PDB-5fw1: Crystal structure of SpyCas9 variant VQR bound to sgRNA and TGAG ...

ID or keywords:

Entry

Database: PDB / ID: 5fw1

Title

Crystal structure of SpyCas9 variant VQR bound to sgRNA and TGAG PAM target DNA

Components

CRISPR-ASSOCIATED ENDONUCLEASE CAS9/CSN1
NON-TARGET DNA STRAND
SGRNA
TARGET DNA STRAND

Keywords

HYDROLASE/DNA / HYDROLASE-DNA COMPLEX / CRISPR / CAS9 / ENDONUCLEASE / PAM / GENOME EDITING / RNP / PROTEIN-RNA 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: 2.499 Å

Authors

Anders, C. / Bargsten, K. / Jinek, M.

Citation

Journal: Mol.Cell / Year: 2016
Title: Structural Plasticity of Pam Recognition by Engineered Variants of the RNA-Guided Endonuclease Cas9.
Authors: Anders, C. / Bargsten, K. / Jinek, M.

History

Deposition	Feb 11, 2016	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Apr 20, 2016	Provider: repository / Type: Initial release
Revision 2.0	Oct 23, 2019	Group: Atomic model / Data collection / Other / Category: atom_site / pdbx_database_status Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_database_status.status_code_sf
Revision 2.1	Jan 10, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5fw1.cif.gz	939 KB	Display	PDBx/mmCIF format
PDB format	pdb5fw1.ent.gz	782.8 KB	Display	PDB format
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Validation report

Summary document	5fw1_validation.pdf.gz	487.2 KB	Display	wwPDB validaton report
Full document	5fw1_full_validation.pdf.gz	517.2 KB	Display
Data in XML	5fw1_validation.xml.gz	52 KB	Display
Data in CIF	5fw1_validation.cif.gz	74.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/fw/5fw1 ftp://data.pdbj.org/pub/pdb/validation_reports/fw/5fw1	HTTPS FTP

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Related structure data

Related structure data	5fw2C 5fw3C 4un3S C: citing same article (ref.) S: Starting model for refinement
Similar structure data	6k3z-d 6k4p-d 6k4u-d 6k4q-d 6k57-d 5fw2-d 5fw3-d 5b2r-d 4un5-d 5b2s-d Search similar-shape structures by Omokage search (details) 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	#181 - Jan 2015 Cascade and CRISPR similarity (16) #253 - Jan 2021 Expressome similarity (2) #121 - Jan 2010 70S Ribosomes similarity (1) #130 - Oct 2010 Riboswitches similarity (1) #16 - Apr 2001 Aminoacyl-tRNA Synthetases similarity (1) #67 - Jul 2005 TATA-Binding Protein similarity (1) #157 - Jan 2013 Transfer-Messenger RNA similarity (1) #168 - Dec 2013 DNA Helicase similarity (1) #255 - Mar 2021 Cisplatin and DNA similarity (1) #87 - Mar 2007 Zinc Fingers similarity (2) #91 - Jul 2007 Thymine Dimers similarity (1) #229 - Jan 2019 Fluorescent RNA Aptamers similarity (1) #260 - Aug 2021 Ribonuclease P similarity (1) #122 - Feb 2010 Enhanceosome similarity (1) #172 - Apr 2014 RecA and Rad51 similarity (1) #227 - Nov 2018 Telomerase similarity (2) #146 - Feb 2012 Aminoglycoside Antibiotics similarity (1) #15 - Mar 2001 Transfer RNA similarity (1) #249 - Sep 2020 SARS-CoV-2 RNA-dependent RNA Polymerase similarity (1) #112 - Apr 2009 Oct and Sox Transcription Factors similarity (1) #135 - Mar 2011 Integrase similarity (1) #150 - Jun 2012 Sliding Clamps similarity (1) #180 - Dec 2014 TAL Effectors similarity (1) #48 - Dec 2003 Catabolite Activator Protein similarity (1) #84 - Dec 2006 Transposase similarity (1) #10 - Oct 2000 Ribosome similarity (1) #210 - Jun 2017 Adenine Riboswitch in Action similarity (1) #139 - Jul 2011 DNA Methyltransferase similarity (1) #155 - Nov 2012 Vitamin D Receptor similarity (1) #3 - Mar 2000 DNA Polymerase similarity (1) #40 - Apr 2003 RNA Polymerase similarity (1) #73 - Jan 2006 Topoisomerase similarity (1) #105 - Sep 2008 Ribonuclease A similarity (1) #226 - Oct 2018 Aminoglycoside Antibiotics and Resistance similarity (1) #245 - May 2020 Spliceosomes similarity (1) #262 - Oct 2021 Fifty Years of Open Access to PDB Structures similarity (1) #65 - May 2005 Self-splicing RNA similarity (1) #98 - Feb 2008 Small Interfering RNA similarity (1) #119 - Nov 2009 Designed DNA Crystal similarity (1) #125 - May 2010 Parvoviruses similarity (1) #131 - Nov 2010 Inteins similarity (1) #160 - Apr 2013 Actinomycin similarity (1) #190 - Oct 2015 Two-component Systems similarity (1) #23 - Nov 2001 DNA similarity (1) #240 - Dec 2019 Hypoxia-Inducible Factors similarity (1) #257 - May 2021 Fetal Hemoglobin similarity (1) #258 - Jun 2021 Glucocorticoid Receptor and Dexamethasone similarity (1) #31 - Jul 2002 p53 Tumor Suppressor similarity (1) #33 - Sep 2002 HIV Reverse Transcriptase similarity (1) #39 - Mar 2003 lac Repressor similarity (1) #45 - Sep 2003 Estrogen Receptor similarity (1) #55 - Jul 2004 DNA Ligase similarity (1) #7 - Jul 2000 Nucleosome similarity (1) #8 - Aug 2000 Restriction Enzymes similarity (1) #92 - Aug 2007 Anabolic Steroids similarity (1) #104 - Aug 2008 Selenocysteine Synthase similarity (1) #106 - Oct 2008 Poly(A) Polymerase similarity (1) #143 - Nov 2011 Toll-like Receptors similarity (1) #161 - May 2013 Ricin similarity (1) #230 - Feb 2019 Initiation Factor eIF4E similarity (1) #266 - Feb 2022 Oligosaccharyltransferase similarity (1) #81 - Sep 2006 Elongation Factors similarity (1) #89 - May 2007 Aconitase and Iron Regulatory Protein 1 similarity (1) #241 - Jan 2020 Twenty Years of Molecules similarity (2)

PDB pages

PDBj /

wwPDB /

NCBI

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Deposited unit

A: SGRNA

B: CRISPR-ASSOCIATED ENDONUCLEASE CAS9/CSN1

C: TARGET DNA STRAND

D: NON-TARGET DNA 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)	176.637, 66.984, 187.228
Angle α, β, γ (deg.)	90.00, 111.12, 90.00
Int Tables number	5
Space group name H-M	C121

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DNA chain , 2 types, 2 molecules CD

#3: DNA chain	TARGET DNA STRAND Mass: 8543.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#4: DNA chain	NON-TARGET DNA STRAND Mass: 3734.479 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	SGRNA Mass: 26788.984 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#2: Protein	CRISPR-ASSOCIATED ENDONUCLEASE CAS9/CSN1 / SPYCAS9 Mass: 158886.078 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) STREPTOCOCCUS PYOGENES (bacteria) / Strain: M1 / Plasmid: PEC-K-MBP / Production host: ESCHERICHIA COLI (E. coli) / Variant (production host): ROSETTA 2 References: UniProt: Q99ZW2, Hydrolases; Acting on ester bonds

#1: RNA chain

SGRNA

Mass: 26788.984 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)

#2: Protein

CRISPR-ASSOCIATED ENDONUCLEASE CAS9/CSN1 / SPYCAS9

Mass: 158886.078 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

STREPTOCOCCUS PYOGENES (bacteria) / Strain: M1 / Plasmid: PEC-K-MBP / Production host:

ESCHERICHIA COLI (E. coli) / Variant (production host): ROSETTA 2
References: UniProt: Q99ZW2, Hydrolases; Acting on ester bonds

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Non-polymers , 3 types, 316 molecules

#5: Chemical	ChemComp-K / POTASSIUM ION Mass: 39.098 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: K
#6: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 301 / Source method: isolated from a natural source / Formula: H₂O

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Details

Sequence details	GAAS AT THE N-TERMINUS IS DERIVED FROM EXPRESSION VECTOR. D10A AND H840A MUTATIONS HAVE BEEN ...GAAS AT THE N-TERMINUS IS DERIVED FROM EXPRESSION VECTOR. D10A AND H840A MUTATIONS HAVE BEEN ENGINEERED TO INACTIVATE NUCLEASE DOMAINS. D1135V, R1335Q, T1337R MUTATIONS ARE SPECIFIC TO THE VQR SPYCAS9 VARIANT.

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.6 Å³/Da / Density % sol: 52 % / Description: NONE
Crystal grow	pH: 8.5 / Details: 0.1 M TRIS PH 8.5, 0.3 M KSCN, 15% (W/V) PEG 3400

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1
Detector	Type: DECTRIS PILATUS / Detector: PIXEL / Date: Oct 22, 2015
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.5→47.62 Å / Num. obs: 71152 / % possible obs: 99.4 % / Observed criterion σ(I): 1.7 / Redundancy: 3.5 % / R_merge(I) obs: 0.1 / Net I/σ(I): 11.9
Reflection shell	Resolution: 2.5→2.65 Å / Redundancy: 3.6 % / R_merge(I) obs: 0.77 / Mean I/σ(I) obs: 1.7 / % possible all: 98.2

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Processing

Software

Name	Version	Classification
PHENIX	(PHENIX.REFINE)	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4UN3

4un3

Resolution: 2.499→47.622 Å / SU ML: 0.42 / σ(F): 1.21 / Phase error: 28.09 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2544	6915	5 %
R_work	0.2183	-	-
obs	0.2202	71146	99.51 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.499→47.622 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10672	2526	15	301	13514

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	13714
X-RAY DIFFRACTION	f_angle_d	0.787	18973
X-RAY DIFFRACTION	f_dihedral_angle_d	16.478	8029
X-RAY DIFFRACTION	f_chiral_restr	0.045	2169
X-RAY DIFFRACTION	f_plane_restr	0.004	1983

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 (%)
2.4988-2.5272	0.4494	214	0.3771	4009	X-RAY DIFFRACTION	92
2.5272-2.5569	0.3632	230	0.3174	4441	X-RAY DIFFRACTION	100
2.5569-2.5881	0.3907	242	0.3277	4368	X-RAY DIFFRACTION	100
2.5881-2.6209	0.383	232	0.3166	4363	X-RAY DIFFRACTION	100
2.6209-2.6554	0.3145	227	0.2884	4347	X-RAY DIFFRACTION	100
2.6554-2.6917	0.3646	220	0.2944	4478	X-RAY DIFFRACTION	100
2.6917-2.7302	0.3886	225	0.2995	4302	X-RAY DIFFRACTION	100
2.7302-2.7709	0.3535	226	0.287	4483	X-RAY DIFFRACTION	100
2.7709-2.8142	0.3338	250	0.277	4327	X-RAY DIFFRACTION	100
2.8142-2.8603	0.3217	235	0.2759	4382	X-RAY DIFFRACTION	100
2.8603-2.9097	0.2859	229	0.2691	4420	X-RAY DIFFRACTION	100
2.9097-2.9626	0.3313	224	0.2744	4380	X-RAY DIFFRACTION	100
2.9626-3.0195	0.3155	230	0.2857	4351	X-RAY DIFFRACTION	100
3.0195-3.0812	0.3058	228	0.2716	4348	X-RAY DIFFRACTION	100
3.0812-3.1481	0.3113	238	0.277	4438	X-RAY DIFFRACTION	100
3.1481-3.2214	0.2937	223	0.2488	4354	X-RAY DIFFRACTION	100
3.2214-3.3019	0.2449	239	0.2408	4356	X-RAY DIFFRACTION	100
3.3019-3.3912	0.3035	237	0.2292	4392	X-RAY DIFFRACTION	100
3.3912-3.4909	0.2436	231	0.2215	4429	X-RAY DIFFRACTION	100
3.4909-3.6036	0.2619	237	0.2103	4328	X-RAY DIFFRACTION	100
3.6036-3.7323	0.2469	229	0.1965	4386	X-RAY DIFFRACTION	100
3.7323-3.8817	0.1965	224	0.1914	4338	X-RAY DIFFRACTION	100
3.8817-4.0582	0.2311	238	0.1898	4408	X-RAY DIFFRACTION	100
4.0582-4.2721	0.2031	225	0.1775	4381	X-RAY DIFFRACTION	100
4.2721-4.5395	0.1947	228	0.1742	4387	X-RAY DIFFRACTION	100
4.5395-4.8897	0.2161	232	0.171	4370	X-RAY DIFFRACTION	100
4.8897-5.3812	0.2312	227	0.1733	4372	X-RAY DIFFRACTION	100
5.3812-6.1584	0.2626	232	0.19	4414	X-RAY DIFFRACTION	100
6.1584-7.7536	0.2025	231	0.197	4350	X-RAY DIFFRACTION	100
7.7536-47.631	0.189	232	0.1833	4408	X-RAY DIFFRACTION	100

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	0.3287	-0.0022	-0.0897	0.0945	-0.0668	0.4079	0.0677	0.0646	-0.0007	0.0643	-0.0523	-0.0134	-0.0141	0.133	-0	0.2445	-0.0507	-0.0089	0.2578	0.0062	0.2438	185.261	63.4676	39.5485
2	0.1553	0.192	0.0357	0.2466	-0.162	0.4804	0.0758	0.3877	0.1993	0.4358	-0.0309	0.2769	-0.9681	-0.864	0.007	0.7145	0.1778	0.0747	0.6355	-0.018	0.5033	200.2825	60.8551	64.4039
3	0.3506	-0.1928	-0.251	0.0822	0.171	1.0726	0.0315	0.0074	-0.0558	0.0799	-0.0122	0.0108	0.0099	0.1536	0	0.2876	-0.0239	-0.0357	0.283	0.0021	0.3575	188.3358	65.8809	47.7925
4	0.4483	0.2266	0.2715	0.2928	-0.0977	0.4393	-0.0926	0.0243	-0.0337	0.0936	0.0461	-0.0378	-0.1501	0.0639	-0	0.3441	0.0239	0.0015	0.2711	-0.0087	0.3545	171.7304	77.2526	75.3028
5	0.3924	-0.6472	0.2751	0.2892	-0.219	0.4179	-0.0118	-0.0162	-0.0158	0.0948	0.0046	0.0611	0.0266	0.076	-0	0.3655	-0.0318	-0.0163	0.3726	0.0063	0.3996	165.8529	47.1312	66.3036
6	0.5628	0.1456	-0.0779	0.3105	0.009	0.2905	-0.0484	0.1011	-0.0659	0.0242	0.0181	-0.0017	0.1912	-0.1048	0	0.3421	-0.0797	0.014	0.2943	-0.024	0.3177	147.5235	45.9936	39.5608
7	0.5054	-0.15	0.1322	0.2085	-0.0703	0.4395	0.0961	0.0937	0.0275	-0.0582	0.0119	0.0212	0.0627	0.0778	0	0.3328	-0.0148	-0.032	0.318	-0.0335	0.3248	179.3407	62.1923	31.984
8	0.3229	-0.3456	-0.8505	0.4532	0.8534	2.2956	0.2988	-0.388	0.8718	-0.2546	0.39	-1.1883	-0.9498	1.3226	0.108	0.8788	-0.0319	0.2762	0.8468	0.1117	1.1382	138.6227	74.4314	36.2429
9	0.1398	-0.0707	-0.1165	0.1846	-0.0463	0.1078	0.1013	0.2517	-0.3121	0.0289	-0.0118	-0.1329	-0.0352	-0.3296	-0.0003	0.3585	-0.0067	-0.0386	0.4224	-0.1108	0.418	167.5502	43.2821	24.9099
10	0.1042	-0.0973	0.0702	0.0045	-0.0178	0.0084	0.1597	-0.1254	0.2335	0.0264	0.0565	0.0164	0.1344	0.1152	0.0004	0.394	-0.044	0.0069	0.3839	-0.0029	0.3592	169.2921	64.3061	65.2458
11	0.2694	0.042	-0.0403	0.2871	-0.0847	0.0227	0.1483	0.1135	-0.7747	0.1352	0.2386	-0.6853	0.294	0.2622	0.0006	0.4427	-0.0621	-0.0034	0.4117	-0.1297	0.5781	165.612	44.4197	25.8528

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN 'B' AND (RESID 4 THROUGH 236 )
2	X-RAY DIFFRACTION	2	CHAIN 'B' AND (RESID 237 THROUGH 315 )
3	X-RAY DIFFRACTION	3	CHAIN 'B' AND (RESID 316 THROUGH 551 )
4	X-RAY DIFFRACTION	4	CHAIN 'B' AND (RESID 552 THROUGH 750 )
5	X-RAY DIFFRACTION	5	CHAIN 'B' AND (RESID 751 THROUGH 953 )
6	X-RAY DIFFRACTION	6	CHAIN 'B' AND (RESID 954 THROUGH 1364 )
7	X-RAY DIFFRACTION	7	CHAIN 'A' AND (RESID 1 THROUGH 70 )
8	X-RAY DIFFRACTION	8	CHAIN 'A' AND (RESID 71 THROUGH 81 )
9	X-RAY DIFFRACTION	9	CHAIN 'C' AND (RESID 1 THROUGH 10 )
10	X-RAY DIFFRACTION	10	CHAIN 'C' AND (RESID 11 THROUGH 28 )
11	X-RAY DIFFRACTION	11	CHAIN 'D' AND (RESID 2 THROUGH 12 )

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