PDB-6u0y: Crystal Structure of the metallo-beta-lactamase L1 from Stenotrop...

ID or keywords:

Entry

Database: PDB / ID: 6u0y

Title

Crystal Structure of the metallo-beta-lactamase L1 from Stenotrophomonas maltophilia

Components

Putative metallo-beta-lactamase l1 (Beta-lactamase type ii) (Ec 3.5.2.6) (Penicillinase)

Keywords

HYDROLASE / lactam antibiotics / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID

Function / homology

Function and homology information

antibiotic catabolic process / beta-lactamase activity / beta-lactamase / periplasmic space / response to antibiotic / zinc ion binding
Similarity search - Function

Biological species

Stenotrophomonas maltophilia (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.7 Å

Authors

Kim, Y. / Maltseva, N. / Endres, M. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)

Funding support

United States, 1items

Citation

Journal: To Be Published
Title: Crystal Structure of the metallo-beta-lactamase L1 from Stenotrophomonas maltophilia
Authors: Kim, Y. / Maltseva, N. / Endres, M. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)

History

Deposition	Aug 15, 2019	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 11, 2019	Provider: repository / Type: Initial release
Revision 1.1	Dec 18, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2	Oct 11, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	6u0y.cif.gz	451.9 KB	Display	PDBx/mmCIF format
PDB format	pdb6u0y.ent.gz	353 KB	Display	PDB format
PDBx/mmJSON format	6u0y.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	6u0y_validation.pdf.gz	450.9 KB	Display	wwPDB validaton report
Full document	6u0y_full_validation.pdf.gz	452.9 KB	Display
Data in XML	6u0y_validation.xml.gz	44.4 KB	Display
Data in CIF	6u0y_validation.cif.gz	63.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/u0/6u0y ftp://data.pdbj.org/pub/pdb/validation_reports/u0/6u0y	HTTPS FTP

-
Related structure data

Related structure data	5dpxS S: Starting model for refinement
Similar structure data	5hh6-1 7l52-1 2aio-1 2fu6-3 6u13-1 5evb-1 6u2y-1 6uaf-1 5dpx-1 2hb9-1 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-IDP97218

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#187 - Jul 2015 New Delhi Metallo-β-Lactamase similarity (3) #105 - Sep 2008 Ribonuclease A similarity (2)

Deposited unit

A: Putative metallo-beta-lactamase l1 (Beta-lactamase type ii) (Ec 3.5.2.6) (Penicillinase)

B: Putative metallo-beta-lactamase l1 (Beta-lactamase type ii) (Ec 3.5.2.6) (Penicillinase)

C: Putative metallo-beta-lactamase l1 (Beta-lactamase type ii) (Ec 3.5.2.6) (Penicillinase)

D: Putative metallo-beta-lactamase l1 (Beta-lactamase type ii) (Ec 3.5.2.6) (Penicillinase)

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	68.033, 97.229, 91.725
Angle α, β, γ (deg.)	90.000, 105.550, 90.000
Int Tables number	4
Space group name H-M	P12₁1
Space group name Hall	P2yb
Symmetry operation	#1: x,y,z #2: -x,y+1/2,-z

#1: Protein	Putative metallo-beta-lactamase l1 (Beta-lactamase type ii) (Ec 3.5.2.6) (Penicillinase) Mass: 29172.857 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Stenotrophomonas maltophilia (strain K279a) (bacteria) Strain: K279a / Gene: Smlt2667 / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): gold / References: UniProt: B2FTM1, beta-lactamase
#2: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 660 / 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: 2.5 Å³/Da / Density % sol: 50.89 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.1 M HEPES pH 7.5, 10 %(w/v) PEG4000, 5 %(v/v) isopropanol

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
Detector	Type: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Oct 28, 2018
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97918 Å / Relative weight: 1
Reflection	Resolution: 1.7→50 Å / Num. obs: 122234 / % possible obs: 96.6 % / Redundancy: 5.9 % / B_iso Wilson estimate: 26.67 Å² / CC_1/2: 0.99 / R_merge(I) obs: 0.122 / Net I/σ(I): 23.1
Reflection shell	Resolution: 1.7→1.73 Å / R_merge(I) obs: 0.843 / Mean I/σ(I) obs: 2.38 / Num. unique obs: 6033 / CC_1/2: 0.735

-
Processing

Software

Name	Version	Classification
PHENIX	1.13_2998	refinement
SBC-Collect		data collection
HKL-3000		data reduction
HKL-3000		data scaling
HKL-3000		phasing
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDBID 5DPX

5dpx

Resolution: 1.7→48.63 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 0.31 / Phase error: 20.66

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1978	6168	5.05 %	random
R_work	0.1677	-	-	-
obs	0.1693	122193	96.58 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Displacement parameters

B_iso mean: 34.9 Å²

Refinement step

Cycle: LAST / Resolution: 1.7→48.63 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7979	0	44	660	8683

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	8424
X-RAY DIFFRACTION	f_angle_d	0.851	11504
X-RAY DIFFRACTION	f_chiral_restr	0.056	1275
X-RAY DIFFRACTION	f_plane_restr	0.006	1525
X-RAY DIFFRACTION	f_dihedral_angle_d	15.384	5011

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 (%)
1.7-1.72	0.2762	210	0.2518	3749	X-RAY DIFFRACTION	95
1.72-1.74	0.2479	208	0.2466	3820	X-RAY DIFFRACTION	96
1.74-1.76	0.2834	225	0.2406	3856	X-RAY DIFFRACTION	96
1.76-1.78	0.2659	193	0.2246	3820	X-RAY DIFFRACTION	96
1.78-1.8	0.2503	205	0.2266	3836	X-RAY DIFFRACTION	96
1.8-1.83	0.2454	201	0.2098	3848	X-RAY DIFFRACTION	96
1.83-1.86	0.2507	224	0.2046	3704	X-RAY DIFFRACTION	93
1.86-1.88	0.2448	197	0.1984	3688	X-RAY DIFFRACTION	92
1.88-1.91	0.2378	196	0.1882	3893	X-RAY DIFFRACTION	97
1.91-1.94	0.2029	181	0.1842	3926	X-RAY DIFFRACTION	97
1.94-1.98	0.2209	191	0.1877	3860	X-RAY DIFFRACTION	97
1.98-2.01	0.2226	208	0.1879	3853	X-RAY DIFFRACTION	97
2.01-2.05	0.2155	207	0.1783	3867	X-RAY DIFFRACTION	97
2.05-2.09	0.2355	230	0.1792	3912	X-RAY DIFFRACTION	97
2.09-2.14	0.2204	197	0.1731	3868	X-RAY DIFFRACTION	97
2.14-2.19	0.2102	203	0.1728	3902	X-RAY DIFFRACTION	97
2.19-2.24	0.2269	179	0.1675	3678	X-RAY DIFFRACTION	92
2.24-2.31	0.2054	208	0.1656	3863	X-RAY DIFFRACTION	96
2.31-2.37	0.2112	213	0.1676	3933	X-RAY DIFFRACTION	98
2.37-2.45	0.1915	203	0.167	3909	X-RAY DIFFRACTION	98
2.45-2.54	0.2085	215	0.1683	3941	X-RAY DIFFRACTION	98
2.54-2.64	0.2341	199	0.1803	3928	X-RAY DIFFRACTION	98
2.64-2.76	0.2292	221	0.1847	3903	X-RAY DIFFRACTION	98
2.76-2.9	0.2308	200	0.1752	3777	X-RAY DIFFRACTION	94
2.9-3.09	0.1945	219	0.1764	3931	X-RAY DIFFRACTION	98
3.09-3.32	0.2112	209	0.1781	3960	X-RAY DIFFRACTION	99
3.32-3.66	0.1748	190	0.1674	4000	X-RAY DIFFRACTION	98
3.66-4.19	0.1735	213	0.153	3886	X-RAY DIFFRACTION	97
4.19-5.28	0.157	222	0.1248	3913	X-RAY DIFFRACTION	97
5.28-48.63	0.1649	201	0.1522	4001	X-RAY DIFFRACTION	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	1.1296000481	-1.2079000473	0.7380999923	1.3500000238	-0.7412999868	0.587100029	0.0031999999	0.4690999985	-0.594900012	-0.0267999992	0.0864999965	0.1395999938	0.0366999991	-0.4957999885	-0.0800999999	0.2231999934	-0.0306000002	0.0081000002	0.2872000039	-0.0601999983	0.2486000061	-34.9835014343	-17.9713993073	10.8922996521
2	4.7771000862	1.1926000118	-0.2910000086	3.7026000023	-1.1542999744	1.8811000586	0.0571999997	-0.2255000025	-0.1743000001	0.0984999985	-0.332100004	-0.3759999871	0.0243999995	0.1686999947	0.2497999966	0.1757999957	0.0130000003	-0.0049000001	0.247299999	-0.0080000004	0.2727999985	-5.0033998489	-8.2807998657	10.8241996765
3	5.9267997742	3.0102000237	1.7174999714	7.4815998077	1.2954000235	4.1188998222	-0.0201999992	0.0588000007	-0.3738999963	0.0395999998	0.1247000024	-0.6262999773	0.1560000032	0.2356999964	-0.1418000013	0.1396999955	0.0195000004	-0.0071	0.2290000021	-0.0088999998	0.2301999927	-7.5921001434	-5.4254999161	12.3662004471
4	4.1430001259	0.3896000087	-0.0493000001	2.7857000828	-0.5360000134	1.9994000196	-0.0531000011	-0.2442000061	-0.0671000034	0.2931999862	0.0447000004	-0.3415000141	-0.1198000014	0.2041999996	0.0103000002	0.1738000065	0.0071999999	-0.0379000008	0.1993999928	-0.0155999996	0.1826000065	-9.744099617	-5.8164000511	18.9214992523
5	1.402099967	-0.2292000055	-0.2529000044	1.1342999935	-0.4350000024	0.6097999811	-0.0119000003	-0.0691	0.0427000001	0.1676999927	0.0195000004	-0.0957000032	-0.0535999984	0.0324000008	-0.0070000002	0.2013999969	0.0063	-0.0223999992	0.2039999962	-0.0129000004	0.1938000023	-18.5849990845	2.7957000732	16.4782009125
6	6.4739999771	1.1948000193	1.4594000578	2.9342999458	-0.271600008	1.9265999794	-0.0852999985	0.1543000042	0.0060000001	-0.0366999991	-0.0096000005	-0.3465999961	-0.0476999991	0.2443999946	0.0913999975	0.1762000024	0.0126999998	0.0060000001	0.2092999965	0.0137	0.2282000035	-8.1922998428	5.5714001656	5.4619002342
7	8.4898004532	-1.5568000078	1.0870000124	3.5611000061	1.1129000187	2.927200079	0.0667999983	0.4796999991	-0.141900003	-0.1878000051	-0.0329000019	0.3149999976	0.0081000002	0.0278999992	-0.0275999997	0.2405000031	0.0022	-0.0155999996	0.2398000062	0.0212999992	0.2344000041	-30.0972995758	1.8595000505	-1.391100049
8	5.565100193	0.7197999954	1.2236000299	2.0199000835	-0.0020000001	1.6970000267	-0.0904999971	0.4176999927	0.3039000034	-0.2009000033	0.0390000008	-0.1306000054	-0.198300004	-0.0083999997	0.0719000027	0.2486000061	0.0048000002	0.0096000005	0.2648999989	0.0362999998	0.1862999946	-16.4545001984	6.839700222	-2.9403998852
9	3.5130000114	-0.6086000204	1.5289000273	6.5359997749	-3.2281999588	8.6600999832	-0.0175000001	0.4205000103	-0.1431999952	-0.3517000079	-0.2660999894	-0.5250999928	0.7506999969	0.4458999932	0.2233999968	0.2845999897	0.0102000004	0.0364000015	0.2556999922	-0.0538999997	0.304399997	-5.4106001854	-7.2853999138	0.0051000002
10	7.9183001518	1.8789000511	5.2892999649	3.1273999214	1.461599946	5.6147999763	0.3055000007	0.2816999853	0.0131999999	-0.1703000069	-0.3481999934	0.2520000041	0.6035000086	-0.1952999979	0.0834000036	0.4031000137	-0.0002	0.0489000008	0.3610999882	-0.0780000016	0.2481999993	-22.3253993988	-0.3664999902	-10.5061998367
11	4.5342998505	0.5521000028	-2.7846000195	1.1367000341	0.0465000011	1.8815000057	-0.2469000071	-0.0348999985	-0.4528999925	0.0599999987	0.1120000035	-0.0469000004	0.1243000031	-0.0793000013	0.1508000046	0.2217999995	-0.0326000005	-0.0590000004	0.1923000067	0.0263	0.2011000067	-42.9800987244	-17.4542007446	20.8022994995
12	3.5202999115	0.7835000157	-0.8141000271	2.010299921	0.6201999784	2.0954999924	-0.0137	0.2210000008	0.1466999948	-0.0377000012	0.0414000005	0.2053000033	-0.0706999972	-0.1703000069	-0.0165999997	0.1800999939	-0.0073000002	-0.0189999994	0.2178000063	0.0476000011	0.1895000041	-50.4612998962	-7.2353000641	21.8012008667
13	2.4410998821	0.2236000001	-0.799399972	1.4234000444	0.0421000011	1.7738000154	0.064000003	-0.0214000009	0.1328999996	0.058699999	-0.0077999998	0.0076000001	-0.1229000017	0.0719999969	-0.064000003	0.2325000018	-0.0173000004	-0.0165999997	0.2049999982	0.0154999997	0.2182999998	-41.1730995178	-1.8748999834	28.389799118
14	6.9598999023	-2.1503999233	0.2064999938	2.9697999954	-0.3012000024	2.7723999023	-0.0091000004	-0.0820999965	-0.2160000056	0.1599999964	0.0463000014	0.4612999856	0.0706999972	-0.375	-0.0093	0.2958000004	-0.0318000019	0.0245999992	0.3246999979	0.0465999991	0.2518000007	-55.8282012939	-9.1134004593	36.438999176
15	7.1178998947	0.9894999862	1.3467999697	3.8573000431	1.0068999529	2.5940999985	0.2022999972	-0.1855999976	-0.2195000052	0.3971000016	0.0242999997	-0.3296000063	0.0852999985	0.1981000006	-0.2493000031	0.3172999918	-0.0108000003	-0.0817999989	0.3522999883	0.0952999964	0.2727999985	-30.2490005493	-14.0572004318	40.182800293
16	2.0852999687	0.0763999969	0.6104999781	1.9558999538	-0.4487999976	1.4745999575	0.0557999983	-0.2790000141	-0.0579000004	0.2057999969	-0.0183000006	0.0820999965	0.0961999968	-0.1106000021	-0.060800001	0.3325000107	-0.0315000005	0.0142999999	0.3292999864	0.0786999986	0.236499995	-49.5194015503	-16.8999004364	38.4182014465
17	9.7510995865	-3.7823998928	3.4581999779	3.6482000351	-1.7423000336	2.803800106	0.0891999975	-0.5329999924	-0.5745000243	0.0159000009	-0.0148	-0.2118999958	0.2809999883	-0.0153000001	-0.0777999982	0.4544999897	-0.0326999985	0.0054000001	0.3709999919	0.1307999939	0.4539999962	-38.2734985352	-23.0841999054	45.09349823
18	5.2445998192	-1.9981000423	4.8705000877	0.7436000109	-1.8088999987	5.2083997726	-0.3513000011	-0.0074999998	0.5554999709	0.2203000039	0.180399999	-0.3630000055	-0.5950999856	0.2172999978	0.1703999937	0.472600013	-0.068400003	0.0308999997	0.3156999946	-0.1418000013	0.4472999871	-27.7786998749	32.7715988159	32.6068000793
19	3.321199894	0.0670000017	0.6098999977	0.9294999838	-0.4514999986	3.200799942	-0.0033	0.066399999	0.2178999931	0.1494999975	0.1976000071	0.1718000025	-0.4099999964	-0.2270999998	-0.1661999971	0.288500011	0.0595000014	0.1053000018	0.2343000025	0.0855000019	0.369599998	-50.1949005127	26.7075996399	14.8156003952
20	3.6085000038	-0.6236000061	0.1508000046	0.5695000291	-0.3075000048	2.5562000275	0.0515000001	-0.1756000072	0.068599999	0.1176000014	0.1791000068	0.1869000047	-0.1255999953	-0.3106000125	-0.1948000044	0.2951000035	0.0310999993	0.1041999981	0.2414000034	0.0908000022	0.3815999925	-52.4194984436	19.8491001129	20.7241001129
21	3.6807999611	0.5863999724	-0.6564999819	1.3646999598	-0.6222000122	2.7174999714	0.1701000035	-0.0498999991	0.2518999875	0.3492999971	0.065200001	0.2274000049	-0.2155999988	-0.0197999999	-0.2261999995	0.3280000091	0.0353000015	0.0504000001	0.1949999928	0.0167999994	0.2973000109	-41.0875015259	20.0067005157	21.5958003998
22	1.5164999962	-0.1005000025	-0.1389999986	0.6782000065	-0.4133000076	2.242399931	-0.0573000014	-0.0988000035	0.0566999987	0.1764000058	0.0315999985	0.1976999938	-0.0691	-0.0287999995	0.0111999996	0.2153999954	0.0300999992	0.0186999999	0.1448000073	0.0328000002	0.2687000036	-35.7370986938	15.5762996674	14.5209999084
23	3.2922999859	0.1984000057	0.6848999858	1.620200038	-0.0758000016	2.0534000397	0.0219000001	0.121299997	0.0238000005	0.0181000009	0.1700000018	0.4104000032	-0.0719999969	-0.3571000099	-0.1167000011	0.1860000044	0.0294000003	0.0326000005	0.2164999992	0.0877000019	0.3282000124	-44.4970016479	22.8509998322	3.7061998844
24	7.1423001289	-1.4850000143	1.9630999565	2.6710999012	0.0109999999	2.4010999203	0.0542000011	-0.0833000019	0.4889999926	0.056400001	0.0372000001	-0.1058000028	-0.1630000025	0.0678000003	-0.1039000005	0.3158000112	-0.0156999994	0.0518000014	0.1817999929	0.0247000009	0.2921999991	-21.896900177	26.699300766	10.4046001434
25	6.7539000511	-0.6504999995	3.6461999416	1.1505999565	0.1207000017	3.8545999527	0.141900003	0.2637999952	0.1653999984	0.0060000001	-0.1251000017	-0.2067999989	-0.1833000034	0.2210000008	-0.0035999999	0.2752999961	0.0132999998	0.0493000001	0.2231999934	0.060800001	0.279700011	-27.2297000885	25.1744995117	0.7899000049
26	1.1822999716	-0.1655000001	-0.1597000062	3.9028999805	1.0334000587	4.1174998283	0.1763000041	0.1299999952	0.3005999923	0.0722000003	0.0116999997	0.4300000072	-0.6399000287	-0.2694000006	-0.1591999978	0.3221000135	0.0606999993	0.0856000036	0.2195000052	0.0873999968	0.4146000147	-44.8490982056	32.1421012878	5.9105000496
27	2.6854999065	0.2590999901	0.5461000204	3.4704999924	-1.1513999701	2.4565000534	-0.0065000001	0.2494000047	0.5446000099	0.114699997	0.0502999984	0.052099999	-0.4674000144	-0.0790000036	-0.0333000012	0.4120999873	0.0244999994	0.0852999985	0.2003999949	0.0758000016	0.4483999908	-33.4832000732	36.0685005188	2.3954000473
28	1.7533999681	-0.0143999998	1.8260999918	1.0217000246	-0.6445999742	2.8986999989	-0.2351000011	-0.5042999983	0.2134999931	0.3280000091	0.2432000041	-0.1978999972	-0.4778000116	-0.0401000008	0.0430999994	0.4523000121	-0.053199999	0.0423999988	0.4176000059	-0.1379999965	0.4379999936	-23.4713001251	24.3229999542	42.827999115
29	4.2509999275	0.0665000007	0.8389999866	1.2364000082	-1.4774999619	3.3808000088	0.1074000001	-0.4848000109	0.198300004	0.0097000003	0.127700001	-0.481099993	-0.3109999895	0.3152999878	-0.2352000028	0.3465000093	-0.0496000014	-0.0068000001	0.4131000042	-0.1544000059	0.3977000117	-13.9103002548	16.8299999237	41.5433006287
30	3.9335999489	0.814899981	0.0071999999	1.2303999662	-0.2973000109	1.0944999456	0.1677999943	-0.0732000023	0.0808999985	-0.0186000001	0.0003	-0.1975000054	-0.1631000042	0.1755000055	-0.1528999954	0.3291000128	-0.0291000009	-0.0161000006	0.2991000116	-0.0936999992	0.2892000079	-23.3644008636	12.1618003845	35.8833999634
31	1.8637000322	0.3282000124	0.1931000054	2.7516000271	-0.8138999939	1.9630000591	-0.0397999994	-0.3585999906	0.0031000001	0.0454000011	0.1445000023	-0.360799998	-0.056400001	0.0649999976	-0.112499997	0.3014999926	-0.0241999999	-0.0414000005	0.3355999887	-0.0710999966	0.2628000081	-23.0048999786	3.6744000912	39.813999176
32	6.3843998909	-1.4285999537	0.0967999995	2.8320999146	-0.9671999812	1.3113000393	-0.1963	-0.9120000005	0.0976999998	0.3124000132	0.0948999971	-0.4997000098	-0.1400000006	0.1744000018	0.1562999934	0.4420000017	-0.0077999998	-0.0940999985	0.5267000198	-0.0588999987	0.3366000056	-19.2649993896	5.9793000221	51.7692985535
33	7.5015001297	-0.5809999704	1.5454000235	3.964400053	0.3030999899	2.1466999054	0.1351999938	-1.0649000406	0.4302000105	0.6571000218	-0.1075000018	0.2544000149	-0.2443999946	0.0693000033	-0.0226000007	0.3370999992	-0.0353999995	0.0377000012	0.4032999873	-0.0812999979	0.2509999871	-41.9813995361	11.2160997391	47.8241996765
34	8.3706998825	-2.5313999653	2.9312000275	1.9733999968	-1.4201999903	2.9633998871	0.1033999994	-0.8500000238	-0.355399996	0.2547000051	0.0905999988	0.0450000018	0.1143999994	-0.3991999924	-0.1626999974	0.4929000139	-0.0604000017	0.0065000001	0.5613999963	-0.0186999999	0.2485000044	-36.0702018738	4.3677000999	54.6912002563
35	1.4235999584	-0.2198999971	-1.0978000164	3.4941000938	-0.6230999827	2.7404000759	0.2664999962	-0.6754000187	0.0966000035	0.2904999852	-0.0384999998	-0.3695000112	-0.164199993	0.2915000021	-0.2148000002	0.5218999982	-0.0276999995	-0.1075000018	0.6668999791	-0.1537999958	0.4494999945	-18.8703994751	15.646900177	57.6669006348
36	4.3769001961	-1.4325000048	0.3788999915	3.3933999538	-0.0197999999	1.772300005	-0.445600003	-0.3601999879	-0.0111999996	0.617299974	0.0892999992	0.3826000094	-1.0470000505	-0.7228000164	0.2415000051	0.8005999923	0.074000001	0.0410999991	0.8963000178	-0.1785999984	0.3680999875	-38.9888000488	13.2840003967	59.5289001465

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 23 through 35 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 36 through 53 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 54 through 66 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 67 through 90 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 91 through 177 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 178 through 204 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 205 through 222 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 223 through 244 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 245 through 266 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 267 through 287 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 23 through 53 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 54 through 113 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 114 through 177 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 178 through 204 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 205 through 222 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 223 through 266 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 267 through 288 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 24 through 35 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 36 through 77 )
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 78 through 102 )
21	X-RAY DIFFRACTION	21	chain 'C' and (resid 103 through 121 )
22	X-RAY DIFFRACTION	22	chain 'C' and (resid 122 through 177 )
23	X-RAY DIFFRACTION	23	chain 'C' and (resid 178 through 204 )
24	X-RAY DIFFRACTION	24	chain 'C' and (resid 205 through 222 )
25	X-RAY DIFFRACTION	25	chain 'C' and (resid 223 through 235 )
26	X-RAY DIFFRACTION	26	chain 'C' and (resid 236 through 257 )
27	X-RAY DIFFRACTION	27	chain 'C' and (resid 258 through 287 )
28	X-RAY DIFFRACTION	28	chain 'D' and (resid 23 through 53 )
29	X-RAY DIFFRACTION	29	chain 'D' and (resid 54 through 90 )
30	X-RAY DIFFRACTION	30	chain 'D' and (resid 91 through 147 )
31	X-RAY DIFFRACTION	31	chain 'D' and (resid 148 through 177 )
32	X-RAY DIFFRACTION	32	chain 'D' and (resid 178 through 204 )
33	X-RAY DIFFRACTION	33	chain 'D' and (resid 205 through 222 )
34	X-RAY DIFFRACTION	34	chain 'D' and (resid 223 through 236 )
35	X-RAY DIFFRACTION	35	chain 'D' and (resid 237 through 266 )
36	X-RAY DIFFRACTION	36	chain 'D' and (resid 267 through 288 )

-
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://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