PDB-8tti: Trp-6-Halogenase BorH complexed with FAD and Trp

ID or keywords:

Entry

Database: PDB / ID: 8tti

Title

Trp-6-Halogenase BorH complexed with FAD and Trp

Components

Tryptophan 6-halogenase

Keywords

FLAVOPROTEIN / halogenase / oxidoreductase

Function / homology

Function and homology information

monooxygenase activity / nucleotide binding
Similarity search - Function

Biological species

uncultured bacterium (environmental samples)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 1.98 Å

Authors

Lingkon, K. / Bellizzi, J.J.

Funding support

United States, 1items

Citation

Journal: Biorxiv / Year: 2023
Title: Crystallographic and thermodynamic evidence of negative cooperativity of flavin and tryptophan binding in the flavin-dependent halogenases AbeH and BorH.
Authors: Ashaduzzaman, M. / Lingkon, K. / De Silva, A.J. / Bellizzi, J.J.

History

Deposition	Aug 14, 2023	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 30, 2023	Provider: repository / Type: Initial release
Revision 1.1	Sep 13, 2023	Group: Database references / Category: citation / citation_author Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8tti.cif.gz	1 MB	Display	PDBx/mmCIF format
PDB format	pdb8tti.ent.gz	725.1 KB	Display	PDB format
PDBx/mmJSON format	8tti.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/tt/8tti ftp://data.pdbj.org/pub/pdb/validation_reports/tt/8tti	HTTPS FTP

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Related structure data

Related structure data	8fovC 8foxC 8ttjC 8ttkC 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
Related items in Molecule of the Month	#228 - Dec 2018 Directed Evolution of Enzymes similarity (1)

Deposited unit

A: Tryptophan 6-halogenase

B: Tryptophan 6-halogenase

C: Tryptophan 6-halogenase

D: Tryptophan 6-halogenase

hetero molecules

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

1

A: Tryptophan 6-halogenase

hetero molecules

defined by author
Evidence: gel filtration
60.8 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Tryptophan 6-halogenase

hetero molecules

defined by author
60.9 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: Tryptophan 6-halogenase

hetero molecules

defined by author
61.1 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

D: Tryptophan 6-halogenase

hetero molecules

defined by author
61.3 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	73.680, 157.410, 112.830
Angle α, β, γ (deg.)	90.000, 104.060, 90.000
Int Tables number	4
Space group name H-M	P12₁1
Space group name Hall	P2yb

#1: Protein	Tryptophan 6-halogenase Mass: 60202.082 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) uncultured bacterium (environmental samples) Gene: borH / Production host: Escherichia coli (E. coli) / References: UniProt: M9QSI0
#2: Chemical	ChemComp-TRP / TRYPTOPHAN Type: L-peptide linking / Mass: 204.225 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₁H₁₂N₂O₂ / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: SO₄
#4: Chemical	ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂₇H₃₃N₉O₁₅P₂ / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1243 / 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: 2.64 Å³/Da / Density % sol: 53.33 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1 M Bis-Tris pH 6.5 300 mM (NH4)2SO4 19% (w/v) PEG 8000.

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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: 1.033 Å

Detector

Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 8, 2019

Radiation

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

Radiation wavelength

Wavelength: 1.033 Å / Relative weight: 1

Reflection

Resolution: 1.98→54.72 Å / Num. obs: 163198 / % possible obs: 94.6 % / Redundancy: 1.9 % / B_iso Wilson estimate: 30.87 Å² / CC_1/2: 0.98 / CC star: 0.995 / R_merge(I) obs: 0.135 / R_pim(I) all: 0.135 / R_rim(I) all: 0.19 / Net I/σ(I): 3.7

Reflection shell

Diffraction-ID: 1 / Redundancy: 1.9 %

Resolution (Å)	R_merge(I) obs	Mean I/σ(I) obs	Num. unique obs	CC_1/2	R_pim(I) all	R_rim(I) all	% possible all
1.98-2.05	1.316	0.62	16589	0.1	1.316	1.861
2.05-2.13	1.036	0.8	16576	0.191	1.036	1.465	96.4
2.13-2.23	0.746	1.1	16678	0.331	0.746	1.055	96.6
2.23-2.35	0.524	1.5	16465	0.548	0.524	0.741	95.6
2.35-2.49	0.366	2	16375	0.7	0.366	0.518	94.9
2.49-2.69	0.26	2.7	14606	0.707	0.26	0.368	84.7
2.69-2.96	0.147	4.3	16711	0.935	0.147	0.208	96.5
2.96-3.39	0.085	6.3	16887	0.976	0.085	0.121	97.8
3.39-4.27	0.055	8.6	16484	0.986	0.055	0.078	95.1
4.27-54.72	0.046	9.5	15827	0.988	0.046	0.065	90.6

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Phasing

Phasing	Method: molecular replacement

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Processing

Software

Name	Version	Classification
PHENIX	1.19.2_4158	refinement
MOSFLM		data reduction
Aimless		data scaling
PHASER		phasing
PDB_EXTRACT	3.27	data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.98→54.72 Å / SU ML: 0.3649 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 31.8227
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2701	1989	1.22 %
R_work	0.2288	160534	-
obs	0.2293	162523	93.91 %

Solvent computation

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

Displacement parameters

B_iso mean: 44.2 Å²

Refinement step

Cycle: LAST / Resolution: 1.98→54.72 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	16685	0	201	1243	18129

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0028	17391
X-RAY DIFFRACTION	f_angle_d	0.4927	23654
X-RAY DIFFRACTION	f_chiral_restr	0.0408	2459
X-RAY DIFFRACTION	f_plane_restr	0.0047	3088
X-RAY DIFFRACTION	f_dihedral_angle_d	11.3794	6237

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 (%)
1.98-2.03	0.4336	133	0.387	11202	X-RAY DIFFRACTION	92.68
2.03-2.08	0.3992	155	0.3568	11556	X-RAY DIFFRACTION	94.76
2.08-2.14	0.3499	151	0.3248	11671	X-RAY DIFFRACTION	95.86
2.14-2.21	0.3368	133	0.3049	11764	X-RAY DIFFRACTION	96.31
2.21-2.29	0.3193	144	0.2864	11708	X-RAY DIFFRACTION	95.94
2.29-2.38	0.3331	147	0.2734	11531	X-RAY DIFFRACTION	94.74
2.38-2.49	0.3459	146	0.2612	11567	X-RAY DIFFRACTION	95.03
2.49-2.62	0.3201	128	0.2437	10616	X-RAY DIFFRACTION	86.77
2.62-2.79	0.2804	130	0.2302	10764	X-RAY DIFFRACTION	88.52
2.79-3	0.26	144	0.2264	11939	X-RAY DIFFRACTION	97.77
3-3.31	0.2695	148	0.2083	11955	X-RAY DIFFRACTION	97.68
3.31-3.79	0.2214	145	0.1916	11770	X-RAY DIFFRACTION	96.12
3.79-4.77	0.2172	148	0.1726	11288	X-RAY DIFFRACTION	92.14
4.77-54.72	0.2329	137	0.2128	11203	X-RAY DIFFRACTION	90.49

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	4.1362355156	0.864522967096	3.33199516164	2.34262212399	0.423391957804	4.2026756323	-0.19330740383	-0.0610213357972	0.0649214995483	0.126112898273	0.224945491421	0.451182625194	0.220723107878	-0.60294083548	-0.0110722934209	0.222024495502	-0.0667750274207	0.0921055318457	0.344555468762	0.072676831335	0.370812982883	-44.6501084933	46.1855496135	94.0452692103
2	2.88388740323	2.18006483387	-1.17411085599	2.65896907874	0.420574167327	1.75147307863	-0.105894335732	-0.21543180022	-0.0143946765611	0.219090652567	0.0854965617277	-0.182553739761	-0.0224632439889	0.10990703599	0.00716786793074	0.225050793033	0.0441278631006	-0.00445685269734	0.164203031417	0.0229577140403	0.256511591216	-13.2618879008	51.3500989827	103.456396836
3	1.79509672737	-0.23182606374	0.657018768193	1.58018871385	0.234643527175	2.50863659543	-0.0783020781575	0.000761012111034	-0.32234061776	-0.0481199993052	0.149840863173	0.33869043851	0.40476937487	-0.488425475591	-0.0559091861905	0.27249899248	-0.106753347917	0.040771316893	0.279825428238	0.0716347325104	0.455951958201	-40.6524522498	37.2941322302	88.990922954
4	2.19091426353	-0.71447653876	0.861592519102	1.04390638642	-0.463628012906	1.22761370329	-0.121744509182	0.137069700599	-0.269390795097	-0.134100031394	0.197943317652	0.0666748794596	0.177598276058	-0.0608521295324	-0.080409612876	0.249111411679	-0.062214756691	0.0744763212525	0.181240056643	0.0190213188775	0.292517795744	-25.8414761337	38.2644891316	88.2831474598
5	3.93934961668	1.48792768852	0.106989553013	4.87181257526	-0.607832488743	2.82070740554	-0.109518710709	0.149193530462	0.497683920135	0.0378589729284	0.0988512406836	0.187817924274	-0.168281658228	-0.165690291097	0.0140951153791	0.177150352426	0.0080351758869	-0.0122861371659	0.140298361658	0.00880424668727	0.200418051205	-15.8792355409	58.1728140805	89.6120784608
6	4.83541451609	4.36620928517	-1.97014446247	3.77995794321	-1.66254196117	1.83328948756	0.372547530566	-0.526256808077	0.503140935038	0.518661262384	-0.244776400791	0.475944704844	-0.31981796327	0.108182761618	-0.11853708992	0.259731195639	0.052344002306	0.0459689218943	0.247278436781	-0.0555400897084	0.317249456365	-19.6839608807	57.8490960664	111.635785301
7	3.95593079129	0.39658424463	-3.36925539781	1.03677030722	-0.575055910598	4.33080946252	-0.0847567260517	-0.124991261318	0.0385522400972	0.163386412736	0.225546049696	-0.730664402949	-0.0366358904482	0.73723439625	-0.119393503671	0.257036473819	-0.0120948281027	-0.0257202091636	0.44075204863	-0.201957779353	0.741811966138	26.7054648165	159.166400718	94.1802171664
8	2.15041389554	1.83667383129	1.00091594071	1.71335087155	0.343997677799	2.3990584789	0.0796470311546	-0.177973522596	0.11502532995	0.147020669109	-0.0522655330539	0.0778854316342	0.148976778945	-0.182713168028	-0.0518334910431	0.202914507535	0.0447520362678	-0.00123448559003	0.163865073883	0.0126538526514	0.235123587503	-4.62609332103	154.006536135	103.664486334
9	1.74934766256	-0.0138529036023	-0.497466587964	1.34266620022	0.187627929792	1.82610168728	0.0124533258078	-0.00155029926184	0.451361921467	-0.146778022559	0.201762872714	-0.646072535473	-0.418349098197	0.50530554496	-0.180066695722	0.320801092948	-0.0967570231967	0.0658334169238	0.367517232132	-0.110937500162	0.764122858016	22.6181742889	168.010148269	89.2676447692
10	1.39097498683	-0.788621479836	-0.633545993548	1.30272594145	0.373906729305	1.22681743029	-0.0375923802621	0.0320188693285	0.42122461926	-0.0947149308621	0.185699507644	-0.417218767937	-0.203032695677	0.167797118617	-0.164625123603	0.226633478027	-0.0312468801836	-0.0151075321335	0.209266756627	-0.0267904082425	0.511951183312	7.99598107595	166.899803299	88.134388072
11	3.14646097442	1.4027455883	-0.00416641289355	3.18114681559	0.903386351492	2.48466877096	0.0127523411431	0.0162847593918	-0.278603421021	-0.0543392604991	0.0135694818578	-0.350050317026	0.177925753355	0.233793950711	-0.0159526471035	0.214679403185	0.0395514205324	0.0346655217437	0.141954277132	0.00781619352379	0.269862970767	-2.25475961081	147.11824125	90.0362409406
12	4.92535017253	4.0240268463	2.27085369946	4.15319841142	1.61208072721	2.37840932111	0.448508993615	-0.43441547865	-0.507407625224	0.752350226187	-0.204528809802	-0.608569973842	0.441593145329	-0.104218625617	-0.245572108565	0.342232459665	0.086431252707	-0.0513876459996	0.197439050656	0.0149134972703	0.320255104839	1.68049150071	147.521783867	111.908885085
13	6.55409451112	-0.716250901958	-0.303944984637	2.20126450514	-0.0206517651478	3.64489635725	0.044406172572	-0.0753668607011	-0.44159550652	0.00101095361513	0.0101963468412	0.190017466416	0.462535664528	-0.0168690001749	-0.0641037704595	0.280477667569	-0.00704902019869	-0.0319821505968	0.135629760306	-0.0285398987397	0.402954677321	-9.50569784709	122.53602803	81.5005733152
14	3.47401246814	0.393939409828	0.388144741289	1.9960907613	-0.0441069477993	0.980801863341	0.110786546965	0.0265612253195	-0.515371939271	0.0109848432808	-0.0532901458608	-0.352024107108	0.332713926297	0.388070658125	-0.0490278265279	0.337640168988	0.14146998452	-0.000233439074946	0.343595133067	-0.0316208677244	0.49093606533	22.3236593505	122.080898564	75.5944003415
15	3.26973311968	-1.25824015594	-0.787849748716	1.62266349299	0.477482593098	1.77791973513	0.155939286054	0.492716319989	-0.576763273412	-0.264775854728	-0.136468302931	0.11062714856	0.33989898866	-0.0250460333367	-0.00885307773558	0.317264276596	0.0200385710804	-0.0467251983288	0.266958294782	-0.110599054161	0.412147671895	-0.566603145324	124.179755646	67.4463725766
16	2.78259239825	1.52784387888	-0.966120013631	4.25317422561	-0.29077873704	3.70772256729	0.235189831173	0.0151935128888	-0.0268542425058	0.542067049583	-0.169056850319	0.338642712386	-0.142896996942	-0.387323818707	-0.108045717851	0.255014106627	0.0419614799321	0.0740506744133	0.376921021072	-0.0875863702294	0.542677657291	14.2698009096	137.636462242	78.2030411544
17	2.45438464632	0.943065010508	-0.03853191006	3.23567967317	0.652145625394	1.57374506757	0.14968870608	-0.157322573988	-0.276385523702	0.333484305938	0.026648647411	-0.572051618573	0.261390631193	0.413339512074	-0.163821315367	0.302827540334	0.0924725355811	0.000571594735662	0.369286542446	-0.0646996498857	0.556952143621	27.4235688951	127.144389451	80.3072651729
18	4.29807441249	-0.184668151244	0.488568641161	2.67585047688	-1.06995852688	3.97446005331	-0.176684677217	-0.186858446164	0.691642904875	0.0628332997456	0.263673666623	0.0387179127945	-0.410791049117	-0.127360584599	-0.116567654282	0.288177489532	-0.0452633829442	-0.0168966668058	0.226496736559	0.0309604435346	0.709416488607	-8.6747314778	82.9242170987	81.3721006443
19	2.06555621705	0.568048285019	-0.672051122995	2.93995671224	0.511016465081	1.02542707451	-0.00534801771143	0.0804818345294	0.942844366019	-0.000822393023865	-0.0196994215145	0.588976406627	-0.328158442997	-0.250607792981	0.0298966187063	0.363430119887	0.054430207457	-0.055047045544	0.360599146261	0.130597544685	0.870394156137	-39.3468818955	83.4937252744	75.4908088039
20	2.40366877119	0.458309970859	-0.279345565941	2.77267219859	0.47164624171	2.30347234052	-0.104219073823	0.314873935697	0.750863665069	-0.27287579207	0.0400245518024	-0.438995232111	-0.516292802713	0.453030151659	0.060441565286	0.363067808626	-0.119848197687	-0.0554399182395	0.462134002188	0.210918285078	0.734085918846	-0.106189263638	82.4073677648	72.0913762978
21	1.2025750369	-0.278169863054	0.160740573167	0.870297200364	-0.274562839645	1.32843684148	0.174356598906	0.591061325324	0.656136338016	-0.503819113101	-0.214073114734	0.211350077788	-0.541209405238	-0.210355905643	0.00608703528053	0.538518084237	0.000682458449507	-0.107944830739	0.450589890514	0.296274279576	0.900171469015	-27.3171506329	87.3859983638	63.6674450963
22	1.29397201315	-0.696458643131	0.399503387425	1.83480009958	-0.192879561311	0.946100444396	0.0165128706548	0.546974436089	0.657809732346	-0.382877109789	-0.00166008598935	0.119377306801	-0.305999826989	0.0463115443704	-0.00405775024306	0.398148751631	-0.0429957088504	-0.0256162758517	0.434283444672	0.304797224184	0.737925753295	-20.0589714914	82.323685642	64.7229530192
23	3.28605560232	0.0289911273817	0.736039256697	1.68440159028	-0.607529374367	0.431825265631	-0.0111637845878	0.280146446578	0.309060039022	-0.263216108512	0.118340419869	0.306991260784	0.036681646327	-0.105840331421	-0.110423152234	0.300126340741	-0.0315700637493	-0.0648679070337	0.317428101865	0.149202488996	0.442995154347	-29.5665755982	68.3888119199	68.2883082561
24	1.3518396988	1.12918684345	-1.62459435286	3.03616382314	-1.81284401073	2.87217469427	-0.0437003442049	-0.0279016806346	0.136967718176	0.0282112057879	0.0144682860138	-0.452320456726	0.114008850811	0.10199752964	-0.0411991547352	0.259508574523	-0.0023570822268	-0.0681847782094	0.305654079685	0.142825032417	0.631375842776	-38.5719274402	67.7772522508	76.1366309602
25	4.05271815328	3.33184459408	-0.0773031172982	7.30891201878	-0.633911888435	1.30884029681	0.227070131173	-0.325026539425	1.38347484204	0.942546710863	-0.145104427458	1.19338831062	-0.401755469175	-0.461984931611	-0.0877474573834	0.467481480547	0.059576797549	0.0567470269386	0.496821176696	-0.120283050431	0.925067644756	-45.0228126239	86.1851271605	84.4192759763

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

ID	Refine TLS-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	chain 'A' and (resid 2 through 80 )	A	A	2 - 80	1 - 73
2	2	chain 'A' and (resid 81 through 161 )	A	A	81 - 161	74 - 154
3	3	chain 'A' and (resid 162 through 271 )	A	A	162 - 271	155 - 264
4	4	chain 'A' and (resid 272 through 427 )	A	A	272 - 427	265 - 420
5	5	chain 'A' and (resid 428 through 491 )	A	A	428 - 491	421 - 484
6	6	chain 'A' and (resid 492 through 600 )	A	A	492 - 528	485 - 521
7	7	chain 'B' and (resid 2 through 80 )	B	G	2 - 80	1 - 73
8	8	chain 'B' and (resid 81 through 161 )	B	G	81 - 161	74 - 154
9	9	chain 'B' and (resid 162 through 272 )	B	G	162 - 272	155 - 265
10	10	chain 'B' and (resid 273 through 427 )	B	G	273 - 427	266 - 420
11	11	chain 'B' and (resid 428 through 491 )	B	G	428 - 491	421 - 484
12	12	chain 'B' and (resid 492 through 600 )	B	G	492 - 528	485 - 521
13	13	chain 'C' and (resid 2 through 63 )	C	N	2 - 63	1 - 56
14	14	chain 'C' and (resid 64 through 161 )	C	N	64 - 161	57 - 154
15	15	chain 'C' and (resid 162 through 427 )	C	N	162 - 427	155 - 420
16	16	chain 'C' and (resid 428 through 466 )	C	N	428 - 466	421 - 459
17	17	chain 'C' and (resid 467 through 527 )	C	N	467 - 527	460 - 520
18	18	chain 'D' and (resid 2 through 66 )	D	Q	2 - 66	1 - 59
19	19	chain 'D' and (resid 67 through 172 )	D	Q	67 - 172	60 - 164
20	20	chain 'D' and (resid 173 through 242 )	D	Q	173 - 242	165 - 234
21	21	chain 'D' and (resid 243 through 272 )	D	Q	243 - 272	235 - 264
22	22	chain 'D' and (resid 273 through 381 )	D	Q	273 - 381	265 - 373
23	23	chain 'D' and (resid 382 through 455 )	D	Q	382 - 455	374 - 447
24	24	chain 'D' and (resid 456 through 491 )	D	Q	456 - 491	448 - 483
25	25	chain 'D' and (resid 492 through 527 )	D	Q	492 - 527	484 - 519

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