PDB-3zxu: Crystal structure of the Ctf19-Mcm21 kinetochore heterodimer from...

ID or keywords:

Entry

Database: PDB / ID: 3zxu

Title

Crystal structure of the Ctf19-Mcm21 kinetochore heterodimer from yeast

Components

CTF19
MCM21

Keywords

CELL CYCLE /

COMA COMPLEX /

PROTEIN COMPLEX /

CELL DIVISION

Function / homology

Function and homology information

centromere complex assembly / meiotic cell cycle /

kinetochore /

cell division /

nucleus
Similarity search - Function

Biological species

KLUYVEROMYCES LACTIS (yeast)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 3.7 Å

Authors

Schmitzberger, F. / Harrison, S.C.

Citation

Journal: Embo Rep. / Year: 2012
Title: Rwd Domain: A Recurring Module in Kinetochore Architecture Shown by a Ctf19-Mcm21 Complex Structure.
Authors: Schmitzberger, F. / Harrison, S.C.

History

Deposition	Aug 15, 2011	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Mar 14, 2012	Provider: repository / Type: Initial release
Revision 1.1	Mar 6, 2019	Group: Data collection / Experimental preparation / Other Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3zxu.cif.gz	500.6 KB	Display	PDBx/mmCIF format
PDB format	pdb3zxu.ent.gz	437.9 KB	Display	PDB format
PDBx/mmJSON format	3zxu.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/zx/3zxu ftp://data.pdbj.org/pub/pdb/validation_reports/zx/3zxu	HTTPS FTP

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Related structure data

Similar structure data	3gpl-1 5kod-1 5kod-4 4eq4-1 3gpl-2 5kod-3 4l39-2 5kod-2 4eq4-2 30046 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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

Deposited unit

A: MCM21

B: CTF19

C: MCM21

D: CTF19

hetero molecules

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

1

A: MCM21

B: CTF19

hetero molecules

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

2

C: MCM21

D: CTF19

hetero molecules

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

Unit cell

Length a, b, c (Å)	239.036, 239.036, 179.487
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	180
Space group name H-M	P6₂22

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Selection details
1	1	1	CHAIN C AND (RESSEQ 99:101 OR RESSEQ 289:291) AND BACKBONE
2	1	1	CHAIN A AND (RESSEQ 99:101 OR RESSEQ 289:291) AND BACKBONE
1	1	2	CHAIN C AND (RESSEQ 282:288) AND BACKBONE
2	1	2	CHAIN A AND (RESSEQ 282:288) AND BACKBONE
1	1	3	CHAIN A AND NOT (RESSEQ 99:101 OR RESSEQ 282:292) AND BACKBONE
2	1	3	CHAIN C AND NOT (RESSEQ 99:101 OR RESSEQ 282:292) AND BACKBONE
1	1	4	CHAIN A AND (RESSEQ 44:46 OR RESSEQ 99:101 OR RESSEQ...
2	1	4	CHAIN C AND (RESSEQ 44:46 OR RESSEQ 99:101 OR RESSEQ...
1	1	5	CHAIN C AND (RESSEQ 282:286 OR RESSEQ 287:288 OR RESSEQ 290:291) AND SIDECHAIN
2	1	5	CHAIN A AND (RESSEQ 282:286 OR RESSEQ 287:288 OR RESSEQ 290:291) AND SIDECHAIN
1	1	6	CHAIN A AND NOT (RESSEQ 44:46 OR RESSEQ 99:101 OR...
2	1	6	CHAIN C AND NOT (RESSEQ 44:46 OR RESSEQ 99:101 OR...
1	1	7	CHAIN B AND (RESSEQ 244:254) AND BACKBONE
2	1	7	CHAIN D AND (RESSEQ 244:254) AND BACKBONE
1	1	8	CHAIN B AND (RESSEQ 259:269) AND BACKBONE
2	1	8	CHAIN D AND (RESSEQ 259:269) AND BACKBONE
1	1	9	CHAIN B AND NOT (RESSEQ 69:72 OR RESSEQ 91:92 OR RESSEQ 244:254 OR RESSEQ 259:269) AND BACKBONE
2	1	9	CHAIN D AND NOT (RESSEQ 69:72 OR RESSEQ 91:92 OR RESSEQ 244:254 OR RESSEQ 259:269) AND BACKBONE
1	1	10	CHAIN B AND (RESSEQ 83 OR RESSEQ 130 OR RESSEQ...
2	1	10	CHAIN D AND (RESSEQ 83 OR RESSEQ 130 OR RESSEQ...
1	1	11	CHAIN B AND NOT (RESSEQ 83 OR RESSEQ 91:92 OR...
2	1	11	CHAIN D AND NOT (RESSEQ 83 OR RESSEQ 91:92 OR...
1	1	12	CHAIN B AND (RESSEQ 69:72 OR RESSEQ 91:92) AND BACKBONE
2	1	12	CHAIN D AND (RESSEQ 69:72 OR RESSEQ 91:92) AND BACKBONE

NCS ensembles :

ID
1
2
3
4
5
6
7
8
9
10
11
12

NCS oper:

ID	Code	Matrix	Vector
1	given	(-0.74117, 0.4525, 0.4959), (0.4307, -0.24611, 0.86829), (0.51494, 0.85713, -0.01248)	0.60654, 0.62171, -0.83024
2	given	(-0.73653, 0.46929, 0.48713), (0.42612, -0.23737, 0.87297), (0.52531, 0.85054, -0.02514)	0.59294, 0.61612, -0.82744

#1: Protein	MCM21 Mass: 33832.305 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) KLUYVEROMYCES LACTIS (yeast) / Strain: NRRL Y-1140 / Gene: KLLA0B10142G / Plasmid: PET3ATR H6 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA2 PLYSS / References: UniProt: Q6CVQ9
#2: Protein	CTF19 Mass: 30838.041 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) KLUYVEROMYCES LACTIS (yeast) / Strain: NRRL Y-1140 / Gene: KLLA0D07612G / Plasmid: PET3ATR H6 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA2 PLYSS / References: UniProt: Q6CRN7
#3: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 48 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 5.7 Å³/Da / Density % sol: 78.5 % / Description: NONE
Crystal grow	Temperature: 293 K / pH: 8.1 Details: 7-10 % (W/V) POLYETHYLENE GLYCOL 8000, 14-20 % (V/V) ETHYLENE GLYCOL, 30 MM CACL2, 30 MM MGCL2, 100 MM BICINE/TRIS PH 8.1-8.5, 0.5 MM TCEP, TEMPERATURE 293 K.

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97914
Detector	Type: ADSC CCD / Detector: CCD / Date: Oct 27, 2010 / Details: MIRRORS
Radiation	Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97914 Å / Relative weight: 1
Reflection	Resolution: 3.7→48.36 Å / Num. obs: 31774 / % possible obs: 97.2 % / Observed criterion σ(I): 0.7 / Redundancy: 18.8 % / B_iso Wilson estimate: 158.26 Å² / R_merge(I) obs: 0.19 / Net I/σ(I): 13.9
Reflection shell	Resolution: 3.7→3.9 Å / Redundancy: 16.7 % / R_merge(I) obs: 4.99 / Mean I/σ(I) obs: 0.7 / % possible all: 85.2

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Processing

Software

Name	Version	Classification
PHENIX	(PHENIX.REFINE)	refinement
XDS		data reduction
SCALA		data scaling
SHELX		phasing

Refinement

Method to determine structure:

SAD
Starting model: NONE

Resolution: 3.7→47.492 Å / SU ML: 0.87 / σ(F): 0 / Phase error: 21.14 / Stereochemistry target values: ML
Details: FOR RESIDUES 1-43 AND 60-58 IN CHAINS A AND C NO SIGNIFICANT ELECTRON DENSITY IS PRESENT THESE PARTS ARE DISORDERED OR FLEXIBLE FOR RESIDUES 1-68 AND 93-96 OR 93-95 IN CHAINS B AND D NO ...

	R_factor	Num. reflection	% reflection
R_free	0.2089	2206	7 %
R_work	0.183	-	-
obs	0.1848	31641	96.68 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 222.628 Å² / k_sol: 0.319 e/Å³

Displacement parameters

B_iso mean: 243 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-29.0736 Å²	0 Å²	0 Å²
2-	-	-29.0736 Å²	0 Å²
3-	-	-	1.0441 Å²

Refinement step

Cycle: LAST / Resolution: 3.7→47.492 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6660	0	3	48	6711

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.011	6782
X-RAY DIFFRACTION	f_angle_d	1.665	9160
X-RAY DIFFRACTION	f_dihedral_angle_d	17.659	2549
X-RAY DIFFRACTION	f_chiral_restr	0.088	1051
X-RAY DIFFRACTION	f_plane_restr	0.008	1162

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Number	Refine-ID	Type	Rms dev position (Å)
1	1	C	24	X-RAY DIFFRACTION	POSITIONAL
1	2	A	24	X-RAY DIFFRACTION	POSITIONAL	0.858
2	1	C	28	X-RAY DIFFRACTION	POSITIONAL
2	2	A	28	X-RAY DIFFRACTION	POSITIONAL	0.136
3	1	A	788	X-RAY DIFFRACTION	POSITIONAL
3	2	C	788	X-RAY DIFFRACTION	POSITIONAL	0.047
4	1	A	238	X-RAY DIFFRACTION	POSITIONAL
4	2	C	238	X-RAY DIFFRACTION	POSITIONAL	0.837
5	1	C	113	X-RAY DIFFRACTION	POSITIONAL
5	2	A	113	X-RAY DIFFRACTION	POSITIONAL	0.276
6	1	A	2260	X-RAY DIFFRACTION	POSITIONAL
6	2	C	2260	X-RAY DIFFRACTION	POSITIONAL	0.132
7	1	B	44	X-RAY DIFFRACTION	POSITIONAL
7	2	D	44	X-RAY DIFFRACTION	POSITIONAL	0.258
8	1	B	44	X-RAY DIFFRACTION	POSITIONAL
8	2	D	44	X-RAY DIFFRACTION	POSITIONAL	0.118
9	1	B	676	X-RAY DIFFRACTION	POSITIONAL
9	2	D	676	X-RAY DIFFRACTION	POSITIONAL	0.047
10	1	B	299	X-RAY DIFFRACTION	POSITIONAL
10	2	D	299	X-RAY DIFFRACTION	POSITIONAL	0.866
11	1	B	1922	X-RAY DIFFRACTION	POSITIONAL
11	2	D	1922	X-RAY DIFFRACTION	POSITIONAL	0.186
12	1	B	24	X-RAY DIFFRACTION	POSITIONAL
12	2	D	24	X-RAY DIFFRACTION	POSITIONAL	0.984

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 (%)
3.7003-3.7808	0.3817	140	0.387	1848	X-RAY DIFFRACTION	99
3.7808-3.8687	0.3957	129	0.3758	1746	X-RAY DIFFRACTION	94
3.8687-3.9654	0.3868	86	0.3355	1180	X-RAY DIFFRACTION	64
3.9654-4.0725	0.3689	144	0.3188	1871	X-RAY DIFFRACTION	100
4.0725-4.1923	0.3136	140	0.2606	1859	X-RAY DIFFRACTION	100
4.1923-4.3275	0.2505	138	0.2329	1879	X-RAY DIFFRACTION	100
4.3275-4.4821	0.2347	140	0.1959	1862	X-RAY DIFFRACTION	100
4.4821-4.6614	0.1753	142	0.1474	1875	X-RAY DIFFRACTION	99
4.6614-4.8733	0.1557	139	0.1278	1868	X-RAY DIFFRACTION	99
4.8733-5.13	0.1777	143	0.1472	1891	X-RAY DIFFRACTION	99
5.13-5.451	0.2172	139	0.1718	1884	X-RAY DIFFRACTION	99
5.451-5.8711	0.2251	143	0.1799	1893	X-RAY DIFFRACTION	99
5.8711-6.4607	0.2151	144	0.1589	1902	X-RAY DIFFRACTION	99
6.4607-7.3925	0.1902	142	0.1539	1909	X-RAY DIFFRACTION	99
7.3925-9.3023	0.1307	145	0.1234	1946	X-RAY DIFFRACTION	99
9.3023-47.4956	0.1946	152	0.1846	2022	X-RAY DIFFRACTION	97

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	6.6019	6.8172	4.6531	7.8447	4.2599	3.8292	0.9817	-1.8612	-0.008	1.0214	-0.2343	0.0588	1.1091	-3.3301	-1.0286	2.4251	0.1765	0.2365	2.3747	0.0581	1.7188	56.0214	138.5699	21.5776
2	4.3995	-5.5954	-2.3696	7.8715	0.689	8.2575	-0.8884	-0.0541	-1.0614	1.2039	1.1853	-0.1445	-0.1704	0.0917	-0.2179	0.8912	-0.0221	-0.0251	1.8	-0.1352	1.6657	58.8139	138.8269	12.3569
3	2.8751	-0.6344	-0.5061	3.5757	0.5852	4.6311	0.3056	0.8851	-0.9519	-0.6573	-0.4889	1.499	0.1819	-0.8151	0.0754	0.7958	0.1797	-0.4157	1.7623	-0.094	1.6943	54.4128	134.3825	-3.9493
4	8.0962	3.5314	-7.3684	3.8721	-2.7586	7.2716	-0.8313	2.1139	2.3727	-0.2627	0.0107	3.2154	-2.3612	-3.0624	0.3779	2.7522	0.9288	-0.0018	1.3181	0.3158	3.4483	19.4748	142.6384	-0.358
5	9.2404	6.3473	-3.6519	4.4564	-3.3469	7.7313	0.2785	1.2713	-1.5144	0.3411	0.226	-2.8847	3.0251	0.6311	-0.9099	1.6773	0.2426	-0.1519	2.2371	0.1627	2.5742	61.4596	120.8977	7.6733
6	3.454	1.5692	-4.0272	6.1073	-3.8893	5.4563	-1.9849	0.0366	-0.5066	1.2192	2.8973	2.1365	2.1078	1.0661	-0.7649	2.0052	0.4526	-0.219	1.9029	0.5867	1.985	69.0875	121.5189	10.4411
7	2.798	1.2036	4.3717	9.9716	-2.5047	8.7541	0.3739	-1.6662	1.4181	0.8016	0.0598	-0.5443	-1.2736	0.9952	-0.4533	1.5108	0.0091	-0.0689	1.7132	-0.5491	1.7967	54.1237	150.5215	13.3243
8	5.871	4.2361	0.6585	9.8099	-4.0927	4.7972	-0.094	-0.5172	1.8613	-0.2601	1.155	1.1477	-0.2977	-0.3629	-1.207	1.3638	0.1708	-0.34	1.4643	-0.0682	2.246	47.1311	154.102	0.0171
9	5.6768	-0.4193	2.0361	5.9297	-1.1992	9.7402	-0.3696	0.2912	1.6452	-0.5321	0.1287	1.0523	-0.7543	-0.8232	0.3179	1.5294	0.2219	-0.1899	1.3082	0.0793	1.8174	43.8283	158.8535	-14.7721
10	6.9524	4.0209	-5.5278	4.1197	-1.834	5.4672	0.7527	0.408	2.018	-0.0137	0.0618	-1.1884	0.4554	-2.1411	-0.2811	1.5598	-0.2993	0.6506	1.6024	0.0639	1.582	47.7365	159.598	-24.4917
11	1.1981	-2.3427	-2.5463	5.4424	4.9161	5.4167	-0.8006	-0.7497	1.7943	-2.1682	1.0692	-2.7988	-1.2458	0.7777	-0.4252	1.3631	-0.318	-0.3176	2.4141	0.1705	2.5062	102.5633	137.4811	-1.6986
12	3.9268	-2.1233	2.6083	4.189	-3.3266	2.9207	-0.4004	-0.5228	1.0816	0.1199	-0.6527	0.5607	0.2372	-0.7022	0.7887	0.6505	0.0231	-0.125	1.7762	-0.4934	1.5686	96.0236	130.6039	0.1228
13	4.82	1.0802	-3.6953	5.6747	0.7505	6.8918	0.3924	1.046	-1.1613	-0.7781	0.213	0.1888	0.8053	0.1484	-0.4528	0.7609	0.2516	-0.2981	1.1824	-0.2107	1.7597	89.205	115.6322	-5.7596
14	6.3329	1.7744	6.0037	2.5236	0.3891	6.6204	0.0483	0.9048	-0.9024	0.0814	0.3277	3.1445	-0.2775	-2.494	-0.2899	1.2992	0.0412	-0.0186	1.5501	0.1518	2.5704	24.322	132.9325	0.0138
15	3.1883	-1.7799	3.799	2.8902	-3.8625	6.1306	-0.0165	-1.8172	-1.4039	0.4061	0.2415	-0.7889	2.1085	2.082	-0.0963	1.3746	0.3248	-1.2178	1.8014	1.0173	2.1354	120.5012	101.476	-16.7147
16	4.6966	1.5292	-4.3665	5.5677	1.271	5.4692	-1.7457	-0.1247	-0.0496	-2.8849	-0.3818	3.1702	-0.5106	-4.2496	2.0554	1.7368	0.0496	-0.1384	2.589	0.0237	1.7309	83.3787	131.7077	-13.5228
17	7.0105	-3.0128	-2.3654	1.6583	1.8532	7.3616	0.084	1.0556	1.1054	-0.7812	-1.099	-2.8496	4.5388	1.7743	0.8201	2.0653	0.1064	-0.3982	1.81	0.6444	1.6862	78.6568	136.9128	-10.4824
18	7.5884	-0.2222	-0.3946	7.9412	-1.2528	9.7236	0.8146	-2.1623	1.6044	0.877	0.3174	0.8939	-1.6954	-0.0842	-0.4099	0.7129	-0.1271	-0.6017	1.7092	-0.1859	1.4198	105.3584	126.5261	7.6003
19	5.3073	5.0547	-5.4943	5.1534	-5.261	5.6343	-1.0845	-0.7029	-1.2197	0.0701	-1.1508	-0.9149	0.8777	0.8836	1.9587	1.0865	0.214	-0.2875	1.6843	-0.1397	1.9291	105.6573	111.071	7.3781
20	5.679	3.3938	-0.163	6.3567	-1.2354	3.6189	-0.2651	0.3175	-0.1644	0.8831	0.1274	-1.1947	-0.2827	0.5932	0.236	1.1959	0.0775	-0.3821	1.7605	0.0007	1.4282	103.1481	95.5529	9.9802
21	3.3619	-4.7179	4.3022	6.7325	-5.8898	5.703	-2.9197	-2.1079	2.2404	-0.9406	3.9565	-4.1717	0.9658	-1.0766	-0.99	1.3495	-0.4046	0.0185	2.5141	-0.0999	2.1876	96.0843	88.5321	12.9493

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN A AND (RESSEQ 44:59)
2	X-RAY DIFFRACTION	2	CHAIN A AND (RESSEQ 99:152)
3	X-RAY DIFFRACTION	3	CHAIN A AND (RESSEQ 153:221)
4	X-RAY DIFFRACTION	4	CHAIN A AND (RESSEQ 283:293)
5	X-RAY DIFFRACTION	5	CHAIN B AND (RESSEQ 69:92)
6	X-RAY DIFFRACTION	6	CHAIN B AND (RESSEQ 97:107)
7	X-RAY DIFFRACTION	7	CHAIN B AND (RESSEQ 108:161)
8	X-RAY DIFFRACTION	8	CHAIN B AND (RESSEQ 162:204)
9	X-RAY DIFFRACTION	9	CHAIN B AND (RESSEQ 205:256)
10	X-RAY DIFFRACTION	10	CHAIN B AND (RESSEQ 257:269)
11	X-RAY DIFFRACTION	11	CHAIN C AND (RESSEQ 44:59)
12	X-RAY DIFFRACTION	12	CHAIN C AND (RESSEQ 99:152)
13	X-RAY DIFFRACTION	13	CHAIN C AND (RESSEQ 153:221)
14	X-RAY DIFFRACTION	14	CHAIN A AND (RESSEQ 222:282)
15	X-RAY DIFFRACTION	15	CHAIN C AND (RESSEQ 283:293)
16	X-RAY DIFFRACTION	16	CHAIN D AND (RESSEQ 69:92)
17	X-RAY DIFFRACTION	17	CHAIN D AND (RESSEQ 96:107)
18	X-RAY DIFFRACTION	18	CHAIN D AND (RESSEQ 108:161)
19	X-RAY DIFFRACTION	19	CHAIN D AND (RESSEQ 162:204)
20	X-RAY DIFFRACTION	20	CHAIN D AND (RESSEQ 205:256)
21	X-RAY DIFFRACTION	21	CHAIN D AND (RESSEQ 257:269)

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