PDB-8ez1: Human Ornithine Aminotransferase (hOAT) co-crystallized with its ...

ID or keywords:

Entry

Database: PDB / ID: 8ez1

Title

Human Ornithine Aminotransferase (hOAT) co-crystallized with its inactivator 3-Amino-4-fluorocyclopentenecarboxylic Acid

Components

Ornithine aminotransferase, mitochondrial

Keywords

TRANSFERASE / hOAT / OAT / inactivator / 3-Amino-4-fluorocyclopentenecarboxylic Acid / covalent modification

Function / homology

Function and homology information

arginine catabolic process to proline via ornithine / ornithine aminotransferase activity / ornithine aminotransferase / arginine catabolic process to glutamate / L-proline biosynthetic process / Glutamate and glutamine metabolism / visual perception / pyridoxal phosphate binding / mitochondrial matrix / mitochondrion ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.91 Å

Authors

Butrin, A. / Shen, S. / Silverman, R. / Liu, D.

Funding support

United States, 1items

Citation

Journal: Molecules / Year: 2023
Title: Structural and Mechanistic Basis for the Inactivation of Human Ornithine Aminotransferase by (3 S ,4 S )-3-Amino-4-fluorocyclopentenecarboxylic Acid.
Authors: Shen, S. / Butrin, A. / Beaupre, B.A. / Ferreira, G.M. / Doubleday, P.F. / Grass, D.H. / Zhu, W. / Kelleher, N.L. / Moran, G.R. / Liu, D. / Silverman, R.B.

History

Deposition	Oct 30, 2022	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 22, 2023	Provider: repository / Type: Initial release
Revision 1.1	Oct 25, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2	Mar 13, 2024	Group: Source and taxonomy / Category: entity_src_gen

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8ez1.cif.gz	591.4 KB	Display	PDBx/mmCIF format
PDB format	pdb8ez1.ent.gz	403.9 KB	Display	PDB format
PDBx/mmJSON format	8ez1.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8ez1_validation.pdf.gz	1.4 MB	Display	wwPDB validaton report
Full document	8ez1_full_validation.pdf.gz	1.4 MB	Display
Data in XML	8ez1_validation.xml.gz	52.9 KB	Display
Data in CIF	8ez1_validation.cif.gz	76 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ez/8ez1 ftp://data.pdbj.org/pub/pdb/validation_reports/ez/8ez1	HTTPS FTP

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Related structure data

Related structure data	1oatS S: Starting model for refinement
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: Ornithine aminotransferase, mitochondrial

B: Ornithine aminotransferase, mitochondrial

C: Ornithine aminotransferase, mitochondrial

hetero molecules

136 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Ornithine aminotransferase, mitochondrial

B: Ornithine aminotransferase, mitochondrial

hetero molecules

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

2

C: Ornithine aminotransferase, mitochondrial

hetero molecules

C: Ornithine aminotransferase, mitochondrial

hetero molecules

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

Unit cell

Length a, b, c (Å)	202.170, 110.290, 57.120
Angle α, β, γ (deg.)	90.000, 103.720, 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

Components on special symmetry positions

ID	Model	Components
1	1	B-861- HOH
2	1	B-876- HOH
3	1	C-604- HOH
4	1	C-672- HOH
5	1	C-777- HOH
6	1	C-782- HOH

#1: Protein	Ornithine aminotransferase, mitochondrial / Ornithine delta-aminotransferase / Ornithine--oxo-acid aminotransferase Mass: 44860.320 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: OAT / Production host: Escherichia coli (E. coli) / References: UniProt: P04181, ornithine aminotransferase
#2: Chemical	ChemComp-X8B / (3E,4E)-4-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)-3-iminocyclopent-1-ene-1-carboxylic acid / 3-Amino-4-fluorocyclopentenecarboxylic Acid Mass: 354.252 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₄H₁₅N₂O₇P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-X8H / (1R,3S,4Z)-3-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)-4-iminocyclopentane-1-carboxylic acid Mass: 358.284 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Formula: C₁₄H₁₉N₂O₇P / Feature type: SUBJECT OF INVESTIGATION / References: ornithine aminotransferase
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 707 / 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: 2.3 Å³/Da / Density % sol: 46.44 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop Details: The crystals with the best morphology and size grew in a final condition containing 10% PEG 6000, 100 mM NaCl, 10% glycerol, 100 mM Tricine pH 7.8.

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.127 Å
Detector	Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 29, 2019
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.127 Å / Relative weight: 1
Reflection	Resolution: 1.91→36.02 Å / Num. obs: 92197 / % possible obs: 98 % / Redundancy: 4.2 % / CC_1/2: 0.992 / Net I/σ(I): 6.1
Reflection shell	Resolution: 1.91→1.96 Å / Num. unique obs: 6637 / CC_1/2: 0.464

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Processing

Software

Name	Version	Classification
PHENIX	1.17.1_3660	model building
PHENIX	1.17.1_3660	refinement
xia2		data reduction
Aimless		data scaling
xia2		data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1OAT

1oat

Resolution: 1.91→36.02 Å / SU ML: 0.2553 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.1943
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2366	4596	4.99 %
R_work	0.1885	87592	-
obs	0.1909	92188	97.89 %

Solvent computation

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

Displacement parameters

B_iso mean: 37.16 Å²

Refinement step

Cycle: LAST / Resolution: 1.91→36.02 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9458	0	48	707	10213

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0121	9729
X-RAY DIFFRACTION	f_angle_d	1.1735	13225
X-RAY DIFFRACTION	f_chiral_restr	0.0697	1463
X-RAY DIFFRACTION	f_plane_restr	0.0073	1694
X-RAY DIFFRACTION	f_dihedral_angle_d	7.5843	1344

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 (%)
1.91-1.93	0.3902	161	0.3233	2773	X-RAY DIFFRACTION	94.1
1.93-1.95	0.2977	158	0.2815	2853	X-RAY DIFFRACTION	96.08
1.95-1.98	0.2844	157	0.2661	2913	X-RAY DIFFRACTION	97.58
1.98-2	0.3175	157	0.2494	2866	X-RAY DIFFRACTION	97.23
2-2.03	0.2888	162	0.2404	2911	X-RAY DIFFRACTION	98.43
2.03-2.06	0.2978	156	0.2259	2938	X-RAY DIFFRACTION	98.57
2.06-2.09	0.2588	135	0.2276	2919	X-RAY DIFFRACTION	98.2
2.09-2.12	0.315	141	0.2276	2924	X-RAY DIFFRACTION	97.89
2.12-2.15	0.2957	158	0.2278	2897	X-RAY DIFFRACTION	98.61
2.15-2.19	0.269	152	0.2271	2956	X-RAY DIFFRACTION	98.17
2.19-2.22	0.2703	142	0.2276	2918	X-RAY DIFFRACTION	98.08
2.22-2.26	0.3411	136	0.2259	2947	X-RAY DIFFRACTION	98.25
2.26-2.31	0.2601	152	0.2235	2947	X-RAY DIFFRACTION	98.63
2.31-2.36	0.2816	174	0.2236	2904	X-RAY DIFFRACTION	98.24
2.36-2.41	0.288	144	0.2218	2950	X-RAY DIFFRACTION	98.85
2.41-2.46	0.2827	157	0.2221	2916	X-RAY DIFFRACTION	98.65
2.46-2.52	0.2805	181	0.2225	2905	X-RAY DIFFRACTION	98.44
2.52-2.59	0.2583	178	0.2206	2891	X-RAY DIFFRACTION	97.21
2.59-2.67	0.2948	148	0.2181	2789	X-RAY DIFFRACTION	94.16
2.67-2.75	0.2829	146	0.2134	2944	X-RAY DIFFRACTION	98.6
2.75-2.85	0.2679	152	0.203	2979	X-RAY DIFFRACTION	98.99
2.85-2.97	0.2606	143	0.1899	2949	X-RAY DIFFRACTION	99.13
2.97-3.1	0.2271	145	0.1773	2946	X-RAY DIFFRACTION	98.85
3.1-3.27	0.1976	159	0.1765	2962	X-RAY DIFFRACTION	98.73
3.27-3.47	0.2312	169	0.1651	2929	X-RAY DIFFRACTION	98.63
3.47-3.74	0.2065	151	0.1549	2954	X-RAY DIFFRACTION	98.95
3.74-4.11	0.1626	150	0.1412	2970	X-RAY DIFFRACTION	98.17
4.11-4.71	0.1672	137	0.1375	2921	X-RAY DIFFRACTION	97.3
4.71-5.93	0.2075	152	0.1684	2871	X-RAY DIFFRACTION	94.94
5.93-36.02	0.193	143	0.1671	3050	X-RAY DIFFRACTION	99.07

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	1.3140504479	0.320319351211	1.27223803748	0.595356532275	0.684907719726	2.13932124502	-0.071402428786	0.324681408015	0.0377892771033	-0.103191311065	0.0978471928302	-0.144032066979	-0.0685757599116	0.496543579218	-0.0342123585762	0.21646815731	-0.0227658988259	-0.0142622217379	0.342303974335	0.0146629040773	0.213350977908	51.7611376284	18.9536534495	-13.3948744762
2	1.03848096815	0.325524257066	0.0853542150469	0.473269744627	0.368631742825	0.52870918562	0.0414997834876	-0.158206341302	-0.160553772778	0.0788030409233	0.0187774768517	-0.0442642959702	0.0887933836088	0.063816725482	-0.051057234516	0.279733128405	0.0306008042856	-0.0454186246125	0.36660681159	0.0542390490604	0.231733121755	36.452630359	0.938244769311	1.8600360408
3	0.331709476955	-0.118330947523	0.0355127656815	0.509897006207	0.119781867366	0.718996145816	-0.0314653824323	-0.0170769186126	0.0294602786702	-0.0581423292784	0.00694875249933	0.044937146648	-0.0243139164541	-0.0676702980565	0.0193495370431	0.19904502516	0.000174120535467	-0.0178208293971	0.211550316001	0.00728169999481	0.152854696001	17.6987221057	20.1304975192	-4.44623873546
4	2.38993774469	0.83782643449	0.553491620249	1.03393063263	0.116723206355	0.676750179521	0.0187444529616	-0.17464188633	0.104819913334	0.102075888838	-0.0797493755344	0.0583971054264	-0.119717062577	-0.155182654121	0.0410778014489	0.234830488877	0.0526282463472	-0.0183242494975	0.28641535317	-0.0265009040457	0.161334154412	20.7782102895	22.8420845261	6.83505209271
5	0.721891786694	0.163628847274	-0.154092747781	0.988387696803	0.420457736274	0.699437082262	0.00392319430268	-0.125202494071	-0.0309260491136	0.14220153055	0.0540290358252	-0.0450581187858	0.0908029730052	0.0226713130911	-0.0611697503441	0.277511951104	0.0114411272546	-0.0243084138898	0.327161529073	0.0477751350202	0.179231462965	31.6233358835	8.2042414108	4.85614206392
6	2.40272781132	-0.210452088102	0.435218574943	3.47823097776	-0.604271841034	2.45901995198	0.00876780322008	-0.106767797832	0.477370114592	0.16492338838	-0.0247475201923	-0.0391750687941	-0.236364403131	0.233420855246	0.0185098003789	0.222526700944	-0.0216413963768	-0.0366933001465	0.337863920566	-0.0358600889956	0.281812274331	44.238176898	33.2868209219	5.272633265
7	0.961241203978	0.320051444656	-0.585182753244	1.7390466504	-0.429433038989	1.39911046882	-0.0094169165711	-0.0266052335882	0.112086305522	0.00159300959576	0.0420592934552	-0.0491316689275	-0.215947989039	0.0996669208714	-0.0112267749109	0.270649844593	-0.0680392553356	-0.0419298408729	0.354821075229	-0.00471724570093	0.228498804059	50.2949374593	29.4398688844	-0.928336649186
8	0.762596006048	-0.765255819078	-0.832979814739	3.96071516637	1.34893504189	1.46332807809	-0.0678882840845	-0.393170539067	-0.24211175052	0.389766312745	0.0723855686816	0.192166245068	0.472260254667	0.214030711816	0.0193710468491	0.324657708043	-0.0136486990982	-0.0060384955743	0.336702689756	0.0935482622604	0.271838248317	24.8429749176	-10.2428624254	3.61943909567
9	0.851753392128	0.524781733413	0.0431297921138	1.63301306831	-0.137536197328	0.573100006522	0.11686553819	-0.0367358636985	-0.225760091768	0.0213335992931	0.0442428274197	-0.0443809289876	0.173638929868	-0.0396926933837	-0.143308034371	0.317565186624	0.0635822600675	-0.080655916133	0.293493325608	0.0105301237104	0.259946604373	38.929887273	-12.4109922692	-10.3337546351
10	0.968806228649	0.270893674521	0.438471904947	0.658520114826	0.053737874573	1.44586846454	-0.0505207162098	0.0476561280871	0.0261501099643	-0.00368914826188	-0.00106870428026	-0.133906818251	-0.00395967224198	0.242278086066	0.0350990448633	0.242964708182	0.0438737768514	-0.00320245083342	0.328103830364	0.00177734316635	0.190481527567	43.9776449569	10.6733583161	-19.5047083054
11	0.790039115742	0.398892119616	-0.171871357071	1.04839520989	0.0954074536038	0.364597962717	0.0662154888719	-0.0485943931162	-0.0252006647975	-0.0555487803763	-0.00680199405024	0.135388231032	-0.00202915158661	0.0139407891086	-0.0531306202973	0.175084446106	0.0067247308685	-0.0221297564842	0.226411718742	0.00631131826727	0.144906098786	17.2485779379	11.2034354521	-22.4640184636
12	0.864572549533	-0.3629157503	0.13834429579	2.75071096615	-0.222318457371	0.535051796157	0.0101235577511	0.0814357668061	-0.0271133081686	-0.109833919988	-0.0264162973689	-0.025602765549	0.0140198108971	-0.0334574529692	0.00799302686621	0.212617070298	0.00747689321236	-0.036435774268	0.256632589669	-0.00247572449851	0.149121391664	20.5548615727	4.85196070182	-32.0845059777
13	0.596632299869	0.16103856015	-0.040193366532	0.675528518252	-0.126479028632	0.796751643569	0.00821106578904	0.174294464569	0.00697216235597	-0.108095949736	-0.0131026925305	-0.0122643471921	0.0304285856372	0.170310834242	0.000644484272227	0.193381508278	0.0434335145589	-0.013582043273	0.274613568147	0.00043172890671	0.14907614357	33.451302746	5.53132616081	-23.6953246513
14	2.05463721775	1.68277061354	0.834723178946	3.45838568419	1.63095683685	1.95114279425	-0.0316831166729	0.3699300195	-0.350066592879	-0.332126858733	0.246985513873	-0.350198236313	0.181333452686	0.347968343808	-0.190431337659	0.330498108319	0.107167778071	-0.0597257530045	0.278491623838	-0.0132832456723	0.218057680411	37.8406761633	-10.883617458	-24.9224962997
15	2.56174573139	-0.330595235721	-0.907322799618	1.6171526468	0.36130584404	3.19989440332	-0.0110748611564	-0.120571900771	-0.516108383766	0.0265239566605	0.049154468915	0.47686461176	0.565956968771	-0.517414561529	-0.0218797704199	0.411765175189	-0.0515981040551	-0.119891941929	0.307050550458	0.0628881466969	0.524013716566	15.5694356955	-19.5059103567	-21.0049917217
16	2.12823461321	0.484538988287	-0.493941086457	1.53845589937	-0.428351313962	1.85377672412	0.0821842663326	0.11235029511	-0.364748870605	-0.0185775488796	0.0622264555611	0.0236239463802	0.559513497674	-0.204673562346	-0.116230542774	0.433375644632	-0.0057028915913	-0.107426672251	0.263220128785	0.00981187986281	0.328500103	25.1265161293	-21.3639192611	-15.6384395238
17	1.0214219534	1.05837242513	-0.328245353363	1.13959204377	-0.3039159036	0.297872709537	0.219444977517	-0.27934109066	0.31877958741	0.290331246159	-0.143551368456	0.0419999753955	-0.213879890939	0.0676043601664	0.0280618725047	0.48940888829	-0.235745294199	0.175451280162	0.589204490734	-0.337168391414	0.750752245689	12.5767483905	60.9684194195	18.8079092925
18	0.215783864739	0.0851252513829	-0.190438550188	0.235316061348	0.0110643761935	0.208893336016	0.35426887622	-0.150279896425	0.388389353167	0.077891428153	0.0920902492458	-0.0624908784398	-0.36218832789	0.0653310108789	0.119801984007	0.547080763032	-0.130100307238	0.335924707126	0.298397924504	-0.022810992665	1.01313491746	8.61059116695	69.6703304109	-0.456438641298
19	1.06629972742	0.00329251846096	-0.219330367733	0.536025263812	0.114404541726	0.710109451733	0.20714536988	0.20360621683	0.407712059946	-0.0567684986068	0.00734524401912	-0.0326395545718	-0.126535892704	-0.149386400792	-0.161239041986	0.22897555805	0.0181069305095	0.0551905687384	0.229623076412	0.0668510996868	0.286981309956	5.44974484645	43.7890141899	-9.46518648836
20	0.368000625659	-0.387075099329	0.182303803196	0.909870504316	-0.0189371849063	0.420549620787	0.233011045417	0.273316161822	0.58217003988	-0.0912204988465	0.0428894920535	0.045776703671	-0.19496410147	-0.0141190345951	-0.204500072095	0.315993263733	0.0153753881091	0.159678025374	0.258574888433	0.0912636359554	0.517475150868	9.11696732506	52.4838441672	-13.9616883395
21	1.3895345007	0.455896818903	-0.19441017235	1.19307550865	0.541652823995	1.52916353042	0.316834399832	-0.2828744473	0.360498967647	0.159167868732	0.077793560045	-0.269080771206	-0.0302754513556	0.352952356242	-0.27759606014	0.368704977313	-0.16843966023	0.169642288162	0.444156120929	-0.196095699336	0.723506701396	31.3969457895	57.4977424206	0.327662706318
22	1.07876453254	0.206348165154	0.315830138384	1.14045639204	0.358818446843	1.25898744934	0.247251047692	-0.0531083356291	0.22430091616	0.175196998101	0.104488407831	-0.213132436893	-0.169672108356	0.188125918144	-0.210343679545	0.46493952513	-0.214349052262	0.2669821808	0.505165548077	-0.185166096811	0.834847319216	29.0002219283	63.0818953938	1.43484874885

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 38 through 82 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 83 through 141 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 142 through 220 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 221 through 263 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 264 through 344 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 345 through 389 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 390 through 439 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 38 through 61 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 62 through 105 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 106 through 141 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 142 through 220 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 221 through 263 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 264 through 326 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 327 through 362 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 363 through 389 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 390 through 439 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 38 through 61 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 62 through 117 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 118 through 220 )
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 221 through 344 )
21	X-RAY DIFFRACTION	21	chain 'C' and (resid 345 through 400 )
22	X-RAY DIFFRACTION	22	chain 'C' and (resid 401 through 439 )

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