PDB-3fm5: X-ray crystal structure of transcriptional regulator (MarR family...

ID or keywords:

Entry

Database: PDB / ID: 3fm5

Title

X-ray crystal structure of transcriptional regulator (MarR family) from Rhodococcus sp. RHA1

Components

Transcriptional regulator

Keywords

TRANSCRIPTION REGULATOR / Transcriptional regulator / MCSG / PF04017 / PSI / MarR / Structural Genomics / Protein Structure Initiative / Midwest Center for Structural Genomics

Function / homology

Function and homology information

DNA-binding transcription factor activity / metal ion binding
Similarity search - Function

Biological species

Rhodococcus jostii (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2 Å

Authors

Nocek, B. / Xu, X. / Zheng, H. / Savchenko, A. / Edwards, A.M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)

Citation

Journal: To be Published
Title: X-ray crystal structure of transcriptional regulator (MarR family) from Rhodococcus sp. RHA1
Authors: Nocek, B. / Xu, X. / Zheng, H. / Savchenko, A. / Edwards, A.M. / Joachimiak, A.

History

Deposition	Dec 19, 2008	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 3, 2009	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Source and taxonomy / Version format compliance

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3fm5.cif.gz	232.6 KB	Display	PDBx/mmCIF format
PDB format	pdb3fm5.ent.gz	202.5 KB	Display	PDB format
PDBx/mmJSON format	3fm5.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3fm5_validation.pdf.gz	478.4 KB	Display	wwPDB validaton report
Full document	3fm5_full_validation.pdf.gz	490.1 KB	Display
Data in XML	3fm5_validation.xml.gz	25.5 KB	Display
Data in CIF	3fm5_validation.cif.gz	35.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/fm/3fm5 ftp://data.pdbj.org/pub/pdb/validation_reports/fm/3fm5	HTTPS FTP

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Related structure data

Similar structure data	2h0j-d 5ep4-d 5ext-d 4eze-2 3ec1-2 4ht6-d 4q0y-1 2w50-d 2zmf-d 3f65-1 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: APC5972

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Transcriptional regulator

B: Transcriptional regulator

C: Transcriptional regulator

D: Transcriptional regulator

hetero molecules

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

1

A: Transcriptional regulator

C: Transcriptional regulator

hetero molecules

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

2

B: Transcriptional regulator

D: Transcriptional regulator

hetero molecules

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

3

Idetical with deposited unit
defined by software

Unit cell

Length a, b, c (Å)	75.114, 75.114, 213.610
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	92
Space group name H-M	P4₁2₁2

Components on special symmetry positions

ID	Model	Components
1	1	B-234- HOH
2	1	C-190- HOH

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Protein , 1 types, 4 molecules ABCD

#1: Protein	Transcriptional regulator Mass: 16355.884 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodococcus jostii (bacteria) / Strain: RHA1 / Gene: RHA1_ro05125 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: Q0S6D0

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Non-polymers , 5 types, 300 molecules

#2: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₈O₃
#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 294 / 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: 2.3 Å³/Da / Density % sol: 46.58 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.2M Mg(OAC), 20% PEG 3350, 4% Glycerol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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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: Jan 28, 2007 / Details: Mirrors
Radiation	Monochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9794 Å / Relative weight: 1
Reflection	Resolution: 1.96→40 Å / Num. obs: 44238 / % possible obs: 97.7 % / Observed criterion σ(I): 2 / Redundancy: 12.2 % / B_iso Wilson estimate: 39 Å² / R_merge(I) obs: 0.085 / Net I/σ(I): 23.7
Reflection shell	Resolution: 1.96→1.99 Å / Redundancy: 6.8 % / R_merge(I) obs: 0.603 / Mean I/σ(I) obs: 3 / Num. unique all: 2024 / % possible all: 91.9

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Processing

Software

Name	Classification
SBC-Collect	data collection
HKL-3000	phasing
SHELXD	phasing
Coot	model building
MLPHARE	phasing
PHENIX	model building
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHENIX	phasing

Refinement

Method to determine structure:

SAD / Resolution: 2→37.136 Å / SU ML: 0.31 / σ(F): 1.89 / Stereochemistry target values: MAXIMUM LIKELIHOOD

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2398	2198	4.99 %	RANDOM
R_work	0.1941	-	-	-
all	0.21	43756	-	-
obs	0.1964	41566	95.85 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 52.7 Å² / k_sol: 0.336 e/Å³

Refinement step

Cycle: LAST / Resolution: 2→37.136 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4072	0	22	294	4388

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004	4174
X-RAY DIFFRACTION	f_angle_d	0.706	5647
X-RAY DIFFRACTION	f_dihedral_angle_d	14.683	1553
X-RAY DIFFRACTION	f_chiral_restr	0.047	672
X-RAY DIFFRACTION	f_plane_restr	0.002	753

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 27

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	% reflection obs (%)
2-2.0253	0.3364	133	0.2564	2487	89
2.0253-2.052	0.2685	142	0.2312	2506	91
2.052-2.0801	0.2357	156	0.2253	2493	90
2.0801-2.1098	0.2736	124	0.2141	2558	92
2.1098-2.1413	0.286	134	0.2222	2538	91
2.1413-2.1748	0.2512	126	0.2187	2527	92
2.1748-2.2104	0.2833	160	0.2112	2503	90
2.2104-2.2485	0.2193	146	0.2055	2541	93
2.2485-2.2894	0.213	124	0.1983	2511	91
2.2894-2.3334	0.2771	138	0.2009	2557	91
2.3334-2.3811	0.2397	126	0.2269	2563	93
2.3811-2.4328	0.2575	103	0.2196	2747	97
2.4328-2.4894	0.2713	129	0.2203	2718	98
2.4894-2.5516	0.228	154	0.22	2704	98
2.5516-2.6206	0.2662	127	0.2191	2754	98
2.6206-2.6977	0.2404	123	0.2251	2766	99
2.6977-2.7847	0.3131	152	0.2203	2756	99
2.7847-2.8842	0.2137	165	0.2118	2736	99
2.8842-2.9997	0.2804	180	0.2137	2742	100
2.9997-3.1361	0.265	171	0.219	2753	100
3.1361-3.3014	0.2326	126	0.2039	2771	100
3.3014-3.5081	0.2219	153	0.1849	2759	100
3.5081-3.7787	0.2008	177	0.1618	2752	100
3.7787-4.1585	0.1948	106	0.152	2807	100
4.1585-4.7592	0.1856	145	0.1452	2783	100
4.7592-5.992	0.2276	139	0.1722	2772	100
5.992-37.142	0.2519	113	0.1805	2742	97

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	-7.1368	6.0021	7.6931	6.6677	-3.0386	7.8819	0.6163	0.6769	-1.8671	-0.7114	0.1635	-2.4874	0.5505	2.0676	-0.7535	0.4195	0.132	0.1132	0.5736	-0.2016	1.1255	13.0762	28.8289	101.1365
2	1.062	0.9911	0.2508	0.9415	0.8388	0.4366	-0.0694	0.1223	-0.3485	0.2521	0.0719	-0.6871	0.2183	0.1169	-0.0417	0.3877	-0.0431	-0.012	0.2782	-0.0362	0.4345	3.6106	32.3418	98.814
3	7.415	-0.9605	2.7844	0.2773	-0.8347	2.085	-0.032	-0.7259	-0.2903	-0.0934	0.1592	0.0355	0.0786	-0.3217	-0.1128	0.3516	-0.045	0.0387	0.2871	-0.0121	0.2953	-7.0445	38.2889	100.4416
4	8.606	-2.2637	-4.6074	8.8593	7.1681	1.4386	-0.7062	-2.3828	0.7687	2.1537	0.3644	-0.714	0.4133	1.012	0.209	0.4584	0.0975	-0.0398	0.6869	-0.0808	0.282	-17.1713	43.6082	100.2125
5	1.9795	5.0118	2.9733	1.254	6.0753	8.4842	0.0313	0.6024	1.2874	0.2891	-1.422	0.6178	0.4732	-1.9818	1.1947	0.421	-0.0855	0.0392	0.971	-0.1025	0.4651	-24.0278	42.3758	98.3978
6	1.9914	3.863	-1.7128	6.6396	-5.1289	2.1338	0.2326	-0.94	-0.4464	0.4204	-1.7106	0.4053	0.4972	-0.0002	1.1295	0.4716	-0.0839	0.0796	0.8301	-0.0872	0.4307	-20.3831	36.0022	93.5962
7	1.9162	-5.1403	2.0935	6.3813	-3.3828	8.6346	-0.1862	-1.2308	0.6809	-1.6996	0.8725	0.6463	-0.5621	-3.1971	-0.3904	0.5146	-0.2867	-0.0865	1.1313	-0.1611	0.4834	-23.7076	36.5929	85.639
8	6.6642	-4.471	4.8447	1.7674	-6.9803	9.8517	0.9413	2.9947	-0.3536	-0.4739	-0.9393	0.9541	0.6638	2.8563	0.1879	0.8911	0.0012	-0.2052	1.7836	-0.2892	0.7329	-25.8747	34.8784	78.4174
9	-0.6327	-0.9204	-1.324	3.4372	-1.1032	-2.3445	-0.5154	0.3726	-0.87	-0.7279	0.9269	0.3918	-0.1515	-0.246	-0.1981	1.3398	-0.479	0.5639	1.2498	-0.481	1.3056	-23.8283	25.36	85.9713
10	2.1059	4.5062	2.0299	2.1119	-8.5398	1.8958	-0.9676	0.2494	-3.8599	2.7668	-2.9459	-0.0476	2.0238	-1.048	3.6023	1.6067	-0.5441	0.4826	0.7456	-0.2478	1.309	-19.4422	25.6838	91.2993
11	2.012	5.6809	-6.6017	7.929	-2.9591	5.2503	-0.9586	0.1104	-1.5082	-0.0319	-0.242	1.0941	1.1499	-2.4504	1.0067	1.0144	-0.3929	0.2818	0.988	0.0159	1.04	-27.1936	27.7481	94.4317
12	2.1053	-8.6812	3.8661	9.5421	2.0075	2.0419	0.0996	2.0326	-2.8227	0.5544	1.5802	2.7104	-0.905	-2.0428	-1.6467	0.5318	-0.2412	0.0018	1.5458	-0.0871	1.0248	-33.1619	35.9605	93.9631
13	5.7059	-0.8842	3.526	1.3839	-0.5473	7.4184	-0.0477	-2.455	1.1153	-1.2257	-0.1795	0.1328	0.2694	-3.2105	0.3152	0.5224	-0.3914	-0.0504	1.1508	-0.2915	0.7372	-33.5537	34.4989	87.44
14	1.2908	-3.1823	1.6161	-5.6212	-2.6048	1.7932	0.4827	-0.0343	-0.1488	-1.0478	-0.5303	2.4791	-0.8043	-0.8769	0.0083	0.6022	-0.1313	-0.1953	0.9886	-0.1033	1.0239	-31.8665	40.6275	84.551
15	8.8096	2.7495	7.4193	9.2885	-8.5644	1.4393	-1.1441	1.3861	1.4044	-1.2451	0.252	0.3813	0.1312	-2.0539	0.6045	0.4426	0.1038	-0.0672	1.4306	0.1434	0.5679	-24.4811	45.9072	87.0091
16	0.7154	1.1121	3.8087	1.9896	-0.024	1.6854	-0.667	0.8348	1.195	-0.1461	0.5432	-0.551	-0.222	-0.7188	0.1857	0.3627	0.0342	-0.0066	0.4981	0.1196	0.814	-13.9445	47.3627	92.9645
17	7.7118	-2.5247	4.0841	7.8498	2.912	-7.9386	-0.0633	1.2126	2.3777	-1.7692	-0.654	2.5069	-0.361	-0.6066	0.4217	0.3835	-0.0105	0.0772	0.0999	-0.144	0.7512	-5.619	47.9203	95.5649
18	2.8406	-5.655	-1.1632	2.6529	0.8959	-5.9683	-0.0606	1.6112	0.0993	-1.1617	-0.39	0.1162	-0.2604	-0.4684	0.2883	0.3237	-0.0945	0.0046	0.4178	0.0607	0.2238	1.1736	47.0598	86.9054
19	3.5948	1.7076	2.5241	0.976	-0.4394	-7.7403	-0.0046	-0.0913	-0.4442	0.1725	-0.2071	0.2414	0.1957	-0.4674	0.1948	0.376	-0.1182	0.0037	0.4498	-0.0012	0.2248	-1.7778	40.1106	85.4835
20	5.9527	7.2001	3.745	5.8333	-7.1559	3.1963	-0.8251	0.9338	-0.1707	-3.0205	0.4419	0.4288	0.9321	0.0162	-0.0489	0.6312	-0.1634	0.0151	0.4277	-0.1505	0.2565	-4.6139	31.0921	83.5015
21	7.4617	-4.7153	4.9909	7.0518	2.2698	7.3043	1.4612	1.8901	-1.3812	-1.8794	-0.3992	-0.0177	-0.2866	0.9704	-1.0092	0.5483	0.1451	0.0362	0.5352	-0.2336	0.4864	-12.7883	-4.855	93.3303
22	2.5515	-0.2546	-1.7001	2.5421	1.1561	1.3289	0.0139	-0.1222	-0.1263	-0.1581	-0.0696	-0.1013	0.215	0.103	0.043	0.2956	-0.0146	0.0317	0.3098	-0.0443	0.2888	-17.6958	1.9694	103.1184
23	-0.7725	0.0107	0.1207	0.8761	-0.3756	4.4824	0.3066	-0.1084	-0.2599	0.1599	-0.1088	0.3398	-0.0262	-0.6822	0.0079	0.2349	-0.0442	0.0128	0.2926	-0.0562	0.2745	-25.0962	6.0678	116.4695
24	2.3615	-0.4004	-1.6652	2.5297	0.3517	2.9194	0.2457	0.2807	0.0726	-0.0698	-0.0653	0.2959	-0.4937	-0.5512	-0.161	0.2981	0.016	0.0337	0.3589	0.0018	0.2617	-26.9631	14.714	116.9981
25	8.0888	-7.1589	-3.6857	2.2767	-1.0055	9.8382	0.356	-0.4822	1.228	0.9155	0.6737	-2.7951	-2.2155	1.318	-0.9491	0.8915	-0.2619	0.2332	0.4275	-0.0911	0.6995	-19.4307	26.7209	117.1256
26	0.4011	2.2481	1.3325	8.6164	6.0063	2.2387	0.5385	-0.2546	0.877	-0.413	0.724	0.944	-3.442	1.0532	-1.1642	1.2212	-0.1301	0.3232	0.7198	0.2406	0.7155	-24.1417	31.1074	110.4103
27	6.9664	-1.5872	9.6493	2.2657	-0.3027	4.1357	1.6082	0.6439	-0.2065	-0.304	-0.2584	0.3838	1.394	-1.8713	-0.8329	0.5964	0.052	0.1491	0.5787	0.0886	0.4336	-24.508	21.5113	105.0554
28	-3.7407	3.2386	0.6822	0.0331	-3.8729	2.1289	0.6611	0.8484	0.2366	-0.0963	0.7838	0.9106	-0.1159	-2.4357	-1.1748	0.4355	0.1682	-0.0092	0.782	0.1214	0.4856	-32.3652	21.8568	107.0958
29	5.762	2.0287	-0.859	1.7537	1.6071	1.8334	0.6253	0.5119	-0.0164	-0.6761	0.0641	0.9336	0.1818	-1.2196	-0.4535	0.5436	0.1632	0.0942	0.5727	0.0242	0.5443	-34.1788	23.0407	116.1906
30	6.567	1.1447	-0.161	2.6325	-6.1719	7.768	0.4954	-0.3462	0.7466	0.8606	0.2846	1.0937	-0.9142	-1.2566	-0.7145	0.6471	0.1749	0.1903	0.3677	0.1332	0.4485	-33.1938	25.0967	120.0319
31	1.9755	8.4082	7.2211	7.1254	1.9236	1.9423	-1.3635	-1.0698	3.1248	-1.2543	0.4192	2.1979	-1.3034	0.3402	0.9662	1.0718	-0.0189	-0.082	0.6975	0.1401	1.2438	-29.7325	39.6934	111.5721
32	8.784	0.1879	5.852	5.2473	-2.8103	3.484	0.1698	-1.1305	0.5323	0.1509	-0.5646	1.5503	-1.6494	-1.4108	0.7496	0.8559	0.4989	0.1141	0.383	0.1692	1.0331	-28.987	34.1992	108.81
33	8.2428	-3.8003	1.695	2.1035	4.4582	8.9528	0.5793	-1.4974	0.4239	0.659	0.1363	-0.7243	-2.4642	0.0584	-0.8979	0.7332	-0.0104	0.175	0.3434	-0.1019	0.3284	-25.5754	26.0773	124.9848
34	1.2787	-4.9097	9.9179	3.4397	7.1364	8.2015	-0.5179	-0.7381	0.627	1.3893	0.7063	-1.7969	-0.2743	0.2555	-0.0021	0.555	-0.0695	0.0822	0.431	0.0092	0.3823	-22.8125	18.2545	126.1217
35	3.1956	0.0459	-6.5026	0.6305	-0.4569	5.4038	-0.2906	-0.9863	-0.5901	0.1478	-0.0738	-0.1187	0.153	1.087	0.2223	0.325	-0.0612	-0.0157	0.4814	0.0254	0.3738	-17.9864	9.2448	121.2784
36	4.3421	-2.6344	7.3096	2.2187	-3.418	8.4431	1.1129	0.1462	-1.4732	-0.4582	0.9642	2.9415	1.6259	-0.2936	-1.5498	0.5724	0.0418	0.0284	0.4383	0.1585	0.7713	-14.2982	0.5462	117.1207
37	5.2449	-2.2284	0.3217	5.3006	-2.8062	2.5455	-0.4367	-1.6192	-0.0485	1.2836	-0.1575	-0.8091	0.2864	0.129	0.4668	0.454	0.0455	-0.0204	0.4362	-0.0065	0.5404	-4.6208	3.4404	114.3599
38	0.4666	-8.3552	2.5039	1.1493	-1.9362	3.1549	0.938	-0.2335	-0.091	0.5959	-0.6247	-0.4796	-0.1952	0.2754	-0.2521	0.2849	-0.0758	-0.0969	0.4206	-0.0142	0.5781	-6.2298	9.8968	109.5442
39	7.3296	-0.9086	0.1974	2.0243	-1.261	1.4937	0.2724	0.2758	-0.0903	-0.3838	-0.5857	0.2981	-0.2903	-0.0167	0.2226	0.2909	-0.0348	0.0836	0.3255	-0.0574	0.5019	-9.3428	14.7572	103.6602
40	6.6663	-0.503	1.6359	3.4775	-7.8034	2.0055	-0.6826	-0.764	-0.1804	0.6015	-1.1939	0.3109	-1.6445	0.8736	0.9054	0.7405	0.1614	0.1996	0.3488	-0.1964	0.4945	-12.6776	21.3057	104.9594
41	9.6373	-6.6393	7.8716	9.5928	-2.5283	-2.2346	1.1432	3.4559	1.6	-1.7584	-0.1995	-0.039	-1.1254	0.9721	-0.5522	0.6168	-0.0728	0.0105	0.8473	0.1842	0.3804	-14.448	38.9948	82.9734
42	6.7078	0.4985	-0.4436	8.2463	-1.411	0.9586	-0.1322	0.2941	0.194	0.4429	-0.2085	0.1143	0.1171	-0.2402	0.3252	0.3432	-0.0595	0.0011	0.3319	0.0011	0.3555	-9.6089	35.7276	90.7275
43	1.9408	-4.2896	2.0235	1.2054	-7.2716	1.9774	0.5869	-0.5224	-1.7729	-0.9631	0.3721	0.5407	1.1095	-0.8994	-0.6962	0.4389	-0.1198	0.0338	0.3142	-0.0277	0.395	-6.5601	26.8471	92.3526
44	5.0512	-2.8763	3.9651	5.3299	2.6986	2.1913	-0.814	-0.8547	0.6823	0.284	0.9277	-0.6171	-0.976	-0.1669	-0.1249	0.3436	-0.059	0.1015	0.2026	0.0356	0.3701	-3.0435	20.3838	99.0153
45	5.8007	1.573	-0.2303	-4.8581	0.8323	1.7597	-0.1038	-0.2718	-0.8824	0.047	-0.0979	-0.1281	-0.1492	-0.0529	0.1535	0.3874	-0.018	0.1113	0.2433	-0.0034	0.4983	-0.1383	18.9455	105.798
46	-3.9404	2.0949	1.5012	4.9161	1.6973	0.5651	-0.1581	0.6515	-0.4454	-0.1598	0.0559	-0.3382	-0.0372	0.3177	0.0713	0.3062	-0.0454	0.0056	0.2451	-0.0114	0.4486	7.333	27.1306	109.3396
47	5.3631	-2.6196	-5.9623	-2.687	0.7737	9.8355	0.5844	0.2677	0.3148	-0.5798	-0.6101	0.0002	-2.2945	-0.2442	-0.0148	0.9187	-0.0247	-0.0894	0.5296	-0.0179	0.6034	12.6718	32.8267	115.8267
48	2.1231	4.8858	9.6735	-5.0522	8.8158	2.3204	0.3634	-2.3278	0.4387	0.8361	-1.02	-0.2575	1.4453	-4.1645	0.5801	0.6591	-0.1195	-0.0779	0.6739	-0.0663	0.4134	2.6355	36.7575	115.6247
49	3.6164	3.541	-2.1661	3.3206	-2.8269	2.2179	-0.1802	0.0463	-0.565	0.847	-0.1557	0.1611	-0.1581	-0.1499	0.3044	0.5521	-0.0318	0.062	0.3787	-0.051	0.4726	-2.7864	33.9679	112.9084
50	2.1501	-9.7359	-6.5635	2.3902	0.9053	0.029	-0.8074	-0.3532	-0.2598	2.3071	0.4476	0.1825	-0.2091	-0.548	0.4368	0.3762	-0.0093	0.0363	0.3229	0.0322	0.5102	-1.871	27.3018	117.5945
51	2.2747	-5.0382	-6.1258	8.774	1.612	2.8148	-0.5953	-0.2756	-0.9901	2.5124	0.7149	0.7557	-0.4154	-1.9227	-0.0843	0.6433	-0.0298	0.0433	0.5325	0.1731	0.5333	2.817	19.0766	118.2235
52	3.0652	-3.5782	-0.4972	6.343	1.8094	4.6008	-0.3946	-0.985	1.0671	1.2013	0.2793	-0.5249	-0.3064	-0.1638	0.0972	0.7628	0.1137	-0.1784	0.4181	-0.0679	0.5265	8.2128	24.1548	120.5843
53	3.1754	-2.5124	1.0246	6.6705	-2.7052	9.5291	0.7765	-0.3427	-0.1941	-1.3033	0.4443	0.1041	0.5773	1.7478	-1.322	1.5645	-0.0637	-0.1346	1.075	-0.349	0.8977	11.2496	36.4871	125.1247
54	3.2313	4.5749	1.658	8.3306	8.4839	8.6191	-0.2399	0.1829	-0.6322	-0.0798	0.2931	-0.9384	0.1726	1.4552	-0.2513	0.3637	-0.0322	-0.1268	0.4672	-0.0302	0.4834	12.1236	25.3535	117.5002
55	5.6695	1.3417	9.7339	0.2455	3.7492	4.7177	-0.7881	1.7439	0.991	0.0647	0.8161	-0.0025	1.1349	1.4257	-0.0708	0.2437	0.1596	0.0506	0.199	0.0401	0.7933	12.8532	18.2631	111.5617
56	-0.6423	2.1022	6.0808	4.53	-1.0678	8.0584	-0.1232	0.8273	-2.544	-1.6294	0.532	-0.5272	0.2128	1.7861	-0.3277	0.1735	-0.0598	0.1156	0.3992	-0.0268	0.5893	10.9786	20.3025	105.351
57	2.3763	-0.1366	-2.4925	-0.3839	-1.9886	5.62	-0.1935	0.1517	-0.6658	-0.1569	-1.0428	-0.0299	0.5437	-0.0576	0.986	0.3505	-0.0288	0.1359	0.2509	-0.0736	0.5725	6.489	20.7517	96.8348
58	9.8972	1.7102	-9.2369	2.123	-6.585	-3.0947	-0.2486	-2.1416	-0.441	-1.8598	-0.3317	-1.3953	2.0516	1.8254	0.3559	0.7769	-0.038	0.2538	0.5919	-0.0938	0.49	2.4068	22.7903	88.7762
59	1.8859	-2.2313	-4.8884	2.7664	4.7325	2.1474	-0.3559	-0.0937	-0.0443	0.5267	-0.1084	0.0374	0.7578	0.9625	0.2958	0.5761	-0.0934	0.1087	0.4642	-0.1187	0.3397	8.0824	33.2934	85.9105
60	3.1368	2.3349	0.057	2.7138	2.2203	-0.5726	-0.0277	-0.301	-0.0443	0.1431	0.1885	-0.6413	0.0798	0.107	-0.1399	0.396	-0.0817	0.0117	0.2688	-0.0198	0.308	4.0451	40.1575	97.1699
61	5.9164	5.5296	1.6834	6.5553	3.0294	0.577	0.5028	-1.1422	0.0414	0.109	-0.3107	-0.3515	-0.423	0.0267	-0.1508	0.386	-0.0556	0.072	0.4572	-0.0398	0.4423	-14.6187	16.1449	113.7372
62	4.2188	0.069	4.3933	0.4064	2.3151	9.1445	-0.0725	-0.2031	0.6619	-0.2495	-0.261	-0.1055	-0.7284	-0.4565	0.1717	0.3079	0.0227	0.0728	0.2707	-0.0055	0.3133	-18.6879	11.3655	99.1665
63	5.3354	-0.9838	-4.4743	-1.1196	5.0802	-1.1361	-0.3138	2.0142	0.1687	-0.5667	0.2411	0.8934	-1.1865	-1.907	0.0158	0.6651	0.0187	0.0057	0.8113	0.1678	0.2465	-24.8807	5.9371	85.4703
64	6.9962	2.9339	5.0072	3.5417	-4.1397	-4.3966	-0.2831	0.9112	0.2354	0.1631	0.0063	0.4317	-0.2594	0.24	0.1283	0.4168	0.083	-0.0144	0.5216	-0.0561	0.303	-24.0475	0.2814	92.2297
65	5.898	-4.5847	-8.5439	7.4167	4.0659	4.2427	-0.026	0.3442	-0.709	0.1685	0.8332	-0.3075	1.4755	0.2468	-0.5334	0.3612	0.1556	-0.0604	0.4538	-0.1422	0.2711	-20.7102	-8.0864	90.0511
66	2.0232	-8.9089	-4.0657	9.0459	9.089	3.6831	0.1615	1.5317	-3.4008	1.9329	-0.2598	-0.5054	1.757	-0.358	0.1136	1.2168	0.0381	-0.3631	0.6277	-0.2563	1.0028	-22.2119	-16.4708	90.7697
67	0.3374	0.4213	1.4493	2.0845	-2.9656	3.2028	0.9611	0.3797	-0.6031	0.6962	0.3806	-0.0292	2.0984	-1.8548	-1.0997	0.6423	-0.2213	-0.1618	0.596	0.0648	0.4391	-26.859	-10.556	99.3923
68	2.1785	-0.1006	-1.2884	2.4717	4.4181	7.3044	0.7932	-0.3145	-0.172	0.0028	-0.7287	-0.08	-0.6648	-1.5504	-0.0065	0.32	0.0187	0.0495	0.5408	-0.0599	0.2735	-27.3767	-5.1874	100.8846
69	-3.8508	3.4286	3.9207	1.6495	2.3739	6.1655	0.2068	0.4385	0.4915	-0.3772	-0.8133	0.3959	-0.7912	-1.0972	0.5626	0.2395	0.1075	0.0007	0.5092	-0.1172	0.3263	-33.2757	-5.275	94.4433
70	1.3688	0.0855	2.3583	-0.1064	0.4891	4.766	0.1036	0.105	0.5138	-0.2352	0.0299	0.0344	-0.5177	-0.7666	-0.057	0.402	0.2404	-0.1178	0.6593	-0.0844	0.2543	-31.5258	-4.9251	83.9125
71	4.1841	2.6549	2.1795	9.1915	-4.0784	4.5139	0.1395	-1.6421	-1.4767	0.4947	0.4669	-0.993	0.1065	-0.7808	-0.451	0.3657	0.0719	-0.1442	0.7687	-0.0185	0.533	-31.557	-15.294	87.4668
72	4.0502	7.244	-1.059	6.5154	8.4177	2.2254	-0.0034	0.2068	-0.801	-0.7712	-1.6999	-1.4205	-1.4455	0.1268	1.3232	1.0164	0.1546	-0.211	0.9405	0.2006	0.892	-31.166	-22.3261	95.5856
73	8.9944	3.3487	-3.3212	9.8013	-0.0161	8.7244	-0.211	0.7024	-1.3726	-1.223	-0.2225	0.3472	0.3249	-0.3964	0.19	0.4029	0.1343	-0.1124	0.4068	-0.1092	0.4233	-27.1663	-14.0693	87.9036
74	2.5788	4.3297	-4.8495	1.9934	-8.2886	4.1286	0.555	2.3932	0.0646	-1.4794	0.474	-0.46	-0.2089	-0.9838	-0.726	0.6317	0.3336	0.073	0.9571	-0.1764	0.2363	-21.5125	-8.6248	78.6825
75	3.2473	2.1356	-7.3464	3.7192	1.69	5.6156	0.1304	0.7143	-0.1568	-1.4667	0.7317	-1.0523	-0.5478	0.6937	-0.7537	0.5435	0.1566	0.1338	0.9693	-0.0845	0.3003	-18.3629	-1.8358	82.3349
76	5.5708	-0.0271	4.8442	2.7844	9.0162	8.2987	0.2473	1.7118	-0.0201	-0.6756	0.3061	-0.1274	-1.2069	-0.0552	-0.3912	0.4693	-0.121	0.1236	0.8811	-0.0064	0.3492	-13.8271	5.6175	87.3072
77	4.4017	-0.998	2.1355	4.7707	7.8357	6.9394	-0.8402	1.1414	0.3121	0.6917	0.8762	-0.796	-0.7228	1.7262	-0.1682	0.7488	-0.2994	0.2807	0.543	0.0223	0.4095	-9.1674	12.5247	93.6262
78	-0.1723	-1.2094	-1.4608	2.0863	-6.8698	6.5964	-0.6789	0.3814	-0.8404	-2.1419	0.2763	-1.6045	1.1385	0.5634	0.3641	0.4764	-0.0206	0.2333	0.3006	-0.1044	0.8889	-1.5889	7.0113	98.4776
79	4.8594	-5.5737	-4.1952	2.1556	1.3499	2.0576	0.8147	-0.1245	-0.2268	-0.5487	0.1147	-1.9594	0.22	0.6879	-0.8768	0.4214	0.0098	-0.0142	0.4192	-0.0428	0.8687	-6.5638	1.6907	103.1902
80	-0.4007	-6.3604	2.2197	9.0574	-5.3071	5.1634	-0.0341	-1.0358	-0.936	0.5024	0.881	-0.0782	1.0894	1.0169	-0.7696	0.3813	0.0974	-0.0277	0.3125	0.0336	0.6077	-12.8561	-4.6362	106.4337

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain A and resid 2:7
2	X-RAY DIFFRACTION	2	chain A and resid 8:15
3	X-RAY DIFFRACTION	3	chain A and resid 16:25
4	X-RAY DIFFRACTION	4	chain A and resid 26:30
5	X-RAY DIFFRACTION	5	chain A and resid 31:36
6	X-RAY DIFFRACTION	6	chain A and resid 37:41
7	X-RAY DIFFRACTION	7	chain A and resid 42:47
8	X-RAY DIFFRACTION	8	chain A and resid 48:53
9	X-RAY DIFFRACTION	9	chain A and resid 54:59
10	X-RAY DIFFRACTION	10	chain A and resid 60:66
11	X-RAY DIFFRACTION	11	chain A and resid 67:73
12	X-RAY DIFFRACTION	12	chain A and resid 74:80
13	X-RAY DIFFRACTION	13	chain A and resid 81:84
14	X-RAY DIFFRACTION	14	chain A and resid 96:102
15	X-RAY DIFFRACTION	15	chain A and resid 103:110
16	X-RAY DIFFRACTION	16	chain A and resid 111:118
17	X-RAY DIFFRACTION	17	chain A and resid 119:122
18	X-RAY DIFFRACTION	18	chain A and resid 123:128
19	X-RAY DIFFRACTION	19	chain A and resid 129:133
20	X-RAY DIFFRACTION	20	chain A and resid 134:142
21	X-RAY DIFFRACTION	21	chain B and resid 4:9
22	X-RAY DIFFRACTION	22	chain B and resid 10:22
23	X-RAY DIFFRACTION	23	chain B and resid 23:30
24	X-RAY DIFFRACTION	24	chain B and resid 31:44
25	X-RAY DIFFRACTION	25	chain B and resid 45:50
26	X-RAY DIFFRACTION	26	chain B and resid 51:56
27	X-RAY DIFFRACTION	27	chain B and resid 57:65
28	X-RAY DIFFRACTION	28	chain B and resid 66:72
29	X-RAY DIFFRACTION	29	chain B and resid 73:77
30	X-RAY DIFFRACTION	30	chain B and resid 78:84
31	X-RAY DIFFRACTION	31	chain B and resid 85:91
32	X-RAY DIFFRACTION	32	chain B and resid 92:96
33	X-RAY DIFFRACTION	33	chain B and resid 97:103
34	X-RAY DIFFRACTION	34	chain B and resid 104:108
35	X-RAY DIFFRACTION	35	chain B and resid 109:118
36	X-RAY DIFFRACTION	36	chain B and resid 119:122
37	X-RAY DIFFRACTION	37	chain B and resid 123:129
38	X-RAY DIFFRACTION	38	chain B and resid 130:134
39	X-RAY DIFFRACTION	39	chain B and resid 135:140
40	X-RAY DIFFRACTION	40	chain B and resid 141:2001
41	X-RAY DIFFRACTION	41	chain C and resid 4:9
42	X-RAY DIFFRACTION	42	chain C and resid 10:16
43	X-RAY DIFFRACTION	43	chain C and resid 17:22
44	X-RAY DIFFRACTION	44	chain C and resid 23:28
45	X-RAY DIFFRACTION	45	chain C and resid 29:38
46	X-RAY DIFFRACTION	46	chain C and resid 39:48
47	X-RAY DIFFRACTION	47	chain C and resid 49:54
48	X-RAY DIFFRACTION	48	chain C and resid 55:60
49	X-RAY DIFFRACTION	49	chain C and resid 61:67
50	X-RAY DIFFRACTION	50	chain C and resid 68:74
51	X-RAY DIFFRACTION	51	chain C and resid 75:79
52	X-RAY DIFFRACTION	52	chain C and resid 80:85
53	X-RAY DIFFRACTION	53	chain C and resid 86:94
54	X-RAY DIFFRACTION	54	chain C and resid 95:100
55	X-RAY DIFFRACTION	55	chain C and resid 101:105
56	X-RAY DIFFRACTION	56	chain C and resid 106:109
57	X-RAY DIFFRACTION	57	chain C and resid 110:118
58	X-RAY DIFFRACTION	58	chain C and resid 119:122
59	X-RAY DIFFRACTION	59	chain C and resid 123:131
60	X-RAY DIFFRACTION	60	chain C and resid 132:143
61	X-RAY DIFFRACTION	61	chain D and resid 4:13
62	X-RAY DIFFRACTION	62	chain D and resid 14:27
63	X-RAY DIFFRACTION	63	chain D and resid 28:36
64	X-RAY DIFFRACTION	64	chain D and resid 37:41
65	X-RAY DIFFRACTION	65	chain D and resid 42:48
66	X-RAY DIFFRACTION	66	chain D and resid 49:54
67	X-RAY DIFFRACTION	67	chain D and resid 55:60
68	X-RAY DIFFRACTION	68	chain D and resid 61:66
69	X-RAY DIFFRACTION	69	chain D and resid 67:74
70	X-RAY DIFFRACTION	70	chain D and resid 75:81
71	X-RAY DIFFRACTION	71	chain D and resid 82:86
72	X-RAY DIFFRACTION	72	chain D and resid 87:93
73	X-RAY DIFFRACTION	73	chain D and resid 94:99
74	X-RAY DIFFRACTION	74	chain D and resid 100:104
75	X-RAY DIFFRACTION	75	chain D and resid 105:109
76	X-RAY DIFFRACTION	76	chain D and resid 110:118
77	X-RAY DIFFRACTION	77	chain D and resid 119:122
78	X-RAY DIFFRACTION	78	chain D and resid 123:130
79	X-RAY DIFFRACTION	79	chain D and resid 131:135
80	X-RAY DIFFRACTION	80	chain D and resid 136:143

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Protein , 1 types, 4 molecules ABCD

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Non-polymers , 5 types, 300 molecules

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-Protein , 1 types, 4 molecules ABCD

-Non-polymers , 5 types, 300 molecules

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

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

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

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Movie

-
Structure viewers

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Viewer log

-
This page

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This web site

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Options

+
Open data

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Basic information

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Structure visualization

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Downloads & links

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Download

-
Validation report

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Related structure data

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Links

-
Assembly

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Components

-
Protein , 1 types, 4 molecules ABCD

-
Non-polymers , 5 types, 300 molecules

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

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News

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

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Aug 12, 2020. Covid-19 info

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Mar 5, 2020. Novel coronavirus structure data

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Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

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Jul 12, 2017. Major update of PDB

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Yorodumi