PDB-4x7d: Crystal structure of 2012 NSW GII.4 P domain in complex with Nano-85

ID or keywords:

Entry

Database: PDB / ID: 4x7d

Title

Crystal structure of 2012 NSW GII.4 P domain in complex with Nano-85

Components

Nano-85 Nanobody
VP1

Keywords

VIRAL PROTEIN / Nanobody / VHH domain / Norovirus / Protruding domain

Function / homology

Function and homology information

Positive stranded ssRNA viruses / Nucleoplasmin-like/VP (viral coat and capsid proteins) / Positive stranded ssRNA viruses / Calicivirus coat protein C-terminal / Calicivirus coat protein C-terminal / Calicivirus coat protein / Calicivirus coat protein / Elongation Factor Tu (Ef-tu); domain 3 / Picornavirus/Calicivirus coat protein / Viral coat protein subunit ...
Similarity search - Domain/homology

Biological species

Norovirus Hu/GII.4/Sydney/NSW0514/2012/AU

Lama glama (llama)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.15 Å

Authors

Koromyslova, A.D. / Hansman, G.S.

Citation

Journal: J.Virol. / Year: 2015
Title: Nanobody binding to a conserved epitope promotes norovirus particle disassembly.
Authors: Koromyslova, A.D. / Hansman, G.S.

History

Deposition	Dec 9, 2014	Deposition site: RCSB / Processing site: PDBE
Revision 1.0	Dec 31, 2014	Provider: repository / Type: Initial release
Revision 1.1	Jan 14, 2015	Group: Database references
Revision 1.2	Feb 18, 2015	Group: Database references
Revision 1.3	Jan 10, 2024	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.4	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	4x7d.cif.gz	338.3 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	4x7d_validation.pdf.gz	462.3 KB	Display	wwPDB validaton report
Full document	4x7d_full_validation.pdf.gz	468.3 KB	Display
Data in XML	4x7d_validation.xml.gz	34.1 KB	Display
Data in CIF	4x7d_validation.cif.gz	49.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/x7/4x7d ftp://data.pdbj.org/pub/pdb/validation_reports/x7/4x7d	HTTPS FTP

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Related structure data

Related structure data	4x7cC 4x7eSC 4x7fC 4oosS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	4x7c-d 5o05-d 4qpg-d 6h71-d 3wfq-4 6h72-d 6b9f-d 3l4j-d Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#136 - Apr 2011 Nanobodies similarity (1) #21 - Sep 2001 Antibodies similarity (1) #256 - Apr 2021 SARS-CoV-2 Spike and Antibodies similarity (1) #156 - Dec 2012 ABO Blood Type Glycosyltransferases similarity (4)

Deposited unit

A: VP1

B: VP1

C: Nano-85 Nanobody

D: Nano-85 Nanobody

hetero molecules

95.2 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)	70.640, 93.580, 136.680
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	chain A
2	1	chain B
1	2	chain C
2	2	chain D

NCS domain segments:

Component-ID: 1

Dom-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	SER	SER	MET	MET	chain A	A	A	224 - 530	1 - 307
2	1	SER	SER	MET	MET	chain B	B	B	224 - 530	1 - 307
1	2	ASP	ASP	VAL	VAL	chain C	C	C	1 - 116	1 - 116
2	2	ASP	ASP	HIS	HIS	chain D	D	D	1 - 121	1 - 121

NCS ensembles :

ID
1
2

Details

The biological unit is a dimer. There is 1 biological unit in the asymmetric unit (chains A & B)

#1: Protein	VP1 Mass: 34060.961 Da / Num. of mol.: 2 / Fragment: UNP residues 225-530 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Norovirus Hu/GII.4/Sydney/NSW0514/2012/AU Plasmid: pMBP / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: K4LM89
#2: Antibody	Nano-85 Nanobody Mass: 13497.894 Da / Num. of mol.: 2 / Fragment: VHH Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lama glama (llama) / Plasmid: pHEN6C / Production host: Escherichia coli (E. coli) / Strain (production host): WK6
#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 419 / 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: 2.37 Å³/Da / Density % sol: 48.21 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: PEG 8000, HEPES

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

ESRF

/ Beamline: ID23-1 / Wavelength: 0.979 Å

Detector

Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 3, 2014

Radiation

Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.979 Å / Relative weight: 1

Reflection

Resolution: 2.15→46.79 Å / Num. obs: 49811 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / B_iso Wilson estimate: 32.4 Å² / R_merge F obs: 0.998 / R_merge(I) obs: 0.083 / R_rim(I) all: 0.097 / Χ²: 0.977 / Net I/σ(I): 11.74 / Num. measured all: 185356

Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)	Highest resolution (Å)	R_merge F obs	R_merge(I) obs	Mean I/σ(I) obs	Num. measured obs	Num. possible	Num. unique obs	R_rim(I) all	% possible all
2.15-2.21		0.782	0.661	2.03	13851	3678	3619	0.767	98.4
2.21-2.27		0.826	0.558	2.39	13531	3524	3518	0.648	99.8
2.27-2.33		0.866	0.497	2.69	13178	3470	3459	0.576	99.7
2.33-2.4		0.918	0.386	3.37	12585	3381	3364	0.449	99.5
2.4-2.48		0.921	0.339	3.74	11939	3243	3234	0.396	99.7
2.48-2.57		0.939	0.27	4.29	10814	3168	3142	0.319	99.2
2.57-2.67		0.955	0.241	5.21	11632	3079	3070	0.28	99.7
2.67-2.78		0.975	0.194	6.42	11218	2925	2923	0.225	99.9
2.78-2.9		0.978	0.166	7.59	10898	2844	2836	0.193	99.7
2.9-3.04		0.989	0.117	10	10167	2699	2680	0.135	99.3
3.04-3.21		0.992	0.088	12.97	9643	2612	2595	0.102	99.3
3.21-3.4		0.994	0.068	15.4	8231	2435	2416	0.08	99.2
3.4-3.63		0.997	0.054	20.6	8872	2301	2294	0.063	99.7
3.63-3.93		0.998	0.044	24.37	8372	2186	2183	0.051	99.9
3.93-4.3		0.998	0.036	28.91	7393	1978	1963	0.041	99.2
4.3-4.81		0.999	0.031	31.6	6272	1813	1792	0.036	98.8
4.81-5.55		0.998	0.032	30.98	5796	1626	1618	0.038	99.5
5.55-6.8		0.998	0.035	29.5	5125	1379	1376	0.041	99.8
6.8-9.62		0.999	0.026	33.76	3649	1103	1089	0.031	98.7
	9.62	0.999	0.02	43.13	2190	664	640	0.023	96.4

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Processing

Software

Name	Version	Classification
XDS		data reduction
PHENIX		refinement
PDB_EXTRACT	3.15	data extraction
XSCALE		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entry 4OOS was used for GII.10 P domain (molecule 1) and recently deposited PDB entry 4X7E for Nano-85 (molecule 2)

4oos

4x7e

Resolution: 2.15→46.79 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.97 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2379	2489	5 %
R_work	0.1955	47249	-
obs	0.1975	49738	99.42 %

Solvent computation

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

Displacement parameters

B_iso max: 104.22 Å² / B_iso mean: 39.688 Å² / B_iso min: 20 Å²

Refinement step

Cycle: final / Resolution: 2.15→46.79 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6340	0	8	419	6767
B_iso mean	-	-	32.11	36.55	-
Num. residues	-	-	-	-	839

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.012	6544
X-RAY DIFFRACTION	f_angle_d	1.264	8937
X-RAY DIFFRACTION	f_chiral_restr	0.057	982
X-RAY DIFFRACTION	f_plane_restr	0.008	1187
X-RAY DIFFRACTION	f_dihedral_angle_d	13.713	2298

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Number	Refine-ID	Rms	Type
1	1	A	2788	X-RAY DIFFRACTION	8.187	TORSIONAL
1	2	B	2788	X-RAY DIFFRACTION	8.187	TORSIONAL
2	1	C	789	X-RAY DIFFRACTION	8.187	TORSIONAL
2	2	D	789	X-RAY DIFFRACTION	8.187	TORSIONAL

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 18

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
2.1501-2.1915	0.3405	134	0.3071	2535	2669	98
2.1915-2.2362	0.3124	137	0.2789	2609	2746	100
2.2362-2.2849	0.3117	137	0.2669	2605	2742	100
2.2849-2.338	0.333	138	0.2531	2610	2748	100
2.338-2.3965	0.3021	136	0.2417	2589	2725	100
2.3965-2.4613	0.2779	136	0.2375	2576	2712	100
2.4613-2.5337	0.2999	138	0.2415	2622	2760	99
2.5337-2.6155	0.2593	136	0.2218	2577	2713	99
2.6155-2.7089	0.2864	136	0.2252	2602	2738	100
2.7089-2.8174	0.2544	139	0.2243	2630	2769	100
2.8174-2.9456	0.2806	138	0.2217	2627	2765	100
2.9456-3.1008	0.2754	137	0.2085	2591	2728	100
3.1008-3.2951	0.2403	137	0.1945	2611	2748	99
3.2951-3.5494	0.2533	140	0.1853	2648	2788	99
3.5494-3.9064	0.2014	140	0.17	2668	2808	100
3.9064-4.4713	0.1712	140	0.1479	2654	2794	99
4.4713-5.6319	0.1873	142	0.1503	2681	2823	99
5.6319-46.8011	0.2119	148	0.1821	2814	2962	99

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	3.0012	0.2479	0.6555	0.699	-0.1957	1.135	0.1125	-0.0541	-0.2689	-0.0719	0.001	0.2016	0.1766	-0.1744	-0.1082	0.2865	-0.0316	-0.0245	0.2054	0.0091	0.4152	7.9257	-8.6123	139.8875
2	0.4749	-0.8599	0.437	2.0246	-0.6429	2.0548	0.0082	0.2107	-0.1055	-0.1993	0.119	0.3301	0.2218	-0.2835	-0.148	0.3046	-0.0895	-0.071	0.3821	0.0151	0.5369	-5.8755	-9.7945	130.18
3	2.235	0.2172	-0.0527	0.8554	-0.1178	0.9591	0.027	-0.3231	-0.2267	0.0789	-0.0086	0.0006	0.0979	-0.0157	-0.0073	0.2529	-0.0112	-0.0172	0.1985	0.0326	0.329	14.3836	-9.7667	148.9918
4	2.4396	-0.0168	-1.0678	1.3196	0.4336	1.8386	0.0619	0.1288	0.0843	0.0557	0.0422	0.1016	-0.1163	-0.1083	-0.1212	0.2714	0.0061	-0.0265	0.1977	0.0243	0.33	7.8162	12.2493	136.2114
5	1.4219	0.6463	-0.7356	1.0574	-0.4619	1.4633	0.0076	0.1667	0.3441	0.0256	0.1098	0.315	-0.0933	-0.2167	-0.1385	0.2447	0.0215	0.0095	0.277	0.0466	0.4559	-2.1411	14.8022	135.9276
6	3.3227	-0.0054	0.4708	1.247	-0.1146	1.6299	-0.0136	0.629	-0.1811	-0.2259	0.1114	-0.1486	0.0559	0.1358	-0.0658	0.2728	-0.0349	0.0036	0.2792	-0.0512	0.2844	18.5288	7.7919	120.4357
7	1.9242	-0.1132	1.7045	3.6468	-3.4899	5.3699	-0.3464	0.1312	0.9449	-0.573	0.2389	-0.335	0.5511	-0.5247	0.2338	0.5115	-0.0676	0.1268	1.4591	0.0253	0.6164	48.2761	16.273	108.0742
8	5.3078	2.5256	-3.6759	1.9983	-4.4505	8.6984	-0.7933	-1.0165	0.4056	-0.2846	1.0477	0.7934	0.4592	-1.2756	-0.6416	0.1743	-0.0358	0.0402	1.3433	0.4159	0.8229	44.3199	25.1367	93.4906
9	3.5097	-1.2194	1.2758	3.5326	-2.7886	6.1571	-0.2569	0.9326	0.5036	-0.4462	-0.2394	-0.711	-0.0737	0.8828	0.3937	0.4526	-0.1719	0.04	0.8129	-0.0236	0.4396	36.0869	18.3724	106.3499
10	3.4815	1.6337	-2.4523	2.9369	1.3394	4.6287	-0.4666	0.3848	0.017	-0.8695	0.4544	-0.8955	-0.2706	0.7561	-0.2841	0.6691	-0.1055	0.1091	1.4398	-0.05	0.5257	36.2521	19.7985	96.7835
11	0.4557	-0.4415	-0.9602	0.6367	0.0717	5.9928	-0.0866	1.1203	-0.0899	-0.2495	0.1048	-0.6027	-0.5415	0.9511	0.5234	0.4268	-0.1974	0.0709	0.8281	0.0085	0.5279	39.241	16.8412	113.9626
12	-0.0197	0.0185	-0.0521	0.0595	-0.3041	1.176	-0.712	-0.2586	0.2832	-0.0327	-0.4674	-0.8988	-0.71	-1.1423	1.0702	0.5705	-0.1377	-0.0333	0.7226	0.1211	0.9603	45.1913	23.7729	106.9392
13	6.6787	2.3669	-5.8285	6.9568	-3.4104	7.311	-0.3143	-1.0672	-0.9405	0.2095	-0.3149	-0.1875	0.1903	0.7824	0.5124	0.3735	0.0561	-0.0528	0.5182	0.1468	0.5816	51.907	-18.0684	158.2325
14	0.9023	2.0408	-1.4589	8.7668	-7.4187	6.4902	-0.0976	-0.0602	-0.0029	1.0606	-0.6944	-0.9401	-0.8714	0.8057	0.807	0.4556	-0.039	-0.1111	0.5894	0.1287	0.4824	48.689	-22.5371	171.9013
15	2.8512	-1.5858	0.3989	6.5843	-3.7753	4.0178	0.1255	-0.1942	0.1266	-0.0469	0.0322	-0.0885	0.5435	0.2448	-0.1594	0.42	-0.0167	-0.1381	0.4794	0.0997	0.3931	42.3301	-17.4849	158.2672
16	5.3766	-3.9042	0.7984	7.5722	-0.8305	0.4401	0.2476	0.4886	-1.1733	-1.1011	0.0913	0.6677	0.4689	0.1418	-0.4834	0.9153	0.0984	-0.0148	0.6941	-0.0558	0.7296	40.8734	-36.2153	161.4323
17	4.8261	-3.6917	0.6761	8.0592	-0.6382	0.1881	0.0888	0.0997	-0.3751	-0.3079	0.3493	0.2624	0.4093	-0.1225	-0.3442	0.4915	-0.071	0.0143	0.5713	0.1752	0.4484	36.9803	-21.567	163.3936
18	4.4801	-3.8383	3.4435	5.8935	-4.2765	5.4527	0.0686	-0.9365	-1.0978	0.0918	0.3946	0.8416	0.308	-0.571	-0.3734	0.4066	-0.0473	0.0207	0.6875	0.2156	0.3936	33.056	-19.3965	166.2443
19	7.1732	-2.9049	0.2022	2.1474	-2.7975	8.1443	-0.0922	-1.0648	-0.4031	0.7134	0.5026	0.9284	-0.2448	-0.2639	-0.4236	0.459	0.0266	0.0251	0.5766	0.0949	0.4381	38.0985	-18.5097	171.4292
20	3.2747	1.5028	-2.2561	5.9302	3.7282	6.6305	0.279	-0.3619	0.4817	0.6664	-0.2627	-0.1215	-0.4666	0.4561	-0.2306	0.4655	-0.0287	-0.0744	0.5359	0.1067	0.5276	45.4247	-13.4805	167.3615
21	2.4145	-2.6103	2.5514	5.2428	-5.1001	4.96	-0.228	-0.4353	-0.3681	0.6166	0.6989	1.4141	0.4489	-0.6951	-0.8996	0.6551	0.0179	0.0186	0.5485	0.2382	0.6417	40.9723	-30.9041	175.6977
22	1.6318	-2.7342	3.1432	4.4584	-5.2869	6.063	0.7303	0.2611	-0.4199	-0.5139	-0.3265	0.1628	1.1445	0.2885	-0.212	0.5105	0.0312	-0.1298	0.4899	0.1006	0.6141	43.4103	-21.2256	158.322
23	1.4518	-0.527	0.5578	4.8873	-2.0049	5.0763	-0.1062	0.9835	0.4061	-0.1751	0.3316	0.3392	-0.4195	-0.033	-0.3805	0.2886	-0.0146	-0.0114	0.3819	0.1289	0.3856	38.5731	-10.7306	144.1561
24	2.0951	1.9719	-3.4939	1.7861	-3.29	5.806	-0.0618	-0.4633	-0.2715	-0.0431	-0.961	-0.4559	0.86	1.8731	1.02	0.616	0.0951	-0.0348	0.5885	0.1759	0.6233	49.0576	-28.4078	167.0705

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 224 through 303 )	A
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 304 through 380 )	A
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 381 through 530 )	A
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 224 through 323 )	B
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 324 through 437 )	B
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 438 through 530 )	B
7	X-RAY DIFFRACTION	7	chain 'C' and (resid 1 through 6 )	C
8	X-RAY DIFFRACTION	8	chain 'C' and (resid 7 through 20 )	C
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 21 through 63 )	C
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 64 through 91 )	C
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 92 through 106 )	C
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 107 through 116 )	C
13	X-RAY DIFFRACTION	13	chain 'D' and (resid 1 through 7 )	D
14	X-RAY DIFFRACTION	14	chain 'D' and (resid 8 through 26 )	D
15	X-RAY DIFFRACTION	15	chain 'D' and (resid 27 through 39 )	D
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 40 through 45 )	D
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 46 through 52 )	D
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 53 through 63 )	D
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 64 through 72 )	D
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 73 through 82 )	D
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 83 through 90 )	D
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 91 through 100 )	D
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 101 through 106 )	D
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 107 through 121 )	D

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