PDB-8z8r: norbelladine 4'-O-methyltransferase S52T complexed with Mg and SAH

ID or keywords:

Entry

Database: PDB / ID: 8z8r

Title

norbelladine 4'-O-methyltransferase S52T complexed with Mg and SAH

Components

Norbelladine 4'-O-methyltransferase

Keywords

TRANSFERASE / O-methyltransferase family protein / NpN4OMT

Function / homology

Function and homology information

norbelladine O-methyltransferase / alkaloid metabolic process / S-adenosylmethionine-dependent methyltransferase activity / O-methyltransferase activity / methylation / metal ion binding
Similarity search - Function

Biological species

Narcissus pseudonarcissus MK-2014 (plant)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.79 Å

Authors

Saw, Y.Y.H. / Nakashima, Y. / Morita, H.

Funding support

Japan, 2items

Citation

Journal: Acs Catalysis / Year: 2024
Title: Structure-Based Catalytic Mechanism of Amaryllidaceae O-Methyltransferases
Authors: Hnin, S.Y.Y. / Nakashima, Y. / Kodama, T. / Morita, H.

History

Deposition	Apr 22, 2024	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Aug 7, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8z8r.cif.gz	504.2 KB	Display	PDBx/mmCIF format
PDB format	pdb8z8r.ent.gz	341.5 KB	Display	PDB format
PDBx/mmJSON format	8z8r.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/z8/8z8r ftp://data.pdbj.org/pub/pdb/validation_reports/z8/8z8r	HTTPS FTP

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Related structure data

Related structure data	8xdoC 8xdpC 8xdqC 8xdrC 8xdsC 8xdtC 8xduC 8xdvC 8xdyC 8xe0C 8xe2C 8xe3C 8xe4C 8xe5C 8z8oC 8z8pC 8z8sC 8zfwC 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

Deposited unit

A: Norbelladine 4'-O-methyltransferase

B: Norbelladine 4'-O-methyltransferase

C: Norbelladine 4'-O-methyltransferase

D: Norbelladine 4'-O-methyltransferase

hetero molecules

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

1

A: Norbelladine 4'-O-methyltransferase

hetero molecules

D: Norbelladine 4'-O-methyltransferase

hetero molecules

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

2

B: Norbelladine 4'-O-methyltransferase

C: Norbelladine 4'-O-methyltransferase

hetero molecules

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

Unit cell

Length a, b, c (Å)	64.352, 79.723, 91.517
Angle α, β, γ (deg.)	90.000, 94.010, 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

#1: Protein	Norbelladine 4'-O-methyltransferase / NpN4OMT Mass: 27411.109 Da / Num. of mol.: 4 / Mutation: S52T Source method: isolated from a genetically manipulated source Source: (gene. exp.) Narcissus pseudonarcissus MK-2014 (plant) Gene: N4OMT / Production host: Escherichia coli M15 (bacteria) References: UniProt: A0A077EWA5, norbelladine O-methyltransferase
#2: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₈O₃
#3: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₄H₂₀N₆O₅S / Feature type: SUBJECT OF INVESTIGATION
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1006 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	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: 2.14 Å³/Da / Density % sol: 42.41 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 25% (w/v) PEG 8000, 0.2M MgCl2, 0.1M Tris-HCl (pH 8.0)

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.035 Å
Detector	Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Mar 4, 2023
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.035 Å / Relative weight: 1
Reflection	Resolution: 1.79→45.65 Å / Num. obs: 86494 / % possible obs: 99.5 % / Redundancy: 4.3 % / B_iso Wilson estimate: 16.89 Å² / CC_1/2: 0.995 / R_merge(I) obs: 0.101 / Net I/σ(I): 10.8
Reflection shell	Resolution: 1.79→1.82 Å / Redundancy: 4.4 % / R_merge(I) obs: 0.658 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 4513 / CC_1/2: 0.65 / % possible all: 98.3

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Processing

Software

Name	Version	Classification
PHENIX	1.17.1_3660	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.79→45.65 Å / SU ML: 0.1798 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.2613
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.1887	2000	2.31 %
R_work	0.1578	84475	-
obs	0.1585	86475	99.45 %

Solvent computation

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

Displacement parameters

B_iso mean: 20.88 Å²

Refinement step

Cycle: LAST / Resolution: 1.79→45.65 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7776	0	12	1006	8794

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0044	8169
X-RAY DIFFRACTION	f_angle_d	0.7745	11146
X-RAY DIFFRACTION	f_chiral_restr	0.0502	1249
X-RAY DIFFRACTION	f_plane_restr	0.0043	1434
X-RAY DIFFRACTION	f_dihedral_angle_d	20.5484	3028

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 (%)
1.79-1.83	0.2886	131	0.2468	5979	X-RAY DIFFRACTION	98.5
1.83-1.88	0.2531	165	0.2168	5917	X-RAY DIFFRACTION	98.91
1.88-1.94	0.2373	131	0.1902	6001	X-RAY DIFFRACTION	99.03
1.94-2	0.2216	130	0.1796	6017	X-RAY DIFFRACTION	99.23
2-2.07	0.2405	153	0.178	6005	X-RAY DIFFRACTION	99.52
2.07-2.16	0.2181	136	0.1695	5995	X-RAY DIFFRACTION	99.32
2.16-2.26	0.2078	143	0.1603	6008	X-RAY DIFFRACTION	99.72
2.26-2.37	0.1961	143	0.1568	6053	X-RAY DIFFRACTION	99.65
2.37-2.52	0.2092	148	0.1589	6034	X-RAY DIFFRACTION	99.73
2.52-2.72	0.2073	139	0.1563	6047	X-RAY DIFFRACTION	99.9
2.72-2.99	0.1804	144	0.1614	6066	X-RAY DIFFRACTION	99.73
2.99-3.42	0.1695	148	0.1449	6067	X-RAY DIFFRACTION	99.65
3.42-4.31	0.1347	140	0.1241	6113	X-RAY DIFFRACTION	99.87
4.31-45.65	0.1612	149	0.148	6173	X-RAY DIFFRACTION	99.54

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	0.0115420085451	0.0382664504403	-0.00156896531027	0.129260024255	0.0420426128186	0.0435859951923	-0.0299239060756	-0.177278804943	-0.33729677913	0.166673081779	0.0844114547049	-0.184500589395	0.103609811562	0.245998924836	7.25883487615E-5	0.206927324401	-0.00421682425678	-0.038409554455	0.252462867772	-0.034411995729	0.335045250289	10.8150585006	2.19328458754	46.3985097349
2	0.0655586461115	-0.0150450220021	-0.0305055125617	0.023196964483	-0.0745796538228	0.00259355815393	-0.0471684834863	-0.127172475173	0.0382231617193	0.143753781867	-0.02631963204	-0.0161768759479	-0.0181297335654	-0.0331079940843	-0.000144931340265	0.107062561532	0.0145386952848	-0.0133878316474	0.124814568718	-0.00495473805707	0.100406240659	-4.94655938168	-10.2413642294	50.8750359572
3	0.315285991517	-0.0799235440472	-0.0117522085141	0.0768463608458	-0.0855292336587	0.208919672068	-0.0142767171147	-0.382828620643	0.30337268398	-0.0790033190637	0.15638399429	0.0339859795656	0.0547131667706	0.0661369697198	0.0728588548759	0.094267188862	0.0166865559065	-0.00687108611781	0.166274376167	-0.0565862231801	0.115445698826	9.62429489066	-11.1875216305	52.836716914
4	0.0655610129652	0.0191735343367	-0.00297828386787	0.0288188794712	-0.0183179134783	0.0215214082965	-0.0391766555878	0.0438273724498	-0.05967001656	-0.00102241359681	0.0415291634926	-0.0497028472231	-0.0517817611474	0.00717315572521	-2.03683578019E-6	0.0941842432155	-0.008859832334	0.00436860163992	0.0874016508927	-0.00566010690951	0.110298592278	3.88069489593	-20.3051132266	37.3170693603
5	0.190515698656	0.0656969775685	-0.0776085312067	0.116410812897	0.0461108151954	0.120815161148	-0.0906536416849	-0.118171909482	-0.0373815085926	0.00904189619077	0.0419049954493	-0.0773428678063	-0.0016212429562	0.0391240016542	-0.0537463047522	0.0880158408734	0.0165861478642	-0.014462006857	0.102172511766	0.00481237031979	0.0971077595541	13.968790388	-20.6201392095	46.129088878
6	0.426863511159	-0.116044402077	0.035406397014	0.101732438933	0.0258225138216	0.0674142710273	-0.016050763184	0.146295399496	-0.0266742118809	-0.0103320556327	-0.00588300566522	-0.0679653839598	0.0334716685956	0.10289265303	0.00999512113562	0.066052122072	-0.00966354094723	0.0125174206551	0.110322517569	0.00520383444493	0.103682629509	17.8689912855	-18.3491408678	32.3023548944
7	0.336573941922	-0.0700374984433	0.0964503042965	0.065778741382	0.000651568104517	0.075624645239	-0.0354502167705	0.0403444740572	0.090953449453	-0.0375225021718	0.110712178709	-0.172989273702	-0.0542918820548	0.119112009494	0.0110755818724	0.0955586480277	-0.0248872695396	0.00455386136478	0.0661836581558	-0.0173770968437	0.123027990002	8.7332692711	-2.73209787963	33.9536020139
8	0.217988798873	-0.00597115568526	-0.0613534663057	0.0390753229388	-0.0335815832765	0.0394809395439	0.117937726539	0.116427552681	0.256178919902	-0.0614626331492	-0.0223915928999	-0.173001066641	-0.122452515714	0.0454104717827	0.0189899919061	0.115079443891	-0.016793266152	0.0201589805471	0.0886368740338	0.00493999796254	0.157230145766	12.4206952431	1.28713255203	30.6627665568
9	0.056694389636	-0.126454436084	0.0242359300791	0.0655844667258	-0.141275454807	0.149272674568	-0.0560833638263	0.0903107764462	0.0424329192346	0.0156262643644	-0.0491260955766	-0.0235352576793	0.0305968788756	-0.016354524859	-0.0619199800544	0.106667059808	-0.0154183531284	0.00256969736407	0.118553150285	-0.00697858554573	0.0669691172485	4.46872481472	-11.1076587381	26.6045297557
10	0.0842343039044	0.0412593236953	0.0365807689891	0.338799029069	-0.092520293589	-0.020374942778	-0.0630141759542	0.0157613781974	0.0263913203477	0.0794038234947	0.023362699413	-0.240357071609	-0.0714716678231	0.0364306212536	-0.00737852053648	0.115891842902	0.00535402596558	0.013681120643	0.105061306509	-0.00111511559028	0.143690891085	32.7838667481	-7.78360916614	89.1265805058
11	0.207807967922	-0.0299985155152	-0.195006227409	0.173436478107	-0.176961247487	0.305673014195	-0.0645953253519	-0.0283420196014	-0.00531072229064	-0.00261432526522	0.0655055637549	-0.0303104640966	-0.0369348364225	0.00225780171076	0.00938817614259	0.11530082938	-0.00142973869015	0.00690128767569	0.0793877783771	-0.0155866310074	0.0924609938036	33.5721088972	-19.8092725645	84.1237440055
12	0.661700398599	-0.0888399286212	-0.368095803161	0.258683705448	0.0892183386946	0.3183676374	-0.039727328418	0.205486448824	-0.10631553802	-0.0961882799484	0.0695570940368	-0.159798612263	0.132964783797	0.00615934083319	0.0249903192492	0.154893687447	-0.0313105027736	0.0198930385207	0.129164024232	-0.0311516335739	0.120458138021	35.4536962483	-23.3152546116	71.5052387102
13	0.307464709217	-0.149554223966	-0.0892663501042	0.149378679485	0.0505929514324	0.255022743371	-0.00407609993722	0.118921310913	0.0845457385766	-0.0535182026965	0.0282765684641	0.00500805337813	-0.0329086196801	-0.055465608918	0.0440338720832	0.131109148503	-0.0264304436678	-0.00512308534851	0.106467121998	0.0121081833261	0.074748370944	24.814334723	-8.02925978241	72.5426072528
14	0.678559459159	0.194324227906	-0.103518575282	0.190878970215	-0.208331540637	0.369220508623	-0.00228110242222	0.0897034148872	0.110238768518	0.00777185854566	0.047598109676	0.0630298530806	-0.069380597061	-0.115404624229	0.0191790040387	0.105402237259	0.00833509338964	-0.00789679591253	0.131709904082	0.024032684438	0.111641824324	3.22188735374	-10.7249429448	83.7859202682
15	0.175486708356	-0.0128438096475	0.00430515108829	0.159226458891	-0.161258388867	0.100245139622	-0.0233259189481	-0.08619297986	-0.117773000456	-0.0254366985926	0.124622010355	0.105560247247	0.0459822380068	-0.124119063155	0.0102593821398	0.143559294987	-0.0138598795483	0.0142940188786	0.140885627521	0.0361194964046	0.138617754105	3.65694153312	-26.2616094333	94.7188595017
16	0.223423556058	0.187637827397	-0.132836886732	0.131890494305	-0.0672395541837	0.181681978735	0.0111836288872	0.00999298447213	0.0128519975559	0.00962791095624	0.0252143529183	0.0250085432333	0.00266748199107	-0.023822879801	0.0239588946951	0.128111864291	0.0133017193664	0.00213977952657	0.070040151994	0.0126405487367	0.0830914567427	14.7757702968	-15.7993513251	97.3766982515
17	0.012048148621	0.0186484228357	-0.0325332142115	0.0228426360385	-0.0702384277052	0.075350159705	0.040177020143	0.0298555370571	0.0972810070027	0.0410306282287	0.00906912557031	-0.0833481813255	0.00273297310597	0.153877809176	1.87321791769E-5	0.199073037864	0.013080218584	-0.0166712221025	0.203316575024	-0.00886420084358	0.214559537295	12.7073141533	-36.8460915975	53.7975919264
18	0.0261117114311	-0.0612418690732	-0.0174909877544	0.0296997514512	-0.00156294255978	0.0486893338939	0.0651312950399	-0.222159760855	0.125682284838	-0.0269700305075	-0.0342705060882	0.0557005955361	-0.0863330282049	0.13897533934	-2.18091075131E-5	0.142562061799	0.00264649402222	-0.0117777139576	0.156099152514	-0.0296680460466	0.136596946967	-3.70580963481	-39.0143221392	65.058581641
19	0.18271470948	-0.16880342706	-0.0448544224264	0.1893500235	-0.00719276170407	0.020487572339	-0.0505344317569	-0.191584614979	0.488349353144	-0.0268056621559	0.076019734124	-0.159145038493	-0.072767721318	-0.0422769172521	-0.00846615590429	0.13903849934	0.00675891204063	-0.00867075063222	0.202348310755	-0.0694204155141	0.171577633668	10.85993136	-40.5884201687	68.2469731528
20	0.0806368756339	0.0186061676631	-0.0893442679236	0.0392141430851	0.00853633436321	0.0413341153325	-0.0839213022506	-0.199302926052	-0.0625857089079	-0.032661063688	0.104367637753	-0.0612871041495	-0.00644758527811	-0.0264940096853	-0.0065381649262	0.0904490749683	0.00654305749245	-0.00463932439915	0.145528995928	0.0180093059519	0.115189171688	2.04070456758	-57.3068020032	64.0506507588
21	0.150575789275	0.079290408182	-0.119706554828	0.184982422439	0.0114438817083	0.138121061376	-0.224030258736	-0.364644402567	-0.019429969258	0.0599455641868	0.163754018821	-0.0954209033849	0.0891317817934	0.129347165598	-0.0327277629071	0.103938336597	0.0376701772305	-0.036501491442	0.23927016211	-0.0098202399104	0.103552732593	12.7274418448	-52.7267566665	70.9992316
22	0.10960865876	0.108454384756	0.025689710969	0.625944300475	0.160602109213	0.215935678225	-0.106649073928	-0.295263210154	-0.456851079484	-0.243720372089	0.258243174397	-0.653968904252	-0.107535283435	0.181364187839	0.044007071671	0.0289828171909	0.0718501492739	-0.104521962128	0.232820308705	0.097079796845	0.119953820002	18.8874802254	-61.9408187721	65.5450457778
23	0.135240049483	-0.0975187065009	0.0266953022039	0.0662433445125	-0.0280922589996	0.0336726796066	-0.0119567682056	-0.0688306817388	-0.101015949643	0.0806649812236	0.0483667429926	-0.0265099116489	0.0851166173849	0.176225264426	0.0320551935328	0.0841323677575	0.0165278225929	0.00125851521819	0.129631741896	0.00545611391704	0.145420627655	13.5169624052	-62.5354892322	56.5269050515
24	0.363569733726	-0.148131130682	0.0990876283205	0.129564061226	-0.0679895020193	-0.0282688430147	-0.0910962256619	0.0179585891052	0.119546613208	-0.0129348982551	0.131700908674	-0.0320338103783	-0.00263781808938	-0.0102231981685	0.00939367866277	0.0937307741898	-0.0234919368773	0.000803213005568	0.065944744557	-0.00359326615868	0.139093792054	9.80892325809	-48.2179466472	48.8238201584
25	0.028514184472	-0.0382898926332	0.0866876776315	0.0483028620678	-0.0337760772903	0.0297565648425	-0.12095434434	0.0689731813595	-0.0620709192442	-0.117793706507	0.0959940499869	-0.175236668356	-0.0215480729007	0.0208557392556	-1.63386606234E-5	0.104640933305	-0.00652372922041	0.00930114403039	0.0875032476865	-0.0020363870666	0.111736489571	13.8517158772	-49.313773958	44.3502043504
26	0.0839425769757	-0.119678063088	0.0765127873651	0.0520914496156	-0.0509751535902	0.12660573272	-0.032835530365	-0.00057973918186	-0.0620084643672	0.015176114975	0.0293926314866	-0.00540545606825	-0.0239144027269	0.0349677454952	-0.00997300819843	0.0869220283898	-0.00861048868503	0.0146255363472	0.0699858317385	-0.0150548629417	0.10683337762	3.48236087501	-58.9287614661	49.9825920937

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid -2 through 18 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 19 through 35 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 36 through 56 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 57 through 78 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 79 through 119 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 120 through 171 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 172 through 198 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 199 through 217 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 218 through 239 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid -2 through 35 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 36 through 92 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 93 through 171 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 172 through 239 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid -2 through 131 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 132 through 171 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 172 through 239 )
17	X-RAY DIFFRACTION	17	chain 'D' and (resid -2 through 18 )
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 19 through 35 )
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 36 through 56 )
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 57 through 78 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 79 through 119 )
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 120 through 142 )
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 143 through 171 )
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 172 through 198 )
25	X-RAY DIFFRACTION	25	chain 'D' and (resid 199 through 217 )
26	X-RAY DIFFRACTION	26	chain 'D' and (resid 218 through 239 )

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