PDB-8fyv: Salmonella enterica serovar Typhimurium chemoreceptor Tsr (taxis ...

ID or keywords:

Entry

Database: PDB / ID: 8fyv

Title

Salmonella enterica serovar Typhimurium chemoreceptor Tsr (taxis to serine and repellents) ligand-binding domain in complex with l-serine

Components

Methyl-accepting chemotaxis protein

Methyl-accepting chemotaxis proteins

Keywords

SIGNALING PROTEIN /

Chemotaxis /

chemoreceptor / chemosensory / Tsr

Function / homology

Function and homology information

chemotaxis / transmembrane signaling receptor activity /

signal transduction /

plasma membrane
Similarity search - Function

Biological species

Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.2 Å

Authors

Baylink, A. / Gentry-Lear, Z. / Glenn, S.

Funding support

United States, 2items

Organization	Grant number	Country
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	1K99AI148587	United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	4R00AI148587-03	United States

Citation

Journal: To Be Published
Title: Bacterial vampirism mediated by chemotaxis
Authors: Baylink, A. / Gentry-Lear, Z. / Glenn, S.

History

Deposition	Jan 26, 2023	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 15, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8fyv.cif.gz	501.2 KB	Display	PDBx/mmCIF format
PDB format	pdb8fyv.ent.gz	346.3 KB	Display	PDB format
PDBx/mmJSON format	8fyv.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/fy/8fyv ftp://data.pdbj.org/pub/pdb/validation_reports/fy/8fyv	HTTPS FTP

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Related structure data

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

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#158 - Feb 2013 Proton-Gated Urea Channel similarity (8) #190 - Oct 2015 Two-component Systems similarity (4)

Deposited unit

A: Methyl-accepting chemotaxis protein

B: Methyl-accepting chemotaxis protein

C: Methyl-accepting chemotaxis protein

D: Methyl-accepting chemotaxis protein

E: Methyl-accepting chemotaxis protein

hetero molecules

91 kDa, 5 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Methyl-accepting chemotaxis protein

B: Methyl-accepting chemotaxis protein

hetero molecules

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

2

C: Methyl-accepting chemotaxis protein

D: Methyl-accepting chemotaxis protein

hetero molecules

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

3

E: Methyl-accepting chemotaxis protein

hetero molecules

E: Methyl-accepting chemotaxis protein

hetero molecules

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

Unit cell

Length a, b, c (Å)	125.807, 75.231, 129.588
Angle α, β, γ (deg.)	90.000, 116.470, 90.000
Int Tables number	5
Space group name H-M	C121
Space group name Hall	C2y
Symmetry operation	#1: x,y,z #2: -x,y,-z #3: x+1/2,y+1/2,z #4: -x+1/2,y+1/2,-z

#1: Protein	Methyl-accepting chemotaxis protein / Methyl-accepting chemotaxis proteins Mass: 18005.994 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria) Gene: DPS76_02420 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A5W2VA06
#2: Chemical	ChemComp-CL / CHLORIDE ION / Chloride Mass: 35.453 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Cl
#3: Chemical	ChemComp-SER / SERINE / Serine Type: L-peptide linking / Mass: 105.093 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: C₃H₇NO₃ / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Na
#5: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 275 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 3.05 Å³/Da / Density % sol: 59.66 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 1.69 M potassium phosphate pH 9.7 / PH range: 8-9.7

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 0.9765 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 4, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9765 Å / Relative weight: 1
Reflection	Resolution: 2.2→58 Å / Num. obs: 55162 / % possible obs: 100 % / Redundancy: 18.8 % / B_iso Wilson estimate: 26.26 Å² / CC_1/2: 0.994 / Net I/σ(I): 7.7
Reflection shell	Resolution: 2.2→2.26 Å / Num. unique obs: 4503 / CC_1/2: 0.838

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Processing

Software

Name	Version	Classification
DIALS		data scaling
PHENIX	1.20.1_4487	refinement
BOS		data collection
DIALS		data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.2→58 Å / SU ML: 0.3822 / Cross valid method: FREE R-VALUE / σ(F): 0.03 / Phase error: 32.1883
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2577	3908	3.63 %
R_work	0.2413	103897	-
obs	0.2419	55162	99.85 %

Solvent computation

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

Displacement parameters

B_iso mean: 52.86 Å²

Refinement step

Cycle: LAST / Resolution: 2.2→58 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5529	0	50	275	5854

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0019	5705
X-RAY DIFFRACTION	f_angle_d	0.4198	7734
X-RAY DIFFRACTION	f_chiral_restr	0.0271	844
X-RAY DIFFRACTION	f_plane_restr	0.0022	1022
X-RAY DIFFRACTION	f_dihedral_angle_d	3.7395	770

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 (%)
2.2-2.23	0.4183	130	0.3913	3730	X-RAY DIFFRACTION	99.92
2.23-2.26	0.6219	136	0.6097	3622	X-RAY DIFFRACTION	99.26
2.26-2.28	0.3948	156	0.4417	3741	X-RAY DIFFRACTION	99.62
2.28-2.32	0.326	135	0.3463	3689	X-RAY DIFFRACTION	99.95
2.32-2.35	0.3006	147	0.3141	3766	X-RAY DIFFRACTION	99.9
2.35-2.38	0.4284	117	0.3087	3676	X-RAY DIFFRACTION	99.74
2.38-2.42	0.3874	160	0.2986	3685	X-RAY DIFFRACTION	99.71
2.42-2.46	0.2719	135	0.2728	3697	X-RAY DIFFRACTION	99.51
2.46-2.5	0.3091	127	0.2876	3730	X-RAY DIFFRACTION	99.87
2.5-2.55	0.3081	148	0.2698	3704	X-RAY DIFFRACTION	100
2.55-2.6	0.2886	141	0.2623	3746	X-RAY DIFFRACTION	99.97
2.6-2.65	0.3391	129	0.2794	3703	X-RAY DIFFRACTION	99.82
2.65-2.71	0.251	166	0.275	3732	X-RAY DIFFRACTION	99.92
2.71-2.77	0.2457	109	0.2575	3666	X-RAY DIFFRACTION	99.84
2.77-2.84	0.3272	160	0.2604	3720	X-RAY DIFFRACTION	99.92
2.84-2.92	0.271	125	0.2344	3761	X-RAY DIFFRACTION	100
2.92-3	0.2193	157	0.2472	3681	X-RAY DIFFRACTION	99.87
3-3.1	0.252	123	0.2426	3718	X-RAY DIFFRACTION	100
3.1-3.21	0.3317	150	0.2429	3735	X-RAY DIFFRACTION	100
3.21-3.34	0.2852	130	0.2427	3700	X-RAY DIFFRACTION	99.92
3.34-3.49	0.2577	146	0.2145	3751	X-RAY DIFFRACTION	99.95
3.49-3.68	0.2365	136	0.1945	3691	X-RAY DIFFRACTION	99.9
3.68-3.91	0.1792	140	0.2018	3682	X-RAY DIFFRACTION	99.9
3.91-4.21	0.1963	150	0.1739	3705	X-RAY DIFFRACTION	99.9
4.21-4.63	0.1859	145	0.1616	3726	X-RAY DIFFRACTION	99.97
4.63-5.3	0.1773	132	0.1691	3735	X-RAY DIFFRACTION	100
5.3-6.67	0.222	139	0.2107	3708	X-RAY DIFFRACTION	100
6.68-58	0.1903	139	0.1892	3697	X-RAY DIFFRACTION	99.4

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	2.65937696617	0.204809655162	0.241892766986	3.05711278724	-1.04547894419	3.19963540783	-0.159161023921	0.612519635697	0.392188637299	-0.190878112046	0.0751695707702	-0.0597566978511	0.011896840315	0.222728820946	0.0303513080161	0.183983965498	-0.00766542935116	-0.0211187649259	0.395377195711	0.0809920623355	0.286513020959	22.2641653688	13.3368449108	45.8013471271
2	3.66584276566	4.09011625342	0.259421949436	5.98076741506	-2.10363004784	3.7153423798	-0.107898716075	1.03694049294	0.0718037749453	-0.352130581022	0.0393077727212	-0.0250276099252	0.0168107782451	0.374234878715	0.0102033407876	0.334524407975	0.077045117941	-0.0203053021027	0.441588407619	-0.0228642664906	0.242427562327	20.8283446186	9.23229806436	39.7742896906
3	2.9568892483	-0.34347785487	3.6666674757	0.0591083725878	-0.368018890902	4.67976717264	-0.304545332561	1.2184880602	0.83504445429	-0.43158769923	0.0965588862581	0.042452788781	-0.327521357093	0.472667218688	0.179169523865	0.737113637153	-0.282338548517	-0.00100205349931	1.20523353918	0.321920388933	0.609231480015	43.810860345	25.2672068522	38.6802378301
4	3.97603498977	2.21850364511	1.01868137309	2.31120185913	-0.141153772273	1.5845269742	-0.242503129524	0.442902062449	-0.335944432178	-0.337523939201	0.142533588314	-0.27877694851	0.13023940269	0.435550870197	0.111495333531	0.236655636958	0.0292314198151	0.0528634027204	0.363154572154	-0.00725933347939	0.247240754035	30.691107373	5.49946372645	47.4251422637
5	7.27650178742	5.08391565458	-1.3893571981	4.21399542499	-3.36364894964	5.03376180391	-0.0227558302178	0.359222871602	0.922127154192	0.602725368298	0.122024287365	0.578208044398	-1.18192208468	0.128767387206	-0.0797917302918	0.461955554626	-0.0619188665052	-0.0154440474764	0.370597260813	0.0556309783672	0.358661402947	36.3344768342	23.2726686934	50.6396527839
6	2.33939714414	-0.210884285044	0.155413874312	0.726002215632	-1.21154663172	3.12596998152	0.0119664173747	-0.0853634570618	0.189097501791	0.280233055934	-0.220189864147	-0.248250291104	-0.120234719733	-0.0672767532877	0.177901630443	0.183306692416	-0.0570124617417	-0.0462675552064	0.271851922629	0.00479292217659	0.269086447619	19.4963749166	15.3633113379	55.1386286511
7	1.71768276309	-0.582688817714	0.882586764976	8.74270604933	-6.04230826992	6.59735882593	-0.573377183076	-0.494827820192	0.456638233366	0.528216863603	0.0394365509097	-0.611305201851	-0.747913504335	-0.246061841164	0.576498509769	0.36270795694	0.00632709075134	-0.137072386811	0.419429602501	-0.0979417477415	0.409700295609	19.384928001	23.0587766097	60.7466407433
8	2.80188822154	-0.189468573803	2.95835942559	0.0601172368991	0.0665635698744	4.45173113468	0.481626460768	-0.310527272676	-0.422915197974	0.83956777774	-0.595809346397	-1.25438577189	-0.911862386669	0.285472463964	0.109079292188	1.10191676679	-0.150598005113	-0.238753310118	0.455054328952	0.0655591480258	0.872838610165	21.0141675377	43.428728026	46.8049131083
9	2.64119320692	-1.5161489097	0.856837410176	4.436078314	-2.72390006314	4.31835290096	-0.346153702194	-0.301806741473	-0.111589902339	0.917834023093	0.65133105277	0.227071391603	-0.736858777288	-1.15910621432	-0.0887626936403	0.161746909686	0.0110097525324	0.00648889747847	0.323124188457	-0.0439310010769	0.222491471977	8.69818894246	21.5012219633	54.0488327223
10	3.84140700206	0.727052051239	-0.4817815015	6.57054090999	-1.6989702301	4.3055217914	-0.0956858238088	-0.00047219540793	0.188775613763	0.0854940617815	-0.503920570896	-1.15001598865	-0.859206869036	0.707612499267	0.507248987182	0.378563331462	-0.0841989240796	-0.0743426272094	0.405928650333	0.0450183044781	0.395652755148	19.0694442681	29.7779528094	41.6557528414
11	2.70511139617	-1.22149425732	-0.784936415814	2.69178233835	0.756328185439	3.59691059684	0.34098251043	0.539069722752	-0.31386589898	-0.480794910793	-0.302616278256	0.128828328475	0.0790618010193	0.131159803337	-0.0498348952018	0.295909324433	0.0438982271351	-0.0106233138492	0.403477591101	-0.00721693850253	0.191816128984	1.1398916273	25.4702638997	26.9930286722
12	6.76047565564	-5.09565031418	0.106443198898	5.29636581058	0.525064682438	2.87265831584	0.53395030127	0.461733689599	-0.316676397433	-0.572556958934	-0.365226820413	0.338434564071	0.162268866577	-0.116920388195	-0.0972396238137	0.423501769115	-0.0134164652076	-0.0493436947931	0.405174908904	-0.0167495660653	0.280162003294	-4.62478221359	22.8650740351	23.6365155833
13	2.18102725403	-2.24746295568	4.26954074356	3.35862117361	-5.04453638796	8.79019863234	0.43018793432	1.96023826798	-1.13174161112	-0.0513646924933	-1.06281391153	0.693295310505	-0.621765334973	0.696349520311	0.705491110155	0.708471249679	0.261734881088	-0.0397453888584	1.32176603863	-0.297750203367	0.568035095875	21.1123334655	8.6689554575	22.0238851732
14	4.83994809567	-1.67418248893	0.210518885879	2.26640072175	-0.291487037413	2.88595671243	0.184962749004	0.00211809619081	-0.441663140089	0.0283146288672	-0.00443657002629	0.214272407234	0.417469588225	-0.211146912799	-0.167754335816	0.311090344078	-0.0520359778272	-0.0403116191035	0.236011159282	-0.0492183064916	0.270823050054	-0.658628808941	16.7170698102	34.2937066383
15	6.84387045634	-2.82808148581	-4.03954898049	3.93201832362	0.352152323076	4.75447925634	0.476466303928	0.826466760017	0.389758788232	-0.529561392399	-0.245912933639	-0.704015172684	0.0127470325411	0.466041633902	-0.174019899663	0.346079287933	0.0673233832552	0.0404264242622	0.63226326753	-0.0672592561004	0.390333384031	17.0024000998	19.6876769356	30.7101896731
16	0.989009318852	-0.0323494067317	1.05718101188	1.545192718	0.18862127572	2.01615346334	-0.0598420318034	-0.238716623381	0.268460447315	-0.0100103647569	-0.058557170266	-0.193486807186	-0.0928622805742	0.528205381465	0.0808527838878	0.200181723069	0.0581599331954	0.00429516053901	0.346516478656	0.0394095107179	0.243214994853	4.16493595989	32.7480561551	32.9625214317
17	7.61005749713	1.12020518176	-5.07617369152	3.23059452992	-0.931010896404	4.20588294838	0.275513631565	0.234408908481	0.504150519863	0.267624811185	-0.106299787225	-0.322918222176	-0.890304382369	0.596428711623	-0.06259439619	0.260397115083	-0.0363940767869	-0.0871487296724	0.536857245582	-0.0157778103107	0.37792847335	11.4399867935	38.5257727851	34.4513095357
18	1.65222761692	-0.807075998605	2.92889835362	2.37006380918	-0.901339870047	5.33482867748	0.300349456386	-0.638068734672	0.344115810652	-0.472396469617	-0.142444866494	-1.35631275833	-0.284094394004	1.99743748748	-0.0440699018364	0.431325965293	-0.13699367857	0.119754346994	1.15825201719	-0.0844380466378	0.836564707343	25.322003063	37.574512749	15.0207327774
19	3.47352530007	1.79554172415	-1.89352076602	2.72642873474	-1.52392250798	6.81557231676	-0.0258065909045	-0.0149010844921	0.36179877801	-0.0663664065675	-0.033342227022	0.163081098302	-0.763707236461	0.357645006362	0.0628255318762	0.310809506102	-0.01216205134	-0.056936904599	0.198398411346	-0.00333633929152	0.232406253424	2.50780730251	43.2213263587	26.6724401117
20	7.48253239509	-0.934599387261	-3.41774163123	1.73942095683	0.605728661007	4.45420056487	-0.329547944647	0.955197163252	-0.692168592008	-0.30376892072	0.123178185914	-0.305877221858	0.168568679487	0.319662583379	0.195974510171	0.391510625361	-0.0298978135274	0.0569691792157	0.606573234273	-0.137625258807	0.336065075176	11.0118872155	32.5106071925	15.1697052603
21	1.85712298092	0.874048014227	0.795054599407	3.64173884449	0.501930660223	3.146105914	0.0138093371516	0.160712721707	0.043909073594	-0.412667220985	0.0522722832059	0.299746957326	-0.136848058307	-0.564287736231	0.0244760095144	0.635949753726	0.00291900301027	-0.0446941929413	0.290527337097	-0.0651600622354	0.277320478291	-4.9077723353	37.5580758512	-0.603081968975
22	2.47389852283	0.574278168364	0.866978204523	3.58686408434	-1.17622803665	5.21397996548	-0.126735937923	0.216829817347	0.0112815058886	-0.599174011099	0.584599986341	0.255590722713	0.255222602366	-1.2827972495	-0.405782164451	0.426490065695	0.0790982156634	-0.00168925946979	0.505714984867	-0.0665101698881	0.223216850431	-10.9283008237	35.5620060279	-1.28449152179
23	1.51329711061	0.741078417807	0.408659942188	4.69013794539	-1.07279144585	6.20789006725	-0.0326494086383	-0.161234065332	0.127909614895	0.0868217591949	0.207173369979	0.192838230742	-0.706408455577	-0.801071840426	-0.151258923814	0.40254971023	0.0738928585049	0.0154231155138	0.523696589125	-0.0744944579183	0.258832988998	-10.4460610304	41.5165080327	8.88849482304
24	2.56924407401	-0.726735496788	1.44599413539	2.16437407442	-0.657326366063	4.8166207696	0.194737663325	-0.149971421739	-0.360368390893	-0.404532201898	0.167059628459	-0.392764175919	0.547364076309	0.0957541960148	-0.258819860626	0.564786535429	-0.0254866917773	-0.102416713023	0.379559966168	-0.00582703599985	0.339346590828	-1.48200980802	25.5773645234	10.35818538

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 42 through 79 )	A	A	42 - 79	1 - 38
2	2	chain 'A' and (resid 80 through 109 )	A	A	80 - 109	39 - 68
3	3	chain 'A' and (resid 110 through 118 )	A	A	110 - 118	69 - 77
4	4	chain 'A' and (resid 119 through 155 )	A	A	119 - 155	78 - 114
5	5	chain 'A' and (resid 156 through 201 )	A	A	156 - 182	115 - 141
6	6	chain 'B' and (resid 42 through 86 )	B	B	42 - 86	1 - 45
7	7	chain 'B' and (resid 87 through 110 )	B	B	87 - 110	46 - 69
8	8	chain 'B' and (resid 111 through 118 )	B	B	111 - 118	70 - 77
9	9	chain 'B' and (resid 119 through 155 )	B	B	119 - 155	78 - 114
10	10	chain 'B' and (resid 156 through 201 )	B	B	156 - 181	115 - 140
11	11	chain 'C' and (resid 43 through 78 )	C	C	43 - 78	1 - 36
12	12	chain 'C' and (resid 79 through 110 )	C	C	79 - 110	37 - 68
13	13	chain 'C' and (resid 111 through 118 )	C	C	111 - 118	69 - 76
14	14	chain 'C' and (resid 119 through 155 )	C	C	119 - 155	77 - 113
15	15	chain 'C' and (resid 156 through 201 )	C	C	156 - 182	114 - 140
16	16	chain 'D' and (resid 42 through 86 )	D	D	42 - 86	1 - 45
17	17	chain 'D' and (resid 87 through 109 )	D	D	87 - 109	46 - 68
18	18	chain 'D' and (resid 110 through 118 )	D	D	110 - 118	69 - 77
19	19	chain 'D' and (resid 119 through 155 )	D	D	119 - 155	78 - 114
20	20	chain 'D' and (resid 156 through 201 )	D	D	156 - 181	115 - 140
21	21	chain 'E' and (resid 42 through 78 )	E	E	42 - 78	1 - 37
22	22	chain 'E' and (resid 79 through 118 )	E	E	79 - 118	38 - 77
23	23	chain 'E' and (resid 119 through 155 )	E	E	119 - 155	78 - 114
24	24	chain 'E' and (resid 156 through 201 )	E	E	156 - 180	115 - 139

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