PDB-7ula: Structure of the Pseudomonas putida AlgKX modification and secret...

ID or keywords:

Entry

Database: PDB / ID: 7ula

Title

Structure of the Pseudomonas putida AlgKX modification and secretion complex

Components

(Alginate biosynthesis protein ...) x 2

Keywords

TRANSFERASE / Acetyltransferase / TPR / complex / SUGAR BINDING PROTEIN

Function / homology

Function and homology information

alginic acid biosynthetic process / acyltransferase activity / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / cell outer membrane / periplasmic space
Similarity search - Function

Biological species

Pseudomonas putida (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.46 Å

Authors

Gheorghita, A.A. / Li, E.Y. / Pfoh, R. / Howell, P.L.

Funding support

Canada, 1items

Citation

Journal: Nat Commun / Year: 2022
Title: Structure of the AlgKX modification and secretion complex required for alginate production and biofilm attachment in Pseudomonas aeruginosa.
Authors: Gheorghita, A.A. / Li, Y.E. / Kitova, E.N. / Bui, D.T. / Pfoh, R. / Low, K.E. / Whitfield, G.B. / Walvoort, M.T.C. / Zhang, Q. / Codee, J.D.C. / Klassen, J.S. / Howell, P.L.

History

Deposition	Apr 4, 2022	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 14, 2022	Provider: repository / Type: Initial release
Revision 1.1	Dec 21, 2022	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2	Oct 25, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	7ula.cif.gz	365.3 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	7ula_validation.pdf.gz	459.8 KB	Display	wwPDB validaton report
Full document	7ula_full_validation.pdf.gz	465.4 KB	Display
Data in XML	7ula_validation.xml.gz	26.8 KB	Display
Data in CIF	7ula_validation.cif.gz	37.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ul/7ula ftp://data.pdbj.org/pub/pdb/validation_reports/ul/7ula	HTTPS FTP

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Related structure data

Related structure data	3e4bS 4kncS S: Starting model for refinement
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	#261 - Sep 2021 DNA-Sequencing Nanopores similarity (1) #22 - Oct 2001 Photosystem I similarity (1) #262 - Oct 2021 Fifty Years of Open Access to PDB Structures similarity (1) #29 - May 2002 Penicillin-binding Proteins similarity (1) #95 - Nov 2007 Multidrug Resistance Transporters similarity (1)

Deposited unit

B: Alginate biosynthesis protein AlgK

A: Alginate biosynthesis protein AlgX

hetero molecules

106 kDa, 2 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)	169.950, 169.950, 143.020
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	97
Space group name H-M	I422
Space group name Hall	I42
Symmetry operation	#1: x,y,z #2: -y,x,z #3: y,-x,z #4: x,-y,-z #5: -x,y,-z #6: -x,-y,z #7: y,x,-z #8: -y,-x,-z #9: x+1/2,y+1/2,z+1/2 #10: -y+1/2,x+1/2,z+1/2 #11: y+1/2,-x+1/2,z+1/2 #12: x+1/2,-y+1/2,-z+1/2 #13: -x+1/2,y+1/2,-z+1/2 #14: -x+1/2,-y+1/2,z+1/2 #15: y+1/2,x+1/2,-z+1/2 #16: -y+1/2,-x+1/2,-z+1/2

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Alginate biosynthesis protein ... , 2 types, 2 molecules BA

#1: Protein	Alginate biosynthesis protein AlgK Mass: 50415.980 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas putida (bacteria) / Gene: algK, PP_1285 / Production host: Escherichia coli (E. coli) / References: UniProt: Q88NC7
#2: Protein	Alginate biosynthesis protein AlgX / Probable alginate O-acetyltransferase AlgX Mass: 54489.246 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas putida (bacteria) / Gene: algX, PP_1282 / Production host: Escherichia coli (E. coli) References: UniProt: Q88ND0, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups

#1: Protein

Alginate biosynthesis protein AlgK

Mass: 50415.980 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Pseudomonas putida (bacteria) / Gene: algK, PP_1285 / Production host:

Escherichia coli (E. coli) / References: UniProt: Q88NC7

#2: Protein

Alginate biosynthesis protein AlgX / Probable alginate O-acetyltransferase AlgX

Mass: 54489.246 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Pseudomonas putida (bacteria) / Gene: algX, PP_1282 / Production host:

Escherichia coli (E. coli)
References: UniProt: Q88ND0, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups

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Non-polymers , 4 types, 38 molecules

#3: Chemical	ChemComp-NI / NICKEL (II) ION Mass: 58.693 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ni
#4: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₃H₈O₃
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 27 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.46 Å³/Da / Density % sol: 50.02 %
Crystal grow	Temperature: 298.15 K / Method: vapor diffusion, sitting drop Details: 0.1 M Tris-HCl pH = 8.5, 0.01 M Nickel (II) chloride, 20% (w/v) PEG2000 MME

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 1.512 Å
Detector	Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 25, 2019
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.512 Å / Relative weight: 1
Reflection	Resolution: 2.46→46 Å / Num. obs: 38142 / % possible obs: 99.87 % / Redundancy: 13.9 % / B_iso Wilson estimate: 61.89 Å² / CC_1/2: 1 / R_merge(I) obs: 0.063 / Net I/σ(I): 33.2
Reflection shell	Resolution: 2.46→2.548 Å / Redundancy: 9 % / R_merge(I) obs: 1.158 / Num. unique obs: 3741 / CC_1/2: 0.666 / % possible all: 99.3

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Processing

Software

Name	Version	Classification
PHENIX	1.18.2_3874+SVN	refinement
XDS		data reduction
XDS		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3E4B, 4KNC

3e4b

4knc

Resolution: 2.46→46 Å / SU ML: 0.4365 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.163
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2535	1916	5.03 %
R_work	0.2154	36189	-
obs	0.2173	38105	99.9 %

Solvent computation

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

Displacement parameters

B_iso mean: 71.53 Å²

Refinement step

Cycle: LAST / Resolution: 2.46→46 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5628	0	31	27	5686

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.005	5781
X-RAY DIFFRACTION	f_angle_d	0.859	7860
X-RAY DIFFRACTION	f_chiral_restr	0.05	861
X-RAY DIFFRACTION	f_plane_restr	0.0054	1053
X-RAY DIFFRACTION	f_dihedral_angle_d	18.9897	817

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 (%)
2.46-2.52	0.409	124	0.3969	2520	X-RAY DIFFRACTION	99.44
2.52-2.59	0.4138	130	0.3561	2557	X-RAY DIFFRACTION	99.56
2.59-2.67	0.3424	145	0.3268	2508	X-RAY DIFFRACTION	99.89
2.67-2.75	0.35	133	0.2925	2599	X-RAY DIFFRACTION	100
2.75-2.85	0.3024	142	0.286	2540	X-RAY DIFFRACTION	100
2.85-2.96	0.3251	128	0.286	2575	X-RAY DIFFRACTION	99.96
2.96-3.1	0.3337	137	0.2618	2554	X-RAY DIFFRACTION	100
3.1-3.26	0.2969	139	0.2396	2574	X-RAY DIFFRACTION	100
3.26-3.47	0.2705	150	0.2177	2562	X-RAY DIFFRACTION	100
3.47-3.73	0.2274	130	0.2024	2584	X-RAY DIFFRACTION	100
3.73-4.11	0.1844	141	0.1748	2598	X-RAY DIFFRACTION	100
4.11-4.7	0.2301	145	0.1676	2601	X-RAY DIFFRACTION	100
4.7-5.92	0.2257	135	0.1914	2643	X-RAY DIFFRACTION	100
5.93-46	0.2226	137	0.2	2774	X-RAY DIFFRACTION	99.76

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	0.741230526868	-0.0732536434686	-1.21257727732	0.0580697765999	0.0442710667205	2.09456867326	0.0573152355564	-0.690487042509	-0.502783647506	0.968973022374	-0.0504423257672	-0.246937770186	0.0118121268579	-0.120344572045	-0.289145729321	0.650482111235	0.306461038554	0.0662187453122	1.61423320741	0.318280476086	1.0265407965	4.60230677489	-35.4422481113	-15.0952032188
2	2.38199277754	-0.755173908917	-2.4342421295	0.905800647784	0.618498515607	2.51386650469	0.875270772586	3.09875679185	0.539537559541	-1.37695958961	-0.614964690263	-0.423453789904	-1.5258683618	-2.20241688026	0.169254667872	1.30055447189	-0.391340970645	-0.27425218208	1.56757253921	0.147187301453	0.743764724503	-0.588103720174	-44.1406027189	-12.732382802
3	2.31466202971	-0.644662024648	1.32903166739	6.5692561425	-0.657256618055	5.21407377068	-0.480723936239	-0.464824549039	0.153334864651	0.281543049414	0.0819518995353	-0.548331102241	0.359796396389	0.131283687282	0.839720801836	1.16119922221	-0.14766202346	-0.111935248125	1.99234418383	0.122722192422	0.662574362875	-1.86323156007	-30.7748845512	-6.04924228619
4	2.09818903578	-0.232462195115	-0.861284855279	1.57782456173	-0.820583511896	1.02923771845	0.168755020097	-1.23161526836	-1.01674973888	0.551933750531	-0.0437391397926	-0.136050400289	-0.0721972213114	-0.301387109572	-0.194932124359	0.607072008551	-0.229037174535	-0.0862782564469	1.05509947317	0.235191683574	0.769138541489	-7.34402646375	-31.6552568033	-17.6719972314
5	3.45476953385	-0.235709054152	1.19115962652	2.24496808206	0.763014623629	3.15044561804	0.177641320529	-1.44135563464	-0.167028679559	1.05653675787	-0.0649470410616	0.0416621852585	0.16504458581	-0.223233210236	-0.144740284653	0.658611766914	-0.0350374553249	0.0671433332664	0.756836863313	0.101636877393	0.610384905297	-8.39284062397	-21.3583237567	-22.3902620283
6	5.89598734506	0.396440514055	-0.192158860218	3.40771755545	0.313682069957	3.72635309071	0.13066769317	-0.95069312938	1.1343720852	0.250175218234	0.232453207238	-0.0983342003136	-0.534663675818	-0.134693268147	-0.16404759185	0.547677014012	-0.0112869040659	0.0960509090619	0.403966013223	-0.00250597942894	0.540942959376	-4.62332444552	-12.2040451266	-28.8303029533
7	3.43172315385	1.15217095089	2.15213861277	0.986891725613	-0.695696519927	5.10447992874	0.0412022997413	0.278464013493	-0.229217802344	0.302121451988	0.525305082306	0.221554914153	0.793530668437	-0.0620333117558	-0.222131866256	0.518116306016	-0.0557228176169	0.00128461889882	0.444699848075	0.0548548827518	0.733762960149	-8.44973746986	-23.3794130461	-35.5892218084
8	2.70202722207	-2.95257939281	0.448076926795	3.49258682271	-0.985795233132	7.24861612042	0.215869304127	0.56414291003	0.548459593004	-0.0948531707085	0.424830944917	0.00738424306893	0.052844283268	0.344197021497	-0.392122704399	0.490997034193	-0.0934456157957	-0.0351045254372	0.533361268758	0.00769232010269	0.511981175696	-5.43643049022	-19.8843360385	-44.90929451
9	3.39710923062	-1.26172867044	-0.170574051433	4.76938790272	-0.710435468258	2.75718026996	0.324031257249	0.837507060904	0.678401895631	-0.866634530936	-0.164447787286	-0.977294582034	0.529725066381	0.708433180053	0.106559075184	1.03799809348	-0.0465680009378	0.133969005682	0.741127774815	0.0104525345886	0.671396882029	0.114969207925	-23.3339445127	-52.9248876132
10	2.54756535545	-0.263413403496	0.103200198975	2.80812347878	0.162054778727	1.41395829775	-0.202470948209	-0.546619578781	0.0150778438774	0.0602879512212	0.192019568803	-0.354547171143	0.162101396912	0.00790851870493	-0.0425108427528	0.459236739571	0.0547765647512	-0.062863594185	0.577500080031	0.00190754569248	0.614464369682	-3.91718646062	-35.416399944	-55.678203805
11	3.0252439975	0.197029462045	0.97690813695	2.53541561412	-1.14970699031	1.85427846506	-0.145805047765	-0.683078713998	-0.313770723217	0.744336688262	0.160097856635	-0.0350535759426	0.0970577855159	-0.198878693556	0.100155787038	0.612095303622	0.050520081352	-0.019433237255	0.529942071286	0.0546542326022	0.514014749412	-6.35239257328	-48.8482068339	-51.1914129165
12	0.11343032583	0.202395831147	0.338523855071	4.31676630725	2.57592509023	2.37946034219	-0.0280246325331	-0.441183733337	-0.0711069347864	0.615163043431	-0.585397432696	0.159236092237	0.783583038353	-0.294509318569	0.108669982275	0.677676978437	-0.158334532132	0.0799150288606	0.762152387595	0.208786065608	0.822335068576	-13.5750059157	-60.5242591682	-54.247819739
13	3.98314245398	2.4299448491	-1.63131325951	4.44970681846	2.6162773735	5.57107983701	0.407276316357	-0.723210887863	-0.384329883294	1.06719243294	-0.167900037893	-0.242315763079	-0.0994713714524	-0.28202841687	0.0337601586965	0.975328058879	-0.00753399106215	0.0639235138142	1.04237587585	0.355693660719	0.500613608164	-11.3690559973	-61.4857289324	-39.8634560129
14	0.449303466868	-0.438892531692	0.143807201831	1.23069626277	-0.915984662498	1.07809346267	0.195861586713	0.0191311786834	-1.205032184	0.11164535048	0.342015033536	-0.0913100697418	0.859777010444	0.12990888205	0.616470681435	0.834962297526	-0.0457430830903	0.0267326450374	0.589484127652	0.0600326719696	0.908035468049	-17.3356595509	-65.4862373599	-65.5143278391
15	1.70838119146	-0.0543566919188	0.108726144368	0.490533118004	0.0648027975614	1.22822309118	-0.0735488553315	0.291729062862	-0.208852988664	-0.195283486547	-0.000749880630568	-0.203542994852	0.266428637041	0.0375737304478	0.0114028107083	0.553559023343	-0.0775722896953	0.033959446143	0.497913922985	-0.0857937828445	0.499052092423	-21.3624666498	-49.6388866201	-87.5329867085
16	1.40992900021	0.300069411354	0.298543736401	1.66860595822	0.428866694888	0.74908914305	-0.132630646273	0.138017807248	0.0138360771236	0.111250675084	0.0318449845464	-0.252506983952	-0.116910621205	-0.0866217610056	0.0615418698058	0.376377464079	-0.0516105901084	0.00743194240508	0.41110150401	-0.00596601488302	0.475942467094	-19.4737008021	-36.8414648299	-80.3439943804
17	1.05425613909	-0.242488669024	0.879932830156	1.16238932606	-0.467891778167	0.483512257351	-0.0267982092435	-0.0824092248444	0.062683480622	0.49793819055	0.0870064262919	0.616712833931	-0.429535607989	0.01328810919	-0.186988851124	0.615825434551	-0.0551836300898	0.0183146851374	0.551106256547	0.0629611241182	0.527416106295	-20.3202987662	-33.4693507938	-72.8101605758
18	1.66862686031	0.878397859042	-0.252997456605	0.865473535635	0.0637471501493	0.95296540158	0.023725726756	0.213117582361	0.147205931858	0.00678478058849	0.0137538551408	-0.0319171557997	0.00133811112439	-0.011047827016	0.106064152599	0.469170280656	-0.054864363384	0.00342787400676	0.466849267627	0.0269290204323	0.454926347674	-32.7995353822	-36.4081649995	-85.4653467156
19	1.07398100459	0.383024338085	0.411617059659	0.207744018496	0.196508367332	0.509377146177	0.00388705459741	0.748283571816	0.23169634448	-0.00424503306389	-0.250408375189	0.297700736422	-0.151170353555	-0.217081730542	0.190600760825	0.65559635086	-0.0488291492639	-0.0607165838157	0.934170885424	0.0552955588966	0.836370716988	-61.2930779647	-37.6593119354	-90.2896789813
20	0.79404028284	-0.408822214103	-0.0637421027502	0.342711160131	0.16902808326	1.02023859275	0.0528618127324	0.422202040557	-0.0402760214044	0.0847811899969	-0.212867075643	0.269207898693	0.205527916691	-0.0947635859474	0.295041916626	0.518598103334	-0.124629098615	-0.0404134369898	0.738624061544	-0.0465360945889	0.600160335438	-56.1425251904	-42.8081917418	-87.943655736
21	2.7549241511	0.511278303583	0.596692042613	2.33454199165	0.67906661412	1.01189761831	0.0496975435343	0.387332180861	-0.460637213911	-0.122552779581	0.122994147148	0.287971179862	0.116058056397	0.0694265344213	0.202801675712	0.503316805562	-0.099275982	-0.0616796793824	0.650716099643	-0.0753187947725	0.521578947694	-53.5690081001	-43.3248128489	-88.672457605
22	1.9998645395	4.59544856211	4.93787592187	1.9999158837	1.99994228476	1.99989592882	-0.33714238619	0.0185008043899	-0.781453855353	0.427619192858	0.217648918773	0.142263964044	0.915739571427	-0.697179307884	0.115725848206	1.09487778223	0.135106174487	-0.603681860566	1.01084149015	0.0875391233373	1.58495001136	-45.1720920157	-24.2985106222	-96.7878723359

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 'B' and (resid 139 through 148 )	B	A	139 - 148	2 - 11
2	2	chain 'B' and (resid 149 through 160 )	B	A	149 - 160	12 - 19
3	3	chain 'B' and (resid 161 through 172 )	B	A	161 - 172	20 - 31
4	4	chain 'B' and (resid 173 through 192 )	B	A	173 - 192	32 - 51
5	5	chain 'B' and (resid 193 through 223 )	B	A	193 - 223	52 - 82
6	6	chain 'B' and (resid 224 through 243 )	B	A	224 - 243	83 - 102
7	7	chain 'B' and (resid 244 through 264 )	B	A	244 - 264	103 - 125
8	8	chain 'B' and (resid 265 through 298 )	B	A	265 - 298	126 - 159
9	9	chain 'B' and (resid 299 through 314 )	B	A	299 - 314	160 - 175
10	10	chain 'B' and (resid 315 through 347 )	B	A	315 - 347	176 - 208
11	11	chain 'B' and (resid 348 through 396 )	B	A	348 - 396	209 - 259
12	12	chain 'B' and (resid 397 through 408 )	B	A	397 - 408	260 - 271
13	13	chain 'B' and (resid 409 through 457 )	B	A	409 - 457	272 - 320
14	14	chain 'A' and (resid 29 through 52 )	A	J	29 - 52	1 - 24
15	15	chain 'A' and (resid 53 through 180 )	A	J	53 - 180	25 - 152
16	16	chain 'A' and (resid 181 through 231 )	A	J	181 - 231	153 - 203
17	17	chain 'A' and (resid 232 through 264 )	A	J	232 - 264	204 - 229
18	18	chain 'A' and (resid 265 through 345 )	A	J	265 - 345	230 - 310
19	19	chain 'A' and (resid 346 through 382 )	A	J	346 - 382	311 - 342
20	20	chain 'A' and (resid 383 through 409 )	A	J	383 - 409	343 - 369
21	21	chain 'A' and (resid 410 through 469 )	A	J	410 - 469	370 - 429
22	22	chain 'A' and (resid 470 through 470 )	A	J	470	430

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