PDB-7qr8: SpCas9 bound to PTPRC off-target1 DNA substrate

ID or keywords:

Entry

Database: PDB / ID: 7qr8

Title

SpCas9 bound to PTPRC off-target1 DNA substrate

Components

(PTPRC off-target1 ...) x 2
CRISPR-associated endonuclease Cas9/Csn1
PTPRC sgRNA

Keywords

HYDROLASE / crispr / cas9 / off-target / ternary complex

Function / homology

Function and homology information

maintenance of CRISPR repeat elements / 3'-5' exonuclease activity / DNA endonuclease activity / defense response to virus / Hydrolases; Acting on ester bonds / DNA binding / RNA binding / metal ion binding
Similarity search - Function

Biological species

Streptococcus pyogenes (bacteria)
synthetic construct (others)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.75 Å

Authors

Pacesa, M. / Jinek, M.

Funding support

Switzerland, 1items

Citation

Journal: Cell / Year: 2022
Title: Structural basis for Cas9 off-target activity.
Authors: Pacesa, M. / Lin, C.H. / Clery, A. / Saha, A. / Arantes, P.R. / Bargsten, K. / Irby, M.J. / Allain, F.H. / Palermo, G. / Cameron, P. / Donohoue, P.D. / Jinek, M.

History

Deposition	Jan 10, 2022	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Oct 26, 2022	Provider: repository / Type: Initial release
Revision 1.1	Nov 23, 2022	Group: Database references / Category: citation / citation_author Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._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
Revision 1.2	Jan 31, 2024	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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Validation report

Summary document	7qr8_validation.pdf.gz	440.8 KB	Display	wwPDB validaton report
Full document	7qr8_full_validation.pdf.gz	455.8 KB	Display
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Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/qr/7qr8 ftp://data.pdbj.org/pub/pdb/validation_reports/qr/7qr8	HTTPS FTP

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Related structure data

Related structure data	7qqoC 7qqpC 7qqqC 7qqrC 7qqsC 7qqtC 7qquC 7qqvC 7qqwC 7qqxC 7qqzC 7qr0C 7qr1C 7qr5C 7qr7C 7zo1C 5fq5S 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
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PDB pages

PDBj /

wwPDB /

NCBI

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Deposited unit

A: PTPRC sgRNA

B: CRISPR-associated endonuclease Cas9/Csn1

C: PTPRC off-target1 target strand

D: PTPRC off-target1 non-target strand

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	178.278, 68.029, 186.741
Angle α, β, γ (deg.)	90.000, 110.740, 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

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PTPRC off-target1 ... , 2 types, 2 molecules CD

#3: DNA chain	PTPRC off-target1 target strand Mass: 8707.598 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: DNA chain	PTPRC off-target1 non-target strand Mass: 3629.365 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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RNA chain / Protein , 2 types, 2 molecules AB

#1: RNA chain	PTPRC sgRNA Mass: 27363.361 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Protein	CRISPR-associated endonuclease Cas9/Csn1 / SpCas9 / SpyCas9 Mass: 158588.781 Da / Num. of mol.: 1 / Mutation: D10A, H840A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus pyogenes (bacteria) / Gene: cas9, csn1, SPy_1046 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: Q99ZW2, Hydrolases; Acting on ester bonds

#1: RNA chain

PTPRC sgRNA

Mass: 27363.361 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

#2: Protein

CRISPR-associated endonuclease Cas9/Csn1 / SpCas9 / SpyCas9

Mass: 158588.781 Da / Num. of mol.: 1 / Mutation: D10A, H840A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Streptococcus pyogenes (bacteria) / Gene: cas9, csn1, SPy_1046 / Production host:

Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q99ZW2, Hydrolases; Acting on ester bonds

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Non-polymers , 3 types, 203 molecules

#5: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Chemical	ChemComp-K / POTASSIUM ION Mass: 39.098 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: K
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 191 / 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: 2.64 Å³/Da / Density % sol: 53 %
Crystal grow	Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.1 M Tris-acetate pH 8.5, 0.3-0.5 M KSCN, 17-19% PEG3350

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
Detector	Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Nov 3, 2017
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.75→48.12 Å / Num. obs: 54916 / % possible obs: 99.9 % / Redundancy: 6.9 % / B_iso Wilson estimate: 58.81 Å² / CC_1/2: 0.998 / R_merge(I) obs: 0.18 / Net I/σ(I): 11.5
Reflection shell	Resolution: 2.75→2.85 Å / R_merge(I) obs: 1.78 / Mean I/σ(I) obs: 1 / Num. unique obs: 5429 / CC_1/2: 0.544

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Processing

Software

Name	Version	Classification
PHENIX	1.20_4459	refinement
Coot		model building
XDS		data reduction
XSCALE		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5FQ5

5fq5

Resolution: 2.75→48.12 Å / SU ML: 0.4046 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.3101
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2502	2741	4.99 %
R_work	0.2215	52147	-
obs	0.2229	54888	99.93 %

Solvent computation

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

Displacement parameters

B_iso mean: 80.35 Å²

Refinement step

Cycle: LAST / Resolution: 2.75→48.12 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10883	2558	12	191	13644

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0038	13938
X-RAY DIFFRACTION	f_angle_d	0.6228	19327
X-RAY DIFFRACTION	f_chiral_restr	0.0447	2205
X-RAY DIFFRACTION	f_plane_restr	0.0033	2030
X-RAY DIFFRACTION	f_dihedral_angle_d	15.491	5651

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 (%)
2.75-2.8	0.4174	137	0.3667	2590	X-RAY DIFFRACTION	99.93
2.8-2.85	0.3575	130	0.3554	2571	X-RAY DIFFRACTION	99.96
2.85-2.9	0.3766	137	0.3418	2566	X-RAY DIFFRACTION	99.89
2.9-2.96	0.3475	135	0.3199	2632	X-RAY DIFFRACTION	99.93
2.96-3.03	0.3499	140	0.3206	2548	X-RAY DIFFRACTION	99.96
3.03-3.1	0.3629	133	0.3216	2629	X-RAY DIFFRACTION	99.93
3.1-3.17	0.3094	139	0.3183	2555	X-RAY DIFFRACTION	100
3.17-3.26	0.2667	140	0.2739	2594	X-RAY DIFFRACTION	99.89
3.26-3.36	0.2604	131	0.2492	2581	X-RAY DIFFRACTION	99.89
3.36-3.46	0.2943	132	0.2397	2609	X-RAY DIFFRACTION	99.96
3.46-3.59	0.2463	141	0.2363	2605	X-RAY DIFFRACTION	99.89
3.59-3.73	0.277	139	0.2257	2580	X-RAY DIFFRACTION	99.93
3.73-3.9	0.2457	133	0.2072	2608	X-RAY DIFFRACTION	100
3.9-4.11	0.1925	140	0.1929	2603	X-RAY DIFFRACTION	100
4.11-4.36	0.1953	136	0.1852	2623	X-RAY DIFFRACTION	99.96
4.36-4.7	0.2166	139	0.1743	2605	X-RAY DIFFRACTION	99.96
4.7-5.17	0.2247	137	0.1763	2621	X-RAY DIFFRACTION	99.96
5.17-5.92	0.2441	138	0.1925	2649	X-RAY DIFFRACTION	100
5.92-7.46	0.2256	141	0.2093	2656	X-RAY DIFFRACTION	99.96
7.46-48.12	0.2089	143	0.1754	2722	X-RAY DIFFRACTION	99.55

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	2.73489768479	0.691036793106	0.0593422254479	3.06639945107	-0.0611945575997	2.45347371104	-0.377125388177	0.243996381907	-0.619816587405	0.41544409721	0.16181870956	0.968298852209	1.98775742843	-1.54294844098	0.31787823871	1.14429051321	-0.307493732624	0.325774412421	1.15206480597	-0.277475127428	1.07185466501	-16.1189094467	4.83492542984	74.8883405368
2	2.83792018816	-0.735429783745	-0.966996443145	1.45975708431	0.512839579815	1.70200973581	0.0652696933341	-0.533818672889	-0.361223631835	0.725484745866	0.269326621116	-0.11787282969	0.3127412684	0.507506925708	-0.34334906114	0.717105996218	-0.0247617545761	0.00564791095765	0.476739627702	-0.0240516667514	0.579926037635	-3.30488895281	6.28992428769	51.1854174761
3	1.33342407216	-0.162798949017	0.2851150998	1.33945667453	0.281143920082	1.23973915335	0.21803542028	0.589347448055	0.224515349875	0.187895198645	-0.0125973528234	-0.249485535094	0.352566668811	0.0991914352185	-0.287090646399	0.421209639101	0.00698388389174	-0.0142816612218	0.577848846678	-0.0128723794852	0.484454595475	13.2863010153	0.0997657094644	23.4218307052
4	1.04001999533	-0.335958982547	-0.666157353755	1.85601734823	0.863442752361	1.30973108293	0.215845240819	0.480169597081	-0.00157292120149	-0.827008650597	-0.15671955775	-0.32436365948	0.276838144959	0.156672699249	-0.0712170699067	1.23203466719	0.393127905195	-0.0322682438241	1.22407449806	-0.237860966491	0.754665762189	26.1275880995	-13.2327060362	3.99738835188
5	0.90561859596	-0.0927114354564	0.363078967901	0.913543340595	-0.124408570027	2.32726513705	0.183202679812	0.536538420889	-0.594789293476	-1.4511479317	-0.234721059074	0.500772589919	0.677205571797	-0.505461515753	0.164649948419	1.37702223863	0.198809614887	-0.20193001	1.13172613131	-0.243431128427	0.797500476838	21.9776422482	-17.1287713931	8.03498183349
6	0.468274743377	0.546369115472	-0.290248065756	1.08736533546	0.355803047806	1.32799114044	-0.00550952365263	0.268688816705	-0.0263749265808	0.132517720498	-0.116093349383	-0.176135299577	-0.0188533537603	0.106979824285	0.0924489646743	0.40477995056	-0.000615851477701	-0.0484896209253	0.598615479777	-0.0535634798708	0.392035051139	17.0795070009	3.21218097965	25.7370446415
7	3.35823288552	-0.0515436309494	0.644005047624	0.800529041309	-0.316449358086	1.83254831846	-0.0128847193382	0.216135931816	-0.416682394946	-0.248266095173	0.0836932128388	0.246471490194	-0.269769233158	-0.0200457153478	-0.0937358256039	0.397273925307	-0.0059892783182	-0.0245122203971	0.370281617202	0.0163224509948	0.428780368954	-2.04465908295	9.56327536078	26.8417033039
8	1.43301063421	0.378932486466	1.25975697538	0.091298704111	0.331723837168	1.10112042392	-0.171199533805	-0.232456249721	0.896507577443	0.00843770137386	-0.15725012947	-0.415708872302	-0.613541021316	-0.251954192971	0.30413114081	0.80821590331	-0.022381884435	-0.094499979936	0.409317283146	0.0254156512691	0.801902479848	-7.59264971034	24.1716726062	28.9453588077
9	2.40174544591	2.01064712206	-0.23127931273	1.71717361548	-0.221362841401	0.336105643014	-0.00158206157301	-0.159646178239	0.68437090492	-0.416851610857	-0.014688991564	-0.0563364776242	-0.611586221598	-0.112709944568	0.0991675914092	0.459416056432	-0.0102585034272	0.023151420612	0.269016080555	0.0421909050044	0.509620058298	-4.88453163735	16.2901743897	35.308452653
10	1.15361047884	-1.16252084156	-1.01088553987	1.94183581708	-0.152031256046	2.58698440672	-0.129780608964	0.461490575984	-0.0757092203844	0.0393265737829	-0.367265481807	-0.317005662479	-0.437296064788	-0.253742929067	0.477166613877	0.456793760004	-0.124022101008	-0.00133513481424	0.479797922089	-0.0229374288317	0.567189363214	-24.4251456941	5.56776852152	39.3988835737
11	2.77096228152	0.641918413977	0.588145735072	0.276358356984	0.917239194749	4.93551317634	-0.0732083339728	-0.00365837112671	1.79484876987	-0.121108478263	0.0176735244204	0.366387829766	-1.95304489572	0.365650352538	0.264599106156	0.948733773271	-0.18692302934	0.00112066879997	0.704270336091	0.214860535634	1.32271520642	-40.029853237	12.6860161513	29.954203816
12	4.01298996782	0.214258589295	-1.0611767912	2.19874060503	-1.01856186114	4.56239160521	-0.140470915678	-0.216418305962	0.118303985817	-0.771495461948	0.236963933975	-0.749663290826	-2.10807903478	0.645296024779	-0.229282549895	1.24431622632	-0.334089000093	0.127789792109	1.17364603178	-0.00332577602187	1.08253295608	-39.2123033233	15.1033392529	36.3067237476
13	1.46624785166	0.147742635899	0.0830160633476	0.286216115014	-0.134103109876	1.18588400902	0.0979120988698	-0.074162465614	-0.073208340095	0.110655932927	-0.0959572581382	-0.05556647759	0.128940513457	0.453687535472	0.00484261527854	0.478004248072	-0.0346102531147	-0.0193379582537	0.452498736124	-0.0228572629599	0.420045549876	15.5003088777	0.626001665879	42.3705937389
14	0.760292838718	-0.421937222197	0.00907169754603	0.496463228915	0.0180160637665	3.92244078079	-0.129810062595	-0.210433401489	0.149117729864	0.126738351792	0.0149747164653	-0.212638237873	-0.362536056074	0.327048452987	0.129634816091	0.556532431117	-0.103706533938	0.0391943877364	0.535295323208	-0.105241727296	0.634471605588	2.24055915066	18.6047454437	72.481756081
15	0.91144184904	0.534819116226	0.536948447643	0.75191465482	0.175259838362	1.53816016843	0.163471199733	-0.358923914481	-0.267477211161	0.206303893012	-0.00181084476986	-0.209766763188	0.373056346311	-0.237562786371	-0.135323184942	0.593979618248	-0.110245422153	-0.0113840796585	0.72531276137	0.0129823558088	0.575940685677	-20.3543381791	-7.11806698934	66.6967719362
16	1.85814660933	0.0968246365896	-0.301467367874	0.569509410003	-0.344941420783	1.54109581056	-0.0263189470029	0.0914749953047	-0.286974696679	-0.149688571445	0.125723253819	0.121424699498	0.500701569144	-0.203487324281	-0.093984448476	0.523761108501	-0.152479321062	-0.0455200570773	0.419316698913	-0.0634044251874	0.489059147454	-25.6158754036	-14.046597297	30.511239436
17	0.869821721741	-1.02153708082	-0.420439903425	2.02610743281	-0.812918128811	1.85021370607	0.186623894879	0.829367850715	-0.868569904176	-0.392837744865	-0.213068751669	0.28543390109	0.879987632323	-1.30174730002	-0.115975924502	0.813655885796	-0.203151424485	-0.0413956493788	1.18976063995	-0.258948363448	0.76321776776	-9.33850996304	-15.2116510973	25.5794487551
18	3.32376791369	-1.32145012158	-0.431500538549	3.61413815306	-0.161019003513	0.153892949566	0.0229686843639	-0.924287873535	0.161939388334	-0.328511835552	-0.037277716958	0.199237704995	0.112879603492	-0.566869555027	-0.318492803349	0.477571235082	-0.0168258065039	0.0596065786823	0.688059493027	-0.0728943367133	0.437904027466	4.14931607835	4.39722144115	50.1543932782
19	1.79649588976	-0.326777687767	-0.952002356179	0.932302905968	-1.07611069593	2.28877259872	0.295799252431	-0.698664722275	-0.239305668442	0.322474074923	0.0930173881958	0.537638016191	0.920958390363	-0.362638482383	-0.441471172638	0.707564576774	-0.227013818044	0.131654811869	0.981726028715	0.043368574084	0.592770126191	-10.9157048245	6.27371232136	62.2544335578
20	0.042317861924	-0.0312179930136	-0.139615875687	0.0345038159003	0.143346459878	0.361167817161	0.415615514268	0.158339888028	0.0925520355794	-0.190546577961	1.04087084506	0.048604358194	1.15379785468	-0.359234372344	-1.27451255539	1.42022613968	-0.148471034143	0.169145963437	1.07803949532	-0.0754743436791	0.873693400182	-13.0945117754	-0.813981458229	78.3515855054
21	0.16033430496	0.0317366550887	0.0342705090552	0.00584047421637	0.0022998388411	0.00699216775807	0.180788530195	0.216212069835	0.276218372137	1.35013453908E-5	0.00392531670606	0.443777237968	0.0778486147148	-0.702039405608	-0.27301895622	0.649445587511	-0.163257100434	0.134170991187	1.72709592529	-0.211028307238	0.927202401356	-22.4668570449	10.8015481259	82.7151012501
22	3.70965146974	-0.849145923496	-1.34904329318	4.63321934795	0.401029603686	3.47036199221	0.219372850739	0.586948818523	-1.49411683536	-0.469342008228	-0.061109437039	-0.27800802792	1.31077512674	0.22190286566	-0.469479871907	0.825180329857	-0.0822645062519	-0.044573548709	0.706534280709	-0.211367055235	0.777168226717	-11.7904872144	-15.0956776018	24.1649964485

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 8 )	A	A	-1 - 8
2	2	chain 'A' and (resid 9 through 18 )	A	A	9 - 18
3	3	chain 'A' and (resid 19 through 28 )	A	A	19 - 28
4	4	chain 'A' and (resid 29 through 33 )	A	A	29 - 33
5	5	chain 'A' and (resid 34 through 43 )	A	A	34 - 43
6	6	chain 'A' and (resid 44 through 48 )	A	A	44 - 48
7	7	chain 'A' and (resid 49 through 53 )	A	A	49 - 53
8	8	chain 'A' and (resid 54 through 58 )	A	A	54 - 58
9	9	chain 'A' and (resid 59 through 63 )	A	A	59 - 63
10	10	chain 'A' and (resid 64 through 68 )	A	A	64 - 68
11	11	chain 'A' and (resid 69 through 73 )	A	A	69 - 73
12	12	chain 'A' and (resid 74 through 82 )	A	A	74 - 82
13	13	chain 'B' and (resid 3 through 445 )	B	B	3 - 445	1 - 443
14	14	chain 'B' and (resid 446 through 653 )	B	B	446 - 653	444 - 651
15	15	chain 'B' and (resid 654 through 1088 )	B	B	654 - 1088	652 - 1053
16	16	chain 'B' and (resid 1089 through 1367 )	B	B	1089 - 1367	1054 - 1332
17	17	chain 'C' and (resid -7 through 2 )	C	C	-7 - 2
18	18	chain 'C' and (resid 3 through 7 )	C	C	3 - 7
19	19	chain 'C' and (resid 8 through 12 )	C	C	8 - 12
20	20	chain 'C' and (resid 13 through 17 )	C	C	13 - 17
21	21	chain 'C' and (resid 18 through 20 )	C	C	18 - 20
22	22	chain 'D' and (resid -2 through 7 )	D	D	-2 - 7

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