PDB-7ufw: Pfs230 D1D2 in complex with LMIV230-01

ID or keywords:

Entry

Database: PDB / ID: 7ufw

Title

Pfs230 D1D2 in complex with LMIV230-01

Components

Gametocyte surface protein P230
LMIV230-01

Keywords

CELL INVASION / antibody / Plasmodium falciparum / Pfs230 / transmission blocking

Function / homology

Function and homology information

cell surface / plasma membrane
Similarity search - Function

Biological species

Homo sapiens (human)

Plasmodium falciparum (malaria parasite P. falciparum)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.1 Å

Authors

Tang, W.K. / Tolia, N.H.

Funding support

United States, 1items

Citation

Journal: Immunity / Year: 2023
Title: A human antibody epitope map of Pfs230D1 derived from analysis of individuals vaccinated with a malaria transmission-blocking vaccine.
Authors: Tang, W.K. / Coelho, C.H. / Miura, K. / Nguemwo Tentokam, B.C. / Salinas, N.D. / Narum, D.L. / Healy, S.A. / Sagara, I. / Long, C.A. / Duffy, P.E. / Tolia, N.H.

History

Deposition	Mar 23, 2022	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 15, 2023	Provider: repository / Type: Initial release
Revision 1.1	Mar 1, 2023	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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
Revision 1.2	Oct 25, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3	Oct 9, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	7ufw.cif.gz	771 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	7ufw_validation.pdf.gz	457 KB	Display	wwPDB validaton report
Full document	7ufw_full_validation.pdf.gz	471.5 KB	Display
Data in XML	7ufw_validation.xml.gz	41.1 KB	Display
Data in CIF	7ufw_validation.cif.gz	58.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/uf/7ufw ftp://data.pdbj.org/pub/pdb/validation_reports/uf/7ufw	HTTPS FTP

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Related structure data

Related structure data	7u9eC 7u9wC 7ua2C 7ua8C 7ubsC 7uc8C 7ucqC 7ui1C 7jumS 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

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#21 - Sep 2001 Antibodies similarity (1) #256 - Apr 2021 SARS-CoV-2 Spike and Antibodies similarity (1)

Deposited unit

H: LMIV230-01

I: LMIV230-01

A: Gametocyte surface protein P230

B: Gametocyte surface protein P230

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

1

H: LMIV230-01

A: Gametocyte surface protein P230

defined by author
Evidence: gel filtration
68.2 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

I: LMIV230-01

B: Gametocyte surface protein P230

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

Unit cell

Length a, b, c (Å)	44.440, 151.370, 99.040
Angle α, β, γ (deg.)	90.000, 92.149, 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

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
d_1	ens_1	chain "A"
d_2	ens_1	(chain "B" and (resid 555 through 740 or resid 760 through 887))
d_1	ens_2	(chain "H" and (resid 1 through 141 or resid 143 through 251))
d_2	ens_2	chain "I"

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	ASP	GLY	C	1 - 314
d_2	1	ens_1	ASP	LEU	D	3 - 188
d_2	2	ens_1	GLU	GLY	D	193 - 320
d_1	1	ens_2	GLN	GLY	A	1 - 119
d_1	2	ens_2	SER	ARG	A	121 - 229
d_2	1	ens_2	GLN	ARG	B	1 - 228

NCS ensembles :

ID
ens_1
ens_2

NCS oper:

ID	Code	Matrix	Vector
1	given	(0.998518002185, 0.028251644349, 0.0465149858113), (0.028325298426, -0.999598330302, -0.000924946559974), (0.0464701708897, 0.00224112664558, -0.998917164018)	3.45630241301, -14.1244357892, -48.5341777639
2	given	(0.999379774411, 0.027493751378, 0.0220036390739), (0.0275730763596, -0.999614310987, -0.00330979306319), (0.0219041538845, 0.00391444826521, -0.999752411919)	3.29164463369, -14.1910661188, -48.8364592238

#1: Antibody	LMIV230-01 Mass: 27470.537 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Protein	Gametocyte surface protein P230 Mass: 40738.957 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum) Gene: PFS230, PF230, S230, PF3D7_0209000 / Production host: Homo sapiens (human) / References: UniProt: P68874
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 366 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	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: 2.44 Å³/Da / Density % sol: 49.59 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, hanging drop Details: 0.1 M Hepes, pH 6.5, 1.0 M lithium chloride, 20% PEG 6000

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 11, 2020
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.1→19.92 Å / Num. obs: 75653 / % possible obs: 99.5 % / Redundancy: 9.6 % / B_iso Wilson estimate: 39.67 Å² / CC_1/2: 0.99 / Net I/σ(I): 11
Reflection shell	Resolution: 2.1→2.15 Å / Num. unique obs: 5372 / CC_1/2: 0.8

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Processing

Software

Name	Version	Classification
PHENIX	1.19.2_4158	refinement
XDS		data reduction
XDS		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 7JUM

7jum

Resolution: 2.1→19.92 Å / SU ML: 0.2499 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.9286
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2131	3781	5 %
R_work	0.1899	71785	-
obs	0.1911	75566	99.52 %

Solvent computation

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

Displacement parameters

B_iso mean: 57 Å²

Refinement step

Cycle: LAST / Resolution: 2.1→19.92 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8626	0	0	366	8992

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	8805
X-RAY DIFFRACTION	f_angle_d	0.6717	11901
X-RAY DIFFRACTION	f_chiral_restr	0.0508	1320
X-RAY DIFFRACTION	f_plane_restr	0.0052	1501
X-RAY DIFFRACTION	f_dihedral_angle_d	12.8698	3283

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)
ens_1	d_2	H	X-RAY DIFFRACTION	Torsion NCS	0.415594012739
ens_2	d_2	A	X-RAY DIFFRACTION	Torsion NCS	0.470496197083

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 (%)
2.1-2.13	0.3825	133	0.3104	2522	X-RAY DIFFRACTION	95.03
2.13-2.15	0.2902	135	0.3043	2571	X-RAY DIFFRACTION	97.48
2.15-2.18	0.277	139	0.2739	2637	X-RAY DIFFRACTION	99.04
2.18-2.22	0.2763	141	0.2653	2663	X-RAY DIFFRACTION	99.29
2.22-2.25	0.3346	138	0.2582	2670	X-RAY DIFFRACTION	99.68
2.25-2.28	0.2635	139	0.2386	2633	X-RAY DIFFRACTION	99.86
2.28-2.32	0.2569	141	0.2381	2674	X-RAY DIFFRACTION	99.75
2.32-2.36	0.2783	139	0.2357	2646	X-RAY DIFFRACTION	99.89
2.36-2.4	0.2753	140	0.2386	2645	X-RAY DIFFRACTION	99.79
2.4-2.45	0.2644	141	0.2231	2689	X-RAY DIFFRACTION	99.86
2.45-2.5	0.2519	141	0.2253	2670	X-RAY DIFFRACTION	99.89
2.5-2.55	0.2835	140	0.2272	2651	X-RAY DIFFRACTION	99.64
2.55-2.61	0.2601	143	0.2268	2705	X-RAY DIFFRACTION	99.86
2.61-2.68	0.2616	138	0.2232	2625	X-RAY DIFFRACTION	99.86
2.68-2.75	0.2636	141	0.2149	2668	X-RAY DIFFRACTION	99.86
2.75-2.83	0.2295	140	0.2132	2660	X-RAY DIFFRACTION	99.86
2.83-2.92	0.2605	141	0.2178	2680	X-RAY DIFFRACTION	99.86
2.92-3.03	0.2812	139	0.2116	2647	X-RAY DIFFRACTION	99.89
3.03-3.15	0.2507	142	0.201	2690	X-RAY DIFFRACTION	99.89
3.15-3.29	0.2386	139	0.2024	2634	X-RAY DIFFRACTION	99.71
3.29-3.46	0.2145	141	0.1895	2684	X-RAY DIFFRACTION	99.75
3.46-3.68	0.1997	142	0.1815	2681	X-RAY DIFFRACTION	99.93
3.68-3.96	0.1996	140	0.1708	2674	X-RAY DIFFRACTION	100
3.96-4.35	0.1536	141	0.1436	2674	X-RAY DIFFRACTION	99.96
4.36-4.98	0.1387	142	0.1347	2701	X-RAY DIFFRACTION	99.96
4.98-6.24	0.1808	142	0.1549	2683	X-RAY DIFFRACTION	99.93
6.24-19.92	0.1809	143	0.1823	2708	X-RAY DIFFRACTION	99.65

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	1.76654335231	-0.0339429018848	-0.484275234593	2.51897519446	1.64691173507	4.36837884315	0.0715366479772	-0.0164044633181	0.226732407476	0.0326824933303	0.00446783322479	0.183844646143	-0.189142973908	-0.153675685676	-0.0279887735832	0.281282325345	0.0140836023324	0.0344504998676	0.299453216204	0.05391962949	0.473533313624	-21.4610760087	-24.7534400198	-1.63276567979
2	2.1237423801	0.361327808384	0.100542436112	2.91411278952	2.2080758586	4.94455798473	-0.0390678485947	-0.0749049500096	-0.268870591444	0.307749393596	0.0485242371971	0.0554322211432	0.437154371226	-0.0102311860195	-0.0480153060153	0.296831450267	-0.000922878327211	0.0227268008474	0.217774420041	0.0521831303725	0.379908129142	-19.2270058227	-33.8619485282	1.55484125223
3	1.98509537452	-0.810856761834	-2.83471204304	3.54690907512	1.92346678775	4.13705486345	-0.06536815265	-0.306977466497	0.143455285266	0.420480938226	-0.176660000045	-0.0269916132919	-0.152877236038	0.51365627213	-0.180678414249	0.362534979322	-0.0204976428712	0.0272367261554	0.351554783586	0.0310481455681	0.456525944918	-17.0540143413	-22.2988921885	5.98414515419
4	2.56450565114	-0.159707903427	-1.06286102486	3.37643092159	1.85296203631	3.70523272001	0.0755055012402	-0.00897740365361	0.0643683760601	-0.0498892038029	-0.0758963726721	0.0933782194003	-0.132146431859	0.0379232640807	0.0917208282144	0.24530349213	-0.0277377788751	0.034579224665	0.280283112745	0.0646319558953	0.392398660262	-13.7871075656	-24.921881031	-3.38273169742
5	1.71096998701	-0.0629638072064	0.255119638585	5.47803184696	-1.03439286444	2.84043097746	-0.0788757668055	-0.0601367745151	0.168987188904	0.0685172705507	-0.0213379929571	-0.178692094032	-0.170757100242	0.177673942707	0.0872167744295	0.284138242914	-0.0088213155325	0.0258871719489	0.346698631181	-0.00171327900802	0.502113542219	-1.53339626113	-17.6498302218	-10.4556558473
6	2.22089427781	0.623032994224	-0.32173283098	5.70639155613	-1.23151036155	3.22142171561	0.0108372672377	0.0615250634324	0.199845467084	-0.0775615005682	-0.115233777788	-0.316097802251	-0.178646846339	0.114653747178	0.102207400124	0.224172563993	-0.0269696131812	0.00820370818451	0.320738519461	0.00583117944425	0.405527752994	-3.16582360191	-18.1302046917	-12.7311026429
7	2.27175408974	0.269955115831	0.505193085587	2.81044344399	1.89956144776	3.09630257468	-0.0204939167709	0.00112285045536	-0.229136497018	0.0721154891096	-0.204235762335	0.454366557946	0.105484196359	-0.173018578106	0.172087447755	0.281538804956	0.0207495838473	-0.0128661033769	0.353954730224	0.0227547105283	0.569644236368	-22.4097204202	10.9379265772	-47.1435215062
8	2.93938511354	0.951460369826	2.16158874691	3.25170471496	0.409484413696	3.41463885922	0.419778452289	0.0488997337831	-0.728870525284	-0.332848249213	0.131424157698	-0.496943272701	0.206546470402	0.559531437334	-0.170102527019	0.343711051455	0.0468432386657	-0.0108147009182	0.317409684086	-0.0316493043257	0.517491723495	-10.6402220005	7.72534928462	-49.4808603787
9	2.81211059819	0.573383472555	0.0235520564863	2.3706824186	2.36954920905	6.13180038282	0.0287135196151	0.335872609533	0.38162833405	-0.917069703356	-0.0663065922287	0.171302986804	-0.764892723983	-0.000166052073399	-0.00427913384717	0.348991638567	0.0159517770084	0.0440202739843	0.271257086614	0.0723142016341	0.496010604753	-12.7048468825	20.2115509695	-51.6400494074
10	2.06565072742	-0.226840385185	1.7082961705	2.94650367948	0.66430367994	2.55026652307	0.0437999404972	0.120268819514	-0.14030951196	-0.247992052372	-0.0859185331263	0.173863848601	0.0181803182097	0.0938558056315	-0.0135097932751	0.286395277058	0.0040671228629	0.0126962121151	0.312440205602	0.0215134419114	0.438430249461	-15.6689778071	11.5277501971	-49.5654271234
11	1.51651213016	-0.805863476992	-0.0104739367864	5.38243574839	-1.11380236248	3.3896200932	-0.0357113849487	-0.0647704137064	-0.144403765125	0.139713428726	-0.125832518368	-0.407954047022	0.210450120448	0.264849770416	0.187705517084	0.292379146899	0.0347789804712	0.0366001670934	0.403406683887	0.0380960646127	0.512875942694	0.324728449458	3.54323527277	-35.7819280404
12	2.63574045462	-1.09701009614	0.201544846735	7.0954803441	-2.29313557407	4.38570453432	0.139346701132	0.216272266363	-0.0928534360145	-0.688655425487	-0.308262954002	-0.618616911986	0.480597168429	0.352557626405	0.155430889889	0.31666321256	0.0617621677362	0.0359200025825	0.425172730128	0.0018026581525	0.541955321323	-0.953854356578	4.39241597175	-43.2614737363
13	1.8093898623	0.226343899862	-0.0217228829357	4.99096467233	0.0987907591489	1.87251779225	-0.0727719650199	0.272907592195	-0.0501422649012	-0.418159545817	0.0686816703431	0.0121760599236	0.0359481005493	0.0633143835058	0.0114468783866	0.304831673564	-0.00829999940543	-0.000607058777416	0.311640256504	-0.00990820649922	0.362898060355	-15.0374607506	-48.8142261928	-22.5354895131
14	7.1585704571	0.682755684959	0.546843777208	7.79162154955	0.947047029349	6.66404659789	0.436275204042	-0.666153980932	0.376407836731	1.07408374677	-0.099977404499	-0.249336852424	-0.148511036653	-0.161677196752	0.115359536187	0.886331901156	-0.0508031449913	0.102208073237	0.465525353704	0.0345053092317	0.683544712732	-21.5081483834	-70.5002854732	0.921298504664
15	3.3606201731	0.461338986415	1.01728203614	5.38538930276	0.141207554003	4.39048140516	0.0217942123699	0.061937286861	0.0890910549847	0.264913886812	-0.143309366838	0.131627649672	0.0888436542963	-0.130236644365	0.0805148983248	0.467726836952	-0.00473401311642	0.116667439783	0.318867249254	0.00925633445751	0.489683027204	-30.0820389284	-80.4137892667	-10.9538250799
16	2.24011828424	1.76289639445	-0.584235022144	3.61742585823	-0.682991693143	1.42937980732	0.0151763607138	-0.134327870367	-0.179946148853	0.142463659263	0.0219373164549	-0.159682436326	0.032561993073	0.038452322154	-0.000770771155651	0.495155261661	0.0351171224087	0.095838047728	0.330542389217	-0.0138327573435	0.514137282857	-26.3660981765	-76.577487759	-10.9338237848
17	1.66468478732	-0.724713108423	0.269187621764	4.3951299131	-0.11579916646	2.06284472157	-0.10955913449	-0.278963434482	0.114361929671	0.447663958688	0.141687172284	-0.309882765395	-0.0218146592035	0.137714434119	-0.0307270247847	0.350058136724	0.00467100384888	-0.00094192589099	0.338037720766	-0.0412021541081	0.451479138766	-13.8743332451	34.3209533582	-26.8995394158
18	0.873740189166	1.79329504227	-0.234660476264	4.61251793171	-2.38759425825	4.32564150659	0.139254753611	0.262703160264	-0.535284951673	-0.845252194064	-0.5784396279	-0.583794141901	0.464127817626	0.763865233889	0.210038215861	0.948870529495	0.128139886122	0.0654583309496	0.609703562928	0.00730851419234	0.779759648287	-19.2048892389	53.0716356772	-50.4214268233
19	1.64870509021	-2.13297651076	2.07220509851	8.71579995582	-1.71837292954	2.98075935533	-0.127170947691	0.770059457276	0.0898857397934	-1.67628755081	-0.0988631310433	0.0101241231145	0.304074073129	-0.070172981057	0.056326754777	0.726087281171	0.00618461383265	0.0469885594628	0.466225345099	-0.0170104482147	0.602800173314	-27.8438407933	60.7413582347	-46.8262338743
20	1.85212842516	-1.31968689718	0.794990483968	8.6096934265	-1.09821068211	5.35013685238	-0.242596185391	0.0792954826389	0.222668520761	0.324004549051	-0.0490777243041	0.214632494436	-0.197609529372	-0.391163719281	0.0976779868218	0.441230596098	-0.0154822223998	0.0165442045081	0.343722330235	-0.0118898943659	0.494931999034	-28.7132569499	68.93186885	-36.1635582741
21	2.39959499788	-1.64828070158	0.292178546893	4.11880759131	-0.528548171823	2.07855347496	-0.0287271575024	0.0831510079131	0.0428549421108	-0.0406310684055	-0.0125448820349	-0.110552705869	0.00772481182471	-0.0421978582926	0.0486986809374	0.434184067661	-0.0409607780144	0.0126913876539	0.281366515668	-0.0382255545583	0.505462089338	-25.5433214067	61.7286284402	-39.0386701399

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 'H' and (resid 1 through 45 )	H	A	1 - 45	1 - 45
2	2	chain 'H' and (resid 46 through 83 )	H	A	46 - 83	46 - 83
3	3	chain 'H' and (resid 84 through 98 )	H	A	84 - 98	84 - 98
4	4	chain 'H' and (resid 99 through 146 )	H	A	99 - 146	99 - 124
5	5	chain 'H' and (resid 147 through 191 )	H	A	147 - 191	125 - 169
6	6	chain 'H' and (resid 192 through 251 )	H	A	192 - 251	170 - 229
7	7	chain 'I' and (resid 1 through 32 )	I	B	1 - 32	1 - 32
8	8	chain 'I' and (resid 33 through 45 )	I	B	33 - 45	33 - 45
9	9	chain 'I' and (resid 46 through 67 )	I	B	46 - 67	46 - 67
10	10	chain 'I' and (resid 68 through 146 )	I	B	68 - 146	68 - 123
11	11	chain 'I' and (resid 147 through 233 )	I	B	147 - 233	124 - 210
12	12	chain 'I' and (resid 234 through 251 )	I	B	234 - 251	211 - 228
13	13	chain 'A' and (resid 555 through 734 )	A	C	555 - 734	1 - 180
14	14	chain 'A' and (resid 735 through 777 )	A	C	735 - 777	181 - 204
15	15	chain 'A' and (resid 778 through 823 )	A	C	778 - 823	205 - 250
16	16	chain 'A' and (resid 824 through 887 )	A	C	824 - 887	251 - 314
17	17	chain 'B' and (resid 553 through 734 )	B	D	553 - 734	1 - 182
18	18	chain 'B' and (resid 735 through 773 )	B	D	735 - 773	183 - 206
19	19	chain 'B' and (resid 774 through 794 )	B	D	774 - 794	207 - 227
20	20	chain 'B' and (resid 795 through 823 )	B	D	795 - 823	228 - 256
21	21	chain 'B' and (resid 824 through 887 )	B	D	824 - 887	257 - 320

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