PDB-8s9j: FphA, Staphylococcus aureus fluorophosphonate-binding serine hydr...

ID or keywords:

Entry

Database: PDB / ID: 8s9j

Title

FphA, Staphylococcus aureus fluorophosphonate-binding serine hydrolases A, apo form

Components

Fluorophosphonate-binding serine hydrolase A

Keywords

HYDROLASE / FphA / Staphylococcus aureus / S. aureus / fluorophosphonate-binding / serine hydrolases / lipase

Function / homology

Function and homology information

Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases / hydrolase activity
Similarity search - Function

Biological species

Staphylococcus aureus USA300-CA-263 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.25 Å

Authors

Fellner, M.

Funding support

New Zealand, 1items

Citation

Journal: To Be Published
Title: FphA, Staphylococcus aureus fluorophosphonate-binding serine hydrolases A, apo form
Authors: Fellner, M.

History

Deposition	Mar 28, 2023	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 10, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	8s9j.cif.gz	1.2 MB	Display	PDBx/mmCIF format
PDB format	pdb8s9j.ent.gz	1 MB	Display	PDB format
PDBx/mmJSON format	8s9j.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	8s9j_validation.pdf.gz	513.1 KB	Display	wwPDB validaton report
Full document	8s9j_full_validation.pdf.gz	571.8 KB	Display
Data in XML	8s9j_validation.xml.gz	112.4 KB	Display
Data in CIF	8s9j_validation.cif.gz	154.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/s9/8s9j ftp://data.pdbj.org/pub/pdb/validation_reports/s9/8s9j	HTTPS FTP

-
Related structure data

Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#54 - Jun 2004 Acetylcholinesterase similarity (6)

Deposited unit

A: Fluorophosphonate-binding serine hydrolase A

B: Fluorophosphonate-binding serine hydrolase A

C: Fluorophosphonate-binding serine hydrolase A

D: Fluorophosphonate-binding serine hydrolase A

E: Fluorophosphonate-binding serine hydrolase A

F: Fluorophosphonate-binding serine hydrolase A

G: Fluorophosphonate-binding serine hydrolase A

hetero molecules

368 kDa, 7 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Fluorophosphonate-binding serine hydrolase A

hetero molecules

defined by author&software
Evidence: gel filtration
52.8 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Fluorophosphonate-binding serine hydrolase A

hetero molecules

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

3

C: Fluorophosphonate-binding serine hydrolase A

hetero molecules

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

4

D: Fluorophosphonate-binding serine hydrolase A

hetero molecules

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

5

E: Fluorophosphonate-binding serine hydrolase A

hetero molecules

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

6

F: Fluorophosphonate-binding serine hydrolase A

hetero molecules

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

7

G: Fluorophosphonate-binding serine hydrolase A

hetero molecules

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

Unit cell

Length a, b, c (Å)	313.042, 313.042, 185.672
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	98
Space group name H-M	I4₁22

Components on special symmetry positions

ID	Model	Components
1	1	A-616- HOH

#1: Protein	Fluorophosphonate-binding serine hydrolase A Mass: 52236.898 Da / Num. of mol.: 7 / Fragment: N-terminal GPG from expression tag Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus USA300-CA-263 (bacteria) Gene: pnbA, DD547_02485, EP54_14100, EQ90_00535, GO814_08475, GO942_08205, GQX37_11595, NCTC13131_01802, SAGV69_02939, SAHC1335_00445, SAMEA2077334_00038, SAMEA2078260_00273, SAMEA2078588_00580, ...Gene: pnbA, DD547_02485, EP54_14100, EQ90_00535, GO814_08475, GO942_08205, GQX37_11595, NCTC13131_01802, SAGV69_02939, SAHC1335_00445, SAMEA2077334_00038, SAMEA2078260_00273, SAMEA2078588_00580, SAMEA2080344_00347, SAMEA2081063_01648, SAMEA2081470_00272, SAMEA70146418_00277 Plasmid: F1006 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: A0A0D6GYZ4, Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases
#2: Chemical	... ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 28 / Source method: obtained synthetically / Formula: SO₄
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 400 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 3.11 Å³/Da / Density % sol: 60.45 %
Crystal grow	Temperature: 289.15 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 2uL 7.1 mg/ml FphA (10mM HEPES pH 7.5, 100mM NaCl) were mixed with 1ul of reservoir solution. Sitting drop reservoir contained 30ul of 1.35M ammonium sulfate, 0.09M sodium acetate pH 4.6, 4% ...Details: 2uL 7.1 mg/ml FphA (10mM HEPES pH 7.5, 100mM NaCl) were mixed with 1ul of reservoir solution. Sitting drop reservoir contained 30ul of 1.35M ammonium sulfate, 0.09M sodium acetate pH 4.6, 4% v/v acetone. Crystal appeared after 30 days at 16C and grew larger for another 2 months when it was frozen in a solution of ~25% glycerol, 75% reservoir.

Crystal

Density Matthews: 3.11 Å³/Da / Density % sol: 60.45 %

Crystal grow

Temperature: 289.15 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 2uL 7.1 mg/ml FphA (10mM HEPES pH 7.5, 100mM NaCl) were mixed with 1ul of reservoir solution. Sitting drop reservoir contained 30ul of 1.35M ammonium sulfate, 0.09M sodium acetate pH 4.6, 4% ...

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 28, 2023
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9537 Å / Relative weight: 1
Reflection	Resolution: 2.25→49.5 Å / Num. obs: 212752 / % possible obs: 98.7 % / Redundancy: 7.8 % / CC_1/2: 0.998 / R_merge(I) obs: 0.122 / R_pim(I) all: 0.046 / R_rim(I) all: 0.131 / Χ²: 1.01 / Net I/σ(I): 11 / Num. measured all: 1656348
Reflection shell	Resolution: 2.25→2.28 Å / % possible obs: 97.2 % / Redundancy: 7.4 % / R_merge(I) obs: 1.435 / Num. measured all: 76466 / Num. unique obs: 10338 / CC_1/2: 0.587 / R_pim(I) all: 0.549 / R_rim(I) all: 1.539 / Χ²: 1.01 / Net I/σ(I) obs: 1.4

-
Processing

Software

Name	Version	Classification
PHENIX	1.20.1-4487	refinement
Aimless	0.7.8	data scaling
XDS	20220220	data reduction
PHASER	2.8.3	phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.25→49.5 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.1 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.277	10754	5.06 %
R_work	0.241	-	-
obs	0.2428	212711	98.47 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 2.25→49.5 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	25380	0	140	400	25920

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008
X-RAY DIFFRACTION	f_angle_d	1.013	35806
X-RAY DIFFRACTION	f_dihedral_angle_d	17.135	9489
X-RAY DIFFRACTION	f_chiral_restr	0.055	3826
X-RAY DIFFRACTION	f_plane_restr	0.009	4618

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.25-2.27	0.3909	328	0.3597	6520	X-RAY DIFFRACTION	96
2.27-2.3	0.3817	371	0.3392	6710	X-RAY DIFFRACTION	99
2.3-2.33	0.3702	371	0.336	6736	X-RAY DIFFRACTION	99
2.33-2.36	0.3589	349	0.3305	6773	X-RAY DIFFRACTION	99
2.36-2.39	0.3658	349	0.3321	6743	X-RAY DIFFRACTION	99
2.39-2.42	0.4109	341	0.3396	6766	X-RAY DIFFRACTION	99
2.42-2.45	0.3764	373	0.3199	6701	X-RAY DIFFRACTION	99
2.45-2.49	0.3537	370	0.3192	6751	X-RAY DIFFRACTION	99
2.49-2.53	0.3616	357	0.3117	6732	X-RAY DIFFRACTION	99
2.53-2.57	0.363	331	0.3146	6758	X-RAY DIFFRACTION	99
2.57-2.62	0.339	330	0.3085	6746	X-RAY DIFFRACTION	99
2.62-2.66	0.3624	326	0.3096	6779	X-RAY DIFFRACTION	99
2.66-2.71	0.343	377	0.3098	6722	X-RAY DIFFRACTION	99
2.71-2.77	0.3219	345	0.3124	6716	X-RAY DIFFRACTION	99
2.77-2.83	0.34	398	0.3117	6693	X-RAY DIFFRACTION	99
2.83-2.9	0.372	322	0.3076	6750	X-RAY DIFFRACTION	99
2.9-2.97	0.3493	360	0.2932	6728	X-RAY DIFFRACTION	99
2.97-3.05	0.3134	341	0.2817	6732	X-RAY DIFFRACTION	99
3.05-3.14	0.3043	334	0.2835	6764	X-RAY DIFFRACTION	99
3.14-3.24	0.3153	368	0.2653	6716	X-RAY DIFFRACTION	99
3.24-3.35	0.3209	350	0.2693	6714	X-RAY DIFFRACTION	98
3.35-3.49	0.2877	370	0.2442	6717	X-RAY DIFFRACTION	98
3.49-3.65	0.2432	347	0.2213	6754	X-RAY DIFFRACTION	98
3.65-3.84	0.2529	370	0.2091	6694	X-RAY DIFFRACTION	98
3.84-4.08	0.2306	338	0.1963	6772	X-RAY DIFFRACTION	98
4.08-4.4	0.2205	397	0.178	6682	X-RAY DIFFRACTION	98
4.4-4.84	0.2097	398	0.1713	6699	X-RAY DIFFRACTION	98
4.84-5.54	0.2536	373	0.1954	6750	X-RAY DIFFRACTION	97
5.54-6.97	0.2308	417	0.2138	6715	X-RAY DIFFRACTION	97
6.97-49.5	0.2008	353	0.1853	6924	X-RAY DIFFRACTION	96

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	0.8266	-0.5571	0.6699	2.2567	-0.9096	1.5989	0.0082	-0.1963	-0.0355	0.2427	-0.0129	-0.179	-0.1583	0.0748	0.0069	0.4273	-0.1013	0.267	0.4186	-0.2442	0.8574	59.7471	-83.6408	-25.8103
2	2.522	0.9408	1.2152	0.3494	0.4548	0.5852	-0.1726	-0.5016	0.3794	0.1125	0.2279	0.3819	-0.5453	-0.1073	-0.0476	0.5593	-0.0453	0.3014	0.4646	-0.2274	0.9227	44.1728	-72.455	-29.1315
3	0.3525	-0.1156	0.2487	0.6333	0.0986	0.8242	0.0728	-0.0077	0.1928	0.003	0.0216	0.0032	-0.2963	0.0979	-0.0892	0.4608	-0.1448	0.3249	0.4	-0.2479	0.9549	55.4598	-74.675	-40.3404
4	1.3967	-1.0024	0.2797	2.1118	0.0034	1.1693	0.1227	0.0223	0.1763	0.0004	0.0375	0.1038	-0.2818	-0.1129	-0.1572	0.5313	-0.1072	0.364	0.3676	-0.1863	0.8919	40.5254	-74.6989	-51.8077
5	1.4216	-2.1907	0.1782	6.7263	-0.1006	0.843	0.2186	0.0866	0.5304	-0.1741	-0.0276	-0.3016	-0.4106	0.1248	-0.1827	0.5538	-0.1103	0.2887	0.4171	-0.1752	0.8686	41.9992	-68.6128	-59.3538
6	1.5367	-0.4762	-0.1062	1.7766	-0.1871	1.5729	-0.0016	0.1028	-0.3094	0.0047	0.0776	0.1996	-0.0811	-0.0503	-0.079	0.3981	-0.0845	0.2427	0.3224	-0.1885	0.8969	35.5128	-86.5371	-47.6337
7	2.2234	-0.5939	0.4705	1.4798	0.0282	0.287	-0.0953	-0.3711	-0.1659	0.2682	0.1554	-0.0561	0.0171	-0.0895	-0.0575	0.7779	0.6009	0.148	1.08	0.2118	0.4726	0.704	-55.9814	15.212
8	0.8913	-0.4642	-0.2802	0.9271	0.4099	0.4395	-0.1036	-0.3027	0.0265	0.0824	0.0811	-0.1461	-0.1455	0.0437	-0.0062	0.7591	0.6922	0.244	0.8892	0.1206	0.4673	4.5306	-50.9411	7.532
9	1.1006	0.7258	0.7431	0.9226	-0.0743	1.1929	-0.2555	-0.5178	0.1575	0.1329	0.0154	-0.0828	-0.522	-0.2131	0.2393	1.0827	0.5605	0.0905	0.9064	0.0025	0.6224	15.8466	-38.8831	9.7003
10	1.1243	-0.1843	0.5524	0.5884	-0.4918	0.5646	-0.1846	-0.4306	0.129	-0.0191	0.1397	-0.1927	-0.5309	-0.1265	0.0488	1.0375	0.5058	0.1413	0.891	-0.0318	0.5592	8.9026	-34.113	8.2866
11	0.7775	-1.3998	-0.8728	3.8347	2.2769	1.3546	-0.1166	-0.1661	0.2124	-0.5167	0.2063	-0.3818	-0.301	0.0881	-0.092	1.346	0.4759	0.1456	0.8301	0.0084	0.5352	9.6833	-26.4629	-5.0718
12	1.1216	-0.7372	-0.2623	1.8606	0.7075	0.7795	-0.0092	-0.041	0.1552	-0.2587	-0.0032	-0.0849	-0.2558	-0.1454	-0.0067	1.046	0.6806	0.2078	0.7232	0.0395	0.3939	-4.7654	-42.7162	-10.3274
13	2.2193	0.0574	0.9284	0.1423	-0.3857	1.5777	-0.101	0.2405	-0.0701	-0.7159	0.2297	-0.6478	-0.7757	0.1318	-0.138	1.1143	0.05	0.4269	0.3823	-0.0512	0.8088	30.2787	-58.2337	-24.5157
14	2.0499	-0.3592	0.5182	0.3464	0.9988	4.3181	-0.2738	-0.2594	0.2098	-0.2286	0.3318	-0.5857	-0.6169	0.1111	-0.0768	0.7464	0.1203	0.3111	0.4527	-0.1116	0.9734	39.2205	-58.7688	-6.872
15	1.4977	-0.1831	-0.0992	0.9628	1.1311	1.3343	0.0279	-0.0125	-0.4561	-0.3226	0.3384	-0.6084	-0.0038	0.3702	-0.3679	0.5776	0.0395	0.3118	0.4747	-0.1454	1.1264	40.6514	-77.1446	-16.761
16	1.2553	-0.3813	0.3106	1.2526	0.8486	1.6626	-0.1756	-0.2297	-0.1962	-0.1059	0.2828	-0.4077	-0.3302	-0.0398	-0.1147	0.5664	0.1736	0.3289	0.4096	0.067	0.8319	29.6594	-68.9656	-8.853
17	0.9773	0.8098	0.867	0.8361	0.4009	1.3454	0.0186	-0.2678	-0.5482	0.2133	0.1787	-0.6684	0.0654	0.0397	-0.1973	0.6126	0.2591	0.1665	0.5857	0.1445	1.0422	38.8537	-77.2266	4.506
18	1.183	-0.4929	1.2511	3.0636	0.875	2.7149	-0.0866	-0.5011	-0.5457	0.3396	0.3554	-0.2775	0.1955	0.0655	-0.2702	0.4834	0.1735	0.269	0.598	0.2587	0.9588	24.1573	-88.5112	-4.8107
19	1.707	-1.633	0.4466	4.3529	1.209	2.677	-0.3251	-0.9674	-0.7402	0.9147	0.6612	-0.431	0.4734	0.0655	-0.3383	0.5972	0.226	0.0886	0.8886	0.3942	1.1062	24.6858	-93.5751	3.5313
20	2.3137	-1.2615	-0.2012	1.8096	1.2992	2.1581	0.0299	-0.2418	-0.4992	-0.0862	0.1953	-0.1506	-0.09	-0.2623	-0.2101	0.4353	0.1405	0.263	0.4395	0.2078	0.9024	17.2857	-85.9174	-15.8646
21	3.1241	0.3079	0.5742	1.7413	1.3165	1.9691	-0.0179	-0.1694	-0.5225	-0.3961	0.064	-0.0888	-0.5527	-0.611	-0.0402	0.5423	0.2293	0.2574	0.5567	0.1516	0.5863	-11.4103	-90.158	-41.6202
22	1.0668	1.0761	0.4175	1.0906	0.4279	1.9704	-0.0176	-0.5486	-0.5091	0.0198	-0.0973	0.0378	-0.0255	-0.9456	0.1298	0.4233	0.1794	0.1624	1.0021	0.2517	0.748	-21.1559	-96.9139	-27.3011
23	2.3724	0.1892	-0.5172	1.8361	1.2399	1.5504	0.0926	-0.5576	-0.5503	-0.007	-0.0454	-0.2966	-0.0718	-0.5219	-0.0333	0.4068	0.184	0.1846	0.7487	0.3108	0.6844	-3.7631	-90.0114	-19.0975
24	0.5736	-0.2425	-0.1749	0.453	0.094	0.2342	-0.1306	0.1023	-0.764	-0.0419	0.0162	0.2806	0.3045	-0.1859	0.1562	0.3505	-0.0839	0.3901	0.4116	-0.2613	1.7293	14.6544	-118.2462	-47.0123
25	0.0414	-0.1414	0.1414	0.4928	-0.4922	0.493	-0.0131	0.7202	-0.7334	-0.2141	-0.0636	0.3167	0.408	-0.3617	0.0924	0.5448	-0.1221	0.2187	0.8028	-0.5195	1.5649	7.3502	-113.4881	-62.6898
26	0.3811	0.6496	0.0479	1.4436	-0.2662	0.3758	-0.3144	0.2798	-0.4802	-0.3931	0.1716	0.198	0.3355	-0.1245	0.1207	0.7805	-0.2254	0.263	0.8678	-0.5642	1.7336	9.616	-124.5826	-67.6503
27	2.3928	-1.9773	-1.0003	2.6977	0.5428	2.2628	0.1452	0.3668	-0.3495	-0.4346	-0.1381	0.3042	0.0241	-0.1191	-0.0024	0.4317	-0.059	0.1601	0.4463	-0.2845	1.1493	24.0202	-106.4979	-65.2359
28	0.9616	-1.5308	0.86	4.4376	0.4797	2.4763	0.2187	0.6658	-1.0449	-0.7698	-0.4635	0.8499	0.579	-0.3008	0.2419	0.8115	0.0608	-0.0027	0.675	-0.3317	1.1385	21.6224	-109.8455	-81.2521
29	3.1506	-3.5215	-2.3372	4.3384	2.284	2.3009	-0.0877	0.3228	-0.3993	-0.2571	-0.0667	0.709	0.1035	-0.0319	0.1516	0.6085	-0.0579	0.0535	0.4992	-0.3107	1.1104	21.3911	-100.7043	-68.7473
30	1.4536	-0.7826	0.3243	1.4856	0.084	1.7192	-0.0299	0.078	-0.038	-0.0764	0.0269	0.0676	-0.1231	0.1651	-0.0093	0.384	-0.0801	0.2518	0.3844	-0.2535	1.062	31.151	-102.5789	-54.4866
31	0.3639	0.3086	-0.5595	0.9415	-0.651	1.3535	0.0447	-0.1831	0.0784	-0.0247	-0.0746	-0.167	-0.1558	0.0632	0.0585	0.8133	0.6763	0.0262	1.3412	0.0274	0.4566	-19.9058	-36.6046	29.9016
32	0.3823	-0.0721	-0.0089	0.1504	-0.0374	0.2353	0.0093	-0.2741	-0.1747	0.0237	-0.0459	-0.0405	0.1708	0.0266	0.0628	0.7187	1.1664	0.1647	1.2751	0.0702	0.4254	-28.0126	-44.9153	24.0116
33	1.1951	0.3912	0.9059	0.4973	0.0754	0.8068	0.0923	-0.3453	-0.5111	0.2024	0.0279	-0.1088	0.4432	-0.1149	-0.1339	1.216	0.7294	0.1097	1.5333	0.2392	0.6701	-33.5293	-63.3581	32.661
34	0.8509	-0.2985	0.905	0.2653	-0.3977	1.0075	0.0543	-0.2844	-0.3355	-0.0917	-0.1166	-0.0076	0.443	0.0103	0.0321	1.0972	0.7383	0.1964	1.4507	0.3064	0.6638	-32.775	-61.0357	25.0604
35	2.1552	0.36	1.5192	1.0618	-1.0925	2.8843	-0.6346	-0.9725	-0.8344	0.6835	0.3316	-0.0784	1.2777	0.1847	0.2904	1.4234	0.5979	0.2601	1.234	0.2899	0.7618	-45.0656	-64.2289	16.0316
36	1.0097	-0.7373	-0.0529	1.051	-0.101	0.7477	-0.0275	-0.066	-0.244	-0.1679	-0.032	0.2394	0.0548	-0.1224	0.0235	0.947	0.7803	0.0003	1.0031	0.1261	0.4587	-37.5262	-48.037	4.7548
37	0.457	-0.1485	-0.059	0.4895	0.1198	0.0382	0.161	0.3752	-0.2861	-0.5638	-0.1956	0.1773	-0.0949	-0.3426	0.0547	1.3356	0.8021	-0.0304	0.9362	-0.1056	0.5427	-25.801	-58.3234	-37.7762
38	0.9944	0.6589	0.1883	0.4369	0.1241	0.036	-0.0748	0.5382	-0.0533	-0.5708	0.0265	-0.0562	-0.1068	-0.0359	0.0281	1.5584	0.7065	0.1423	1.1509	0.0885	0.5616	-21.6397	-45.6417	-50.3826
39	0.6275	0.4523	0.1145	0.5889	0.3959	1.2561	-0.054	0.3625	-0.083	-0.3865	0.0694	-0.0395	-0.2909	-0.0149	-0.0158	1.7254	0.7157	0.1096	1.2304	0.0062	0.5662	-18.4716	-50.8775	-57.0616
40	0.2008	0.2069	0.4287	0.2149	0.4377	0.9107	0.1358	0.4969	0.3113	-0.6655	-0.0785	-0.2972	-0.5865	0.0066	-0.0775	1.6471	0.5108	0.3408	0.8727	0.1331	0.6134	-3.5561	-42.8502	-45.4143
41	0.5652	-0.6819	-0.0516	1.0123	0.2594	0.2356	0.1941	0.2468	0.2165	-0.6788	-0.2266	-0.3155	-0.4875	-0.0855	0.0099	1.345	0.6044	0.2907	0.765	0.0826	0.4595	-4.6363	-48.0344	-33.653
42	1.4938	-0.9589	-0.5683	1.7713	0.3944	1.2087	0.0781	-0.0193	0.108	-0.2317	-0.0857	-0.1441	-0.3018	-0.0678	-0	1.1077	0.558	0.1719	0.7341	0.0927	0.3982	-8.943	-45.4431	-22.2403

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid -1 through 49 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 50 through 78 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 79 through 285 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 286 through 314 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 315 through 363 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 364 through 450 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid -1 through 69 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 70 through 200 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 201 through 241 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 242 through 314 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 315 through 363 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 364 through 450 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid -1 through 21 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 22 through 49 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 50 through 78 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 79 through 200 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 201 through 285 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 286 through 314 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 315 through 363 )
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 364 through 450 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 0 through 241 )
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 242 through 324 )
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 325 through 450 )
24	X-RAY DIFFRACTION	24	chain 'E' and (resid -1 through 200 )
25	X-RAY DIFFRACTION	25	chain 'E' and (resid 201 through 239 )
26	X-RAY DIFFRACTION	26	chain 'E' and (resid 240 through 285 )
27	X-RAY DIFFRACTION	27	chain 'E' and (resid 286 through 314 )
28	X-RAY DIFFRACTION	28	chain 'E' and (resid 315 through 336 )
29	X-RAY DIFFRACTION	29	chain 'E' and (resid 337 through 363 )
30	X-RAY DIFFRACTION	30	chain 'E' and (resid 364 through 450 )
31	X-RAY DIFFRACTION	31	chain 'F' and (resid -1 through 49 )
32	X-RAY DIFFRACTION	32	chain 'F' and (resid 50 through 209 )
33	X-RAY DIFFRACTION	33	chain 'F' and (resid 210 through 241 )
34	X-RAY DIFFRACTION	34	chain 'F' and (resid 242 through 314 )
35	X-RAY DIFFRACTION	35	chain 'F' and (resid 315 through 363 )
36	X-RAY DIFFRACTION	36	chain 'F' and (resid 364 through 450 )
37	X-RAY DIFFRACTION	37	chain 'G' and (resid -1 through 200 )
38	X-RAY DIFFRACTION	38	chain 'G' and (resid 201 through 241 )
39	X-RAY DIFFRACTION	39	chain 'G' and (resid 242 through 285 )
40	X-RAY DIFFRACTION	40	chain 'G' and (resid 286 through 336 )
41	X-RAY DIFFRACTION	41	chain 'G' and (resid 337 through 411 )
42	X-RAY DIFFRACTION	42	chain 'G' and (resid 412 through 450 )

-
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

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.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

+
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

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
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

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-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

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
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