PDB-7q6n: Structure of WrbA from Salmonella Typhimurium bound to ME0052

ID or keywords:

Entry

Database: PDB / ID: 7q6n

Title

Structure of WrbA from Salmonella Typhimurium bound to ME0052

Components

NAD(P)H dehydrogenase (quinone)

Keywords

FLAVOPROTEIN / NADH dehydrogenase / oxidoreductase / anti-virulence compound

Function / homology

Function and homology information

NADPH dehydrogenase (quinone) activity / NAD(P)H dehydrogenase (quinone) / NADH:ubiquinone reductase (non-electrogenic) activity / NAD binding / FMN binding / NADP binding / flavin adenine dinucleotide binding
Similarity search - Function

Biological species

Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.33 Å

Authors

Gabrielsen, M. / Beckham, K.S.H. / Roe, A.J.

Funding support

1items

Citation

Journal: Microbiology (Reading, Engl.) / Year: 2022
Title: Crystal structures of WrbA, a spurious target of the salicylidene acylhydrazide inhibitors of type III secretion in Gram-negative pathogens, and verification of improved specificity of next-generation compounds.
Authors: Zambelloni, R. / Beckham, K.S.H. / Wu, H.J. / Elofsson, M. / Marquez, R. / Gabrielsen, M. / Roe, A.J.

History

Deposition	Nov 8, 2021	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Aug 3, 2022	Provider: repository / Type: Initial release
Revision 1.1	Jan 31, 2024	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	7q6n.cif.gz	535.1 KB	Display	PDBx/mmCIF format
PDB format	pdb7q6n.ent.gz	373.9 KB	Display	PDB format
PDBx/mmJSON format	7q6n.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	7q6n_validation.pdf.gz	3 MB	Display	wwPDB validaton report
Full document	7q6n_full_validation.pdf.gz	3.1 MB	Display
Data in XML	7q6n_validation.xml.gz	34.1 KB	Display
Data in CIF	7q6n_validation.cif.gz	45.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/q6/7q6n ftp://data.pdbj.org/pub/pdb/validation_reports/q6/7q6n	HTTPS FTP

-
Related structure data

Related structure data	7q6mC 7q6oC 2r96S S: Starting model for refinement C: citing same article (ref.)
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	#133 - Jan 2011 Nitric Oxide Synthase similarity (2) #228 - Dec 2018 Directed Evolution of Enzymes similarity (2)

Deposited unit

A: NAD(P)H dehydrogenase (quinone)

B: NAD(P)H dehydrogenase (quinone)

C: NAD(P)H dehydrogenase (quinone)

D: NAD(P)H dehydrogenase (quinone)

hetero molecules

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

1

Idetical with deposited unit
defined by author
Evidence: Established in literature

Unit cell

Length a, b, c (Å)	92.160, 92.810, 93.970
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁
Space group name Hall	P2ac2ab
Symmetry operation	#1: x,y,z #2: x+1/2,-y+1/2,-z #3: -x,y+1/2,-z+1/2 #4: -x+1/2,-y,z+1/2

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
d_1	ens_1	(chain "A" and (resid 1 through 23 or (resid 24...
d_2	ens_1	(chain "B" and (resid 1 through 23 or (resid 24...
d_3	ens_1	(chain "C" and (resid 1 through 23 or (resid 24...
d_4	ens_1	(chain "D" and (resid 1 through 63 or resid 65...
d_1	ens_2	chain "E"
d_2	ens_2	chain "F"
d_3	ens_2	chain "G"
d_4	ens_2	chain "H"

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Beg label comp-ID	End label comp-ID	Label asym-ID	Label seq-ID
d_1	1	ens_1	MET	PRO	A	1 - 63
d_1	2	ens_1	GLU	GLU	A	66
d_1	3	ens_1	LEU	PHE	A	69 - 114
d_1	4	ens_1	SER	ASN	A	116 - 200
d_2	1	ens_1	MET	PRO	B	2 - 64
d_2	2	ens_1	GLU	PHE	B	66 - 112
d_2	3	ens_1	SER	ASN	B	114 - 198
d_3	1	ens_1	MET	PRO	D	2 - 64
d_3	2	ens_1	GLU	PHE	D	66 - 112
d_3	3	ens_1	SER	ASN	D	114 - 198
d_4	1	ens_1	MET	PRO	E	8 - 70
d_4	2	ens_1	GLU	PHE	E	72 - 118
d_4	3	ens_1	SER	SER	E	121
d_4	4	ens_1	THR	ASN	E	124 - 207
d_1	1	ens_2	FMN	FMN	F
d_1	2	ens_2	ME0	ME0	F	2
d_2	1	ens_2	FMN	FMN	G
d_2	2	ens_2	ME0	ME0	G	2
d_3	1	ens_2	FMN	FMN	H
d_3	2	ens_2	ME0	ME0	H	2
d_4	1	ens_2	FMN	FMN	I
d_4	2	ens_2	ME0	ME0	I	2

NCS ensembles :

ID
ens_1
ens_2

NCS oper:

ID	Code	Matrix	Vector
1	given	(-0.994008209446, 0.108857905838, -0.00988108753035), (0.109297272015, 0.988759176743, -0.102026451163), (-0.0013363698419, -0.102495105948, -0.994732610993)	-47.7947857457, 0.806816612356, -35.4325964543
2	given	(-0.907923194638, -0.0258071319598, -0.418341325448), (-0.0267339851093, -0.992504589017, 0.119247368191), (-0.418283117849, 0.119451382246, 0.900428009672)	-49.8387159835, 57.8286117434, -14.6323630965
3	given	(0.902687347172, -0.0816155858099, 0.422486034573), (-0.0843837616702, -0.996358874349, -0.0121808978743), (0.421941860951, -0.0246554184621, -0.906287579258)	8.32756880337, 54.054706105, -26.4951918408
4	given	(-0.848047627081, -0.00303303623462, -0.529911334935), (-0.065684838802, -0.991670268247, 0.110795221138), (-0.525833361582, 0.128766764993, 0.840784393338)	-52.4298667375, 56.2214037368, -20.6995330531
5	given	(-0.992750733951, 0.118634511703, -0.019282968447), (0.120044182078, 0.986629604828, -0.110233466904), (0.00594765401927, -0.11174916335, -0.993718647255)	-48.4338442598, 0.922178129875, -34.8041374969
6	given	(0.887919582189, -0.108912854338, 0.446919238482), (-0.112637913689, -0.993467184705, -0.0183208437039), (0.445994973027, -0.034072614723, -0.894386684248)	9.52696458468, 52.9588050554, -24.8303645772

#1: Protein	NAD(P)H dehydrogenase (quinone) / Flavoprotein WrbA / NAD(P)H:quinone oxidoreductase / NQO Mass: 24675.785 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria) Gene: STM1119 / Production host: Escherichia coli (E. coli) References: UniProt: Q8ZQ40, NAD(P)H dehydrogenase (quinone)
#2: Chemical	ChemComp-8YX / 2-azanyl-4,6-bis(bromanyl)phenol Mass: 266.918 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₆H₅Br₂NO / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE Mass: 456.344 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₇H₂₁N₄O₉P
#4: Chemical	ChemComp-PG4 / TETRAETHYLENE GLYCOL Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₈H₁₈O₅ / Comment: precipitant*YM
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 198 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.39 Å³/Da / Density % sol: 48.59 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.6 Details: 8 % (v/v) Tacsimate pH 8, 20 % (w/v) polyethylene glycol 3350

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97625 Å
Detector	Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 20, 2021
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97625 Å / Relative weight: 1
Reflection	Resolution: 2.33→46.98 Å / Num. obs: 66323 / % possible obs: 100 % / Observed criterion σ(F): 1.35 / Redundancy: 13.3 % / B_iso Wilson estimate: 28.71 Å² / CC_1/2: 0.992 / R_pim(I) all: 0.04 / R_rim(I) all: 0.147 / Net I/σ(I): 17
Reflection shell	Resolution: 2.34→2.4 Å / Mean I/σ(I) obs: 3.8 / Num. unique obs: 2525 / CC_1/2: 0.897 / R_pim(I) all: 0.208 / R_rim(I) all: 0.779 / % possible all: 100

-
Processing

Software

Name	Version	Classification
PHENIX	1.18.2_3874	refinement
PHENIX	1.18.2_3874	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 2R96

2r96

Resolution: 2.33→46.98 Å / SU ML: 0.2538 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.703
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1963	3323	5.01 %	RANDOM
R_work	0.1651	62997	-	-
obs	0.1667	66320	99.93 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 30.79 Å²

Refinement step

Cycle: LAST / Resolution: 2.33→46.98 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5853	0	177	198	6228

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0142	6180
X-RAY DIFFRACTION	f_angle_d	1.5043	8415
X-RAY DIFFRACTION	f_chiral_restr	0.07	926
X-RAY DIFFRACTION	f_plane_restr	0.0089	1066
X-RAY DIFFRACTION	f_dihedral_angle_d	21.4137	2140

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)
ens_1	d_2	A	X-RAY DIFFRACTION	Torsion NCS	0.50686587394
ens_1	d_3	A	X-RAY DIFFRACTION	Torsion NCS	0.456890190691
ens_1	d_4	A	X-RAY DIFFRACTION	Torsion NCS	0.528807519842
ens_2	d_2	A	X-RAY DIFFRACTION	Torsion NCS	0.673560542271
ens_2	d_3	A	X-RAY DIFFRACTION	Torsion NCS	0.116626595242
ens_2	d_4	A	X-RAY DIFFRACTION	Torsion NCS	0.310198196187

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 (%)
2.33-2.37	0.3527	123	0.2411	2609	X-RAY DIFFRACTION	100
2.37-2.4	0.3224	102	0.232	2665	X-RAY DIFFRACTION	99.96
2.4-2.44	0.2404	152	0.2098	2665	X-RAY DIFFRACTION	100
2.44-2.48	0.2338	112	0.1956	2606	X-RAY DIFFRACTION	100
2.48-2.52	0.213	168	0.1972	2600	X-RAY DIFFRACTION	99.86
2.52-2.57	0.2941	128	0.1953	2638	X-RAY DIFFRACTION	99.82
2.57-2.62	0.2449	125	0.1928	2655	X-RAY DIFFRACTION	100
2.62-2.67	0.2285	154	0.2025	2587	X-RAY DIFFRACTION	99.96
2.67-2.73	0.2553	149	0.1876	2642	X-RAY DIFFRACTION	99.96
2.73-2.79	0.2249	168	0.1963	2594	X-RAY DIFFRACTION	100
2.79-2.86	0.2228	146	0.1927	2610	X-RAY DIFFRACTION	99.96
2.86-2.94	0.2705	128	0.1902	2654	X-RAY DIFFRACTION	99.93
2.94-3.02	0.2259	115	0.1785	2610	X-RAY DIFFRACTION	99.96
3.02-3.12	0.1916	134	0.1917	2640	X-RAY DIFFRACTION	99.93
3.12-3.23	0.2052	163	0.1719	2614	X-RAY DIFFRACTION	99.89
3.23-3.36	0.219	122	0.1769	2645	X-RAY DIFFRACTION	99.78
3.36-3.52	0.2217	145	0.1518	2594	X-RAY DIFFRACTION	100
3.52-3.7	0.183	130	0.1504	2640	X-RAY DIFFRACTION	100
3.7-3.93	0.1863	150	0.1355	2627	X-RAY DIFFRACTION	100
3.93-4.24	0.1225	146	0.1254	2645	X-RAY DIFFRACTION	100
4.24-4.66	0.1313	134	0.1155	2605	X-RAY DIFFRACTION	99.89
4.66-5.34	0.1346	131	0.1245	2617	X-RAY DIFFRACTION	99.96
5.34-6.72	0.1903	161	0.1603	2626	X-RAY DIFFRACTION	100
6.72-46.98	0.186	137	0.1696	2609	X-RAY DIFFRACTION	99.42

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	1.96620730592	0.388427998876	0.137015419862	3.77395963929	1.45634402882	2.91956431015	0.121884796872	-0.0168478411144	-0.344955891262	0.161623255265	0.107518584178	-0.457447097282	0.217638184794	-0.0285454498463	-0.0622666401239	0.201701331267	0.020320123654	-0.0325566101376	0.242036912007	0.00479277801813	0.314686703122	-8.75423279814	14.0026304548	-5.72427946859
2	1.75502286418	0.421797629624	0.157936585339	2.60022119628	0.431175758956	1.80415534802	-0.0915998529147	-0.297315107354	-0.477331117554	0.383676503065	0.176810300736	-0.28849308921	0.470492853107	0.202378739079	-0.0191570966788	0.26964247548	0.0666525846112	-0.0490619288202	0.211745260815	0.0307380761638	0.297565818991	-12.3693596443	9.36824229951	-1.729926602
3	2.64515789164	-0.170253000575	-0.122811917047	1.20712701582	-0.376628411481	2.79320684893	0.151017452685	0.0691722160584	-0.107001761238	0.134849409831	0.195895111665	-0.178003122362	-0.24047619914	0.311019808381	-0.0456163331542	0.175604389159	-0.00802582273369	-0.0365795810296	0.316762246585	0.04074689948	0.314516729231	3.24662375736	27.2003878011	-3.95486485184
4	1.14864692715	0.270612067401	0.151357535371	1.16886139014	-0.0981381312678	1.44983060427	-0.0232426671997	0.031566448344	-0.177369984997	-0.0486975348078	0.0754260508764	-0.252260294763	0.194405082094	0.268353775763	-0.0393742350971	0.134269845427	0.0188438097488	-0.00381883001815	0.159601875432	-0.0136925002222	0.226773133338	-10.1657586209	18.3080790953	-13.1341045117
5	1.57033006865	-0.392803253605	-0.139490149491	1.915430426	0.717348971346	1.8456408585	-0.08581531785	0.0180006108742	-0.454170768592	0.00257751979741	-0.0651943187732	0.377778107539	0.147046640397	-0.20076953466	0.051530489582	0.173251784916	-0.0178957000303	0.0145250691762	0.162118235456	0.0350787535636	0.295733955316	-25.5907291615	14.965005512	-9.44541576999
6	2.00142223965	-0.407708349978	-0.443502972418	2.07571485892	0.524600748723	0.542615865712	-0.027744128534	-0.574551195366	0.0170775374675	0.379508605446	-0.10030661649	0.323868002302	0.150849945978	-0.0423524559098	-0.0102642330622	0.173023282503	-0.0149275444147	0.050710559554	0.239963006225	0.033233285324	0.24373383622	-27.1734533372	22.9387188692	-0.829212121379
7	1.76685195713	1.01267076767	0.161443846374	2.76824582483	0.560537092429	1.64408826848	0.0326142004568	-0.525198298033	0.107742860079	0.589752833749	-0.00675779800739	-0.149787753185	-0.0825959882294	0.200577411378	-0.0267070506792	0.207680091472	-0.0113613159628	-0.00479622921152	0.272127461793	-0.0350452104933	0.1951163703	-16.1651587141	26.4372364898	4.77816129861
8	2.26220554205	-0.343669748796	-0.349397395575	3.24228837066	0.851720072742	2.39841695509	-0.0349137695105	-0.105827036639	-0.459093289672	0.222029956546	0.120692965705	-0.0472016788018	0.448908504156	0.0273425143971	0.00453902529194	0.237991925906	-0.0082081036082	-0.012886344792	0.203019856331	0.040893767154	0.287383152782	-21.816717241	8.91348650081	-4.67508453848
9	1.96321593949	0.503470740138	-0.296521789449	0.318584662677	0.600736600404	2.11540521181	-0.0123722787637	0.296024208327	-0.386556610983	-0.502776144191	0.138705698792	0.355056882613	0.26475421764	-0.220015721027	-0.0216820171983	0.300234892036	-0.0833625192674	-0.0998496181994	0.399240453391	-0.101183476579	0.364575680312	-37.398741054	13.0521237568	-30.8519632209
10	1.31378199388	-0.126505739475	0.239258353368	3.80828794708	-0.709515561654	1.76076980971	0.0288862624059	0.37657114069	-0.294175363674	-0.753260664526	-0.0698750745358	0.410948335466	0.200210945007	-0.176161953933	0.00218741860279	0.423197227973	-0.0975626946697	-0.0657104873375	0.421578555734	-0.087680799071	0.312064893915	-32.5939161492	11.4173344763	-37.1846980848
11	4.41359745338	-3.16796376874	0.282137287681	4.07753385026	-0.246877495055	1.15458242071	0.0388671176925	0.219510340788	-0.642187846902	-0.375749535275	-0.120221359797	0.385843164562	0.54039614331	-0.538364283709	0.0105972514995	0.409711216408	-0.119943378526	-0.0396128224739	0.424709427794	-0.116044050766	0.463182178204	-37.2921341089	5.19044424981	-30.8925452469
12	1.56831685211	-0.240025097123	0.165034556338	1.56231334253	-0.10992146136	1.65974309212	-0.0683112716106	0.268011921183	0.113598252285	-0.268062659315	-0.0310159964067	0.393792794564	-0.0106351259662	-0.428264445014	-0.0196688066237	0.305009079586	-0.0805531366219	-0.136858053249	0.497160342217	-0.0278888485218	0.478022833205	-45.0502500882	19.1924230882	-30.7804904199
13	1.49717191104	0.0596944998325	0.0637057097849	1.46507190818	0.124615940609	1.39309116195	-0.0590025167108	0.203845769494	-0.00557543848971	-0.2286684081	0.106832537094	0.206159026961	0.0878115840796	-0.335581455786	-0.0213072562816	0.180795138207	-0.0400071273669	-0.0352652753696	0.231047075159	-0.00806994989919	0.222753417095	-32.9204540345	20.852216155	-22.904096144
14	1.48453364793	-0.257762940479	0.749727839864	2.35066461269	0.310543916529	1.11607116178	-0.223746657351	0.398948545963	-0.341603026677	-0.406887023219	-0.0258908428542	-0.302904444344	0.169752268745	0.00967402105528	-0.00631583025136	0.289298625952	-0.0460214121931	-0.00299553655969	0.229023281752	-0.0452534702361	0.312329931024	-20.8619937027	14.0132683066	-27.2175089057
15	0.574939862777	0.313540680605	-0.408516534865	0.887466637074	-0.16265401386	0.846019992526	0.0973829974014	0.83218386531	-0.0966520000254	-0.788767835956	-0.115671473587	-0.388178532937	0.100169807203	0.0668266546014	-0.0156450472497	0.415124763842	-0.000691504554211	0.0524343492022	0.435251388587	-0.0219611399406	0.292225971527	-18.5063974178	20.7732795507	-36.2016745381
16	0.797683260049	-0.460700114286	0.269938453803	1.28753390809	-0.996022397456	1.09996361262	-0.0489385351982	0.655502400044	0.130795102113	-0.773192114664	-0.0357234121648	0.212164234251	-0.3236644487	-0.15620571019	-0.00979416689819	0.531152039548	-0.0360820491891	-0.0696671833934	0.490412984714	-0.0592559186197	0.251497199786	-28.8370987155	24.7003410182	-42.8766626842
17	2.23494678086	0.142967563548	-0.12956325527	2.55519962392	-0.473029280926	2.78743743656	-0.103360043031	0.187546232419	-0.173415037831	-0.424013506375	0.00290640765	-0.137239732137	0.598222917655	-0.0880652895291	0.0226688827039	0.308081357138	-0.0597255092225	-0.00938016627248	0.306674511546	-0.138173710336	0.324760481992	-25.0484011742	7.56533788733	-31.262417577
18	1.77664227363	-0.071499202576	-0.157623077574	2.47213906205	-0.418182880544	2.44449107248	0.0694763884166	0.195538793889	0.530752068292	-0.198840704811	0.0135285450772	0.394939615574	-0.317355088934	-0.114636177632	-0.0286609398143	0.27134661813	0.117696419293	-0.0121937290446	0.332272851478	0.0404651500032	0.338037487148	-39.5436406421	44.6816544998	-14.5691044943
19	1.77420332454	1.43608754007	-0.717979253813	4.16628155357	-0.901006046824	1.07433941758	0.00948524726146	-0.187032535179	0.352443774162	0.368705170497	0.108747067937	0.625383418334	-0.385246830883	-0.235783586232	-0.0266778254744	0.293827667573	0.10441639746	0.000632967455579	0.28095629789	-0.00766267140224	0.307698878873	-37.6337377262	46.0270030594	-6.77009073972
20	4.3728404713	2.77027505032	1.27894151586	3.73451841684	1.14957776755	1.52236753278	0.141293565839	-0.15404029322	0.519808809731	-0.154871600508	-0.168477169422	0.640636456366	-0.688968373438	-0.223137138036	0.00848375686851	0.425064009375	0.131670990214	-0.0165859908781	0.338602262053	0.0532871848338	0.392471248825	-38.702075667	52.5843171267	-14.3451703211
21	1.64066472975	0.340724014425	-1.19472842845	0.0776175065408	-0.244766514779	0.98681838714	-0.021527450226	0.0764297813211	-0.066592229962	-0.0673542280724	-0.0993438318411	0.651063692276	0.167814253618	-0.525171116031	0.0631271347826	0.263184003125	0.0389531634004	-0.0363240477973	0.513043944723	0.0195118529152	0.486793577701	-51.4713575943	30.7845849793	-16.8454461079
22	1.34704580475	0.176503758182	0.381744297551	2.12079560704	0.355861764387	0.922252495926	-0.223509393227	0.0319311969617	0.12413537596	-0.0319239687903	0.120987463299	0.622364263291	-0.321404269552	-0.693652789109	-0.0231009261853	0.35570384928	0.150912910773	-0.018010694129	0.429663451889	0.10152788441	0.472089292769	-44.2364785691	44.0973034024	-18.9960679617
23	1.29262753347	-0.0215881029645	-0.0954905927062	1.55171703129	0.0638762045971	1.52404876511	-0.0165115126545	0.227695489403	0.10932574823	-0.223089154642	0.0773302852573	0.256084813102	-0.257307819623	-0.322186871517	-0.0331678530063	0.192000405796	0.0337669170937	-0.0367076480713	0.211598802469	0.031349861125	0.212954342324	-32.8302944094	36.3961627104	-20.12816951
24	1.58520805747	0.0973005266732	0.00174101597122	1.63909372413	0.233673064152	1.38868989478	0.0263792862202	-0.164849719324	0.162662292893	0.170576980028	0.0201596289596	0.0535021769231	-0.349443405538	-0.0891885220577	-0.0407351096288	0.227515314571	0.0302767645241	0.00697439275838	0.174064007047	-0.0105078347836	0.218024241556	-28.1538229804	41.546264794	-6.29312024031
25	1.18119624022	0.127172579656	0.0588732278388	2.55627209966	0.114678955461	1.21832699046	-0.0488358342295	0.177957766029	0.380531722293	-0.432115151208	0.179429198861	-0.597306271052	-0.385792061258	0.220077296645	-0.046324970031	0.383168786827	-0.122561092887	0.0976435638821	0.349003802721	0.0275064309336	0.36502548253	-3.68109928807	46.3301690092	-27.4497545654
26	1.66440033887	-0.226320632274	0.047672472638	0.944198300797	0.143921601011	1.35505872015	0.087207409213	0.070797220916	0.305571712867	-0.371409658641	0.00772767523084	-0.637921153168	-0.294662770747	0.367425080283	-0.0183527714971	0.323641834719	-0.126840563074	0.112843350251	0.384394134722	-0.0204138429168	0.351983981926	2.24362152753	37.9500206951	-23.9997112868
27	1.68107372139	-0.255661322317	-0.211517411457	1.79630646565	0.0656892182152	1.27490497663	-0.0168229866519	0.194189497904	0.0482982019428	-0.295439760851	0.1273075482	-0.231154853956	-0.327483960329	0.223792465254	-0.0467561730269	0.23210158775	-0.0604864294279	0.0439069007213	0.198771353115	0.00423615403987	0.195183710447	-10.9030334786	37.035933709	-22.8754669498
28	1.60107273772	-0.108718428911	-0.202831944951	1.80472663468	0.0476285035287	1.5940570026	-0.0320297210933	0.22851244351	0.112946151889	-0.578336875654	0.182906740352	-0.175412018768	-0.349515333849	0.258920832754	-0.0746006131393	0.403968895099	-0.0781169514618	0.0615498450818	0.318294012716	0.0543938403594	0.233279485661	-11.4790596363	40.7898967585	-33.8586704377

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

ID	Refine TLS-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	chain 'A' and (resid 1 through 13 )	A	A	1 - 13	1 - 13
2	2	chain 'A' and (resid 14 through 38 )	A	A	14 - 38	14 - 38
3	3	chain 'A' and (resid 39 through 50 )	A	A	39 - 50	39 - 50
4	4	chain 'A' and (resid 51 through 133 )	A	A	51 - 133	51 - 136
5	5	chain 'A' and (resid 134 through 149 )	A	A	134 - 149	137 - 152
6	6	chain 'A' and (resid 150 through 162 )	A	A	150 - 162	153 - 165
7	7	chain 'A' and (resid 163 through 175 )	A	A	163 - 175	166 - 178
8	8	chain 'A' and (resid 176 through 197 )	A	A	176 - 197	179 - 200
9	9	chain 'B' and (resid 0 through 13 )	B	B	0 - 13	1 - 14
10	10	chain 'B' and (resid 14 through 28 )	B	B	14 - 28	15 - 29
11	11	chain 'B' and (resid 29 through 38 )	B	B	29 - 38	30 - 39
12	12	chain 'B' and (resid 39 through 70 )	B	B	39 - 70	40 - 71
13	13	chain 'B' and (resid 71 through 133 )	B	B	71 - 133	72 - 134
14	14	chain 'B' and (resid 134 through 149 )	B	B	134 - 149	135 - 150
15	15	chain 'B' and (resid 150 through 162 )	B	B	150 - 162	151 - 163
16	16	chain 'B' and (resid 163 through 175 )	B	B	163 - 175	164 - 176
17	17	chain 'B' and (resid 176 through 197 )	B	B	176 - 197	177 - 198
18	18	chain 'C' and (resid 0 through 13 )	C	D	0 - 13	1 - 14
19	19	chain 'C' and (resid 14 through 28 )	C	D	14 - 28	15 - 29
20	20	chain 'C' and (resid 29 through 38 )	C	D	29 - 38	30 - 39
21	21	chain 'C' and (resid 39 through 50 )	C	D	39 - 50	40 - 51
22	22	chain 'C' and (resid 51 through 70 )	C	D	51 - 70	52 - 71
23	23	chain 'C' and (resid 71 through 133 )	C	D	71 - 133	72 - 134
24	24	chain 'C' and (resid 134 through 197 )	C	D	134 - 197	135 - 198
25	25	chain 'D' and (resid -6 through 28 )	D	E	-6 - 28	1 - 35
26	26	chain 'D' and (resid 29 through 50 )	D	E	29 - 50	36 - 57
27	27	chain 'D' and (resid 51 through 162 )	D	E	51 - 162	58 - 172
28	28	chain 'D' and (resid 163 through 197 )	D	E	163 - 197	173 - 207

-
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