFRACTION	77	D	240 - 249
78	X-RAY DIFFRACTION	78	D	250 - 256
79	X-RAY DIFFRACTION	79	D	257 - 266
80	X-RAY DIFFRACTION	80	D	267 - 282

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News

-
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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