PDB-8osy: Trimeric catalytic domain of the E. coli Dihydrolipoamide Acetylt...

ID or keywords:

Entry

Database: PDB / ID: 8osy

Title

Trimeric catalytic domain of the E. coli Dihydrolipoamide Acetyltransferase (E2) of the pyruvate dehydrogenase complex

Components

Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex

Keywords

TRANSFERASE / Pyruvate dehydrogenase complex / Catalytic domain / Trimer

Function / homology

Function and homology information

pyruvate catabolic process / dihydrolipoyllysine-residue acetyltransferase / dihydrolipoyllysine-residue acetyltransferase activity / lipoic acid binding / acetyl-CoA biosynthetic process from pyruvate / pyruvate dehydrogenase complex / pyruvate metabolic process / acetyltransferase activity / glycolytic process / cytoplasm
Similarity search - Function

Biological species

Escherichia coli (E. coli)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.89 Å

Authors

Meinhold, S. / Zdanowicz, R. / Glockshuber, R.

Funding support

Switzerland, 1items

Citation

Journal: Sci Adv / Year: 2024
Title: Dimerization of a 5-kDa domain defines the architecture of the 5-MDa gammaproteobacterial pyruvate dehydrogenase complex.
Authors: Sarah Meinhold / Rafal Zdanowicz / Christoph Giese / Rudi Glockshuber /

Abstract: The pyruvate dehydrogenase complex (PDHc) is a ~5 MDa assembly of the catalytic subunits pyruvate dehydrogenase (E1), dihydrolipoamide acetyltransferase (E2), and dihydrolipoamide dehydrogenase (E3). ...

History

Deposition	Apr 20, 2023	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Feb 7, 2024	Provider: repository / Type: Initial release
Revision 1.1	Feb 21, 2024	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8osy.cif.gz	481.3 KB	Display	PDBx/mmCIF format
PDB format	pdb8osy.ent.gz	331.8 KB	Display	PDB format
PDBx/mmJSON format	8osy.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	8osy_validation.pdf.gz	447.1 KB	Display	wwPDB validaton report
Full document	8osy_full_validation.pdf.gz	462.8 KB	Display
Data in XML	8osy_validation.xml.gz	40.7 KB	Display
Data in CIF	8osy_validation.cif.gz	57.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/os/8osy ftp://data.pdbj.org/pub/pdb/validation_reports/os/8osy	HTTPS FTP

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Related structure data

Related structure data	17119C 17126C 8oqjC 8orbC 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	#153 - Sep 2012 Pyruvate Dehydrogenase Complex similarity (16) #154 - Oct 2012 Citric Acid Cycle similarity (13)

Deposited unit

A: Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex

B: Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex

C: Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex

D: Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex

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

1

A: Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex

B: Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex

C: Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex

defined by author&software
Evidence: equilibrium centrifugation
81.8 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

D: Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex

defined by author&software
81.8 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	148.149, 148.149, 119.954
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	146
Space group name H-M	H3
Space group name Hall	R3
Symmetry operation	#1: x,y,z #2: -y,x-y,z #3: -x+y,-x,z #4: x+1/3,y+2/3,z+2/3 #5: -y+1/3,x-y+2/3,z+2/3 #6: -x+y+1/3,-x+2/3,z+2/3 #7: x+2/3,y+1/3,z+1/3 #8: -y+2/3,x-y+1/3,z+1/3 #9: -x+y+2/3,-x+1/3,z+1/3

#1: Protein	Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex / Dihydrolipoamide acetyltransferase component of pyruvate dehydrogenase complex / E2 Mass: 27260.723 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: aceF, b0115, JW0111 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: P06959, dihydrolipoyllysine-residue acetyltransferase
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 483 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex / Dihydrolipoamide acetyltransferase component of pyruvate dehydrogenase complex / E2

Mass: 27260.723 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Escherichia coli (E. coli) / Gene: aceF, b0115, JW0111 / Production host:

Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P06959, dihydrolipoyllysine-residue acetyltransferase

#2: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 483 / 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: 2.34 Å³/Da / Density % sol: 47.39 %
Crystal grow	Temperature: 277.15 K / Method: vapor diffusion, sitting drop Details: 100 mM Tris-HCl pH 8.5, 200 mM MgCl2, 30 % (w/v) PEG 4000

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.000002 Å
Detector	Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Sep 17, 2020
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.000002 Å / Relative weight: 1
Reflection	Resolution: 1.89→44.96 Å / Num. obs: 157861 / % possible obs: 99.7 % / Redundancy: 5.2 % / B_iso Wilson estimate: 40.63 Å² / CC_1/2: 0.999 / R_rim(I) all: 0.055 / Net I/σ(I): 17.6
Reflection shell	Resolution: 1.89→2 Å / Num. unique obs: 25095 / CC_1/2: 0.653 / R_rim(I) all: 1.008

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Processing

Software

Name	Version	Classification
PHENIX	1.20.1_4487	refinement
XDS		data reduction
XDS		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.89→44.96 Å / SU ML: 0.381 / Cross valid method: FREE R-VALUE / σ(F): 1.3 / Phase error: 28.4711
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2444	7891	5 %
R_work	0.2059	149936	-
obs	0.2078	157827	99.68 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 58.64 Å²

Refinement step

Cycle: LAST / Resolution: 1.89→44.96 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7604	0	0	483	8087

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0055	7754
X-RAY DIFFRACTION	f_angle_d	0.7789	10467
X-RAY DIFFRACTION	f_chiral_restr	0.051	1205
X-RAY DIFFRACTION	f_plane_restr	0.0068	1339
X-RAY DIFFRACTION	f_dihedral_angle_d	4.8426	1034

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 (%)
1.89-1.91	0.8803	239	0.9006	4560	X-RAY DIFFRACTION	91.72
1.91-1.93	0.4801	268	0.451	5067	X-RAY DIFFRACTION	99.83
1.93-1.95	0.6818	259	0.6057	4925	X-RAY DIFFRACTION	99.88
1.95-1.98	0.4593	260	0.4076	4972	X-RAY DIFFRACTION	99.96
1.98-2	0.342	266	0.3405	5042	X-RAY DIFFRACTION	99.92
2-2.03	0.2851	268	0.2777	5069	X-RAY DIFFRACTION	99.98
2.03-2.06	0.3033	260	0.2845	4943	X-RAY DIFFRACTION	99.94
2.06-2.09	0.3497	268	0.2752	5101	X-RAY DIFFRACTION	99.83
2.09-2.12	0.296	258	0.2626	4892	X-RAY DIFFRACTION	99.92
2.12-2.16	0.2759	266	0.2534	5062	X-RAY DIFFRACTION	100
2.16-2.2	0.3025	268	0.2506	5066	X-RAY DIFFRACTION	100
2.2-2.24	0.3064	262	0.2516	4976	X-RAY DIFFRACTION	100
2.24-2.28	0.3212	260	0.2891	4970	X-RAY DIFFRACTION	99.92
2.28-2.32	0.274	268	0.2421	5078	X-RAY DIFFRACTION	100
2.32-2.38	0.2932	262	0.2442	4972	X-RAY DIFFRACTION	100
2.38-2.43	0.2869	266	0.2271	5054	X-RAY DIFFRACTION	100
2.43-2.49	0.2784	262	0.2283	4968	X-RAY DIFFRACTION	100
2.49-2.56	0.2585	266	0.2199	5076	X-RAY DIFFRACTION	100
2.56-2.63	0.2707	262	0.2198	4983	X-RAY DIFFRACTION	99.98
2.63-2.72	0.2861	266	0.228	5025	X-RAY DIFFRACTION	100
2.72-2.82	0.2682	260	0.2248	4938	X-RAY DIFFRACTION	100
2.82-2.93	0.2477	268	0.2248	5122	X-RAY DIFFRACTION	99.96
2.93-3.06	0.3007	262	0.2232	4959	X-RAY DIFFRACTION	99.94
3.06-3.22	0.2325	264	0.2063	5003	X-RAY DIFFRACTION	99.98
3.22-3.43	0.2347	264	0.202	5007	X-RAY DIFFRACTION	99.98
3.43-3.69	0.2245	262	0.1836	5005	X-RAY DIFFRACTION	99.98
3.69-4.06	0.2186	266	0.1645	5040	X-RAY DIFFRACTION	100
4.06-4.65	0.1873	263	0.1487	5028	X-RAY DIFFRACTION	99.98
4.65-5.85	0.181	266	0.1596	5037	X-RAY DIFFRACTION	99.94
5.85-44.96	0.1857	262	0.1651	4996	X-RAY DIFFRACTION	99.81

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	8.15400272991	-6.07916322095	-0.384546111375	2.04425251173	-0.878475856806	0.696976321075	0.224769472605	0.308568660298	0.88491604743	0.00769742453586	-0.237951339559	-1.20974731554	-0.227157586014	0.813092645323	0.0520683268499	0.510354571475	-0.0528766397391	-0.0762318601632	0.664848260401	0.0705889112714	0.721768527224	56.3313078391	17.9700538077	9.68827725565
2	1.77114553085	0.0965707976132	0.326897594763	2.9840376038	-0.28641744702	2.72026438188	0.0293263885979	0.618752902674	-0.00160828602308	-0.55303334569	-0.11051203061	-0.0792385905892	-0.040841520179	0.13096940153	0.0892979070852	0.294570385744	0.0809512248952	-0.0286060704973	0.440382502021	0.000833758731996	0.241805274555	31.74049686	23.2671902319	-7.16419666802
3	3.78589673973	0.342838133977	-1.13552723904	7.30863860235	-2.89129754767	7.00761245561	-0.151255055579	1.02115773914	0.119859666071	-0.890685736467	-0.18070723153	0.529772328142	-0.00931596380549	-0.513534781714	0.323520663938	0.276666770955	0.0976512962817	-0.0639197921071	0.501388124145	0.011394259723	0.331184123846	20.9861391524	26.0873542248	-3.93711332469
4	5.80248780035	-1.18448875775	-1.70436049609	4.41522446484	1.71997141048	2.97819964732	-0.216263388155	-0.416534274554	0.415800966462	0.627293305531	0.168116503352	-0.150546696551	-1.1365328616	0.264593133226	0.0412672557669	0.738462206181	0.029800861647	-0.212131055832	0.42429571851	-0.092207642559	0.368797757974	37.94190805	32.033977838	34.2884594664
5	2.17138238967	-3.22448908638	5.00735387991	4.80207343516	-7.36831110072	2.00426048002	-0.132426078005	-0.0046407599777	0.153696901721	0.209352334921	-0.33941254641	-0.643747919907	0.243364748309	0.891608939111	0.447019234869	0.458879760914	0.0214962232594	-0.146828724473	0.416526463366	0.0269930561942	0.375597090903	48.7792641346	19.118562567	24.9082306441
6	4.75671967211	2.46422345003	0.131426858917	8.23381757961	-1.34135302099	3.18713078425	0.0673251991694	-0.0135764619817	-0.838985458018	-0.0347840747635	-0.0622316268055	0.399153267006	0.616742607943	-0.0123627996507	-0.0028309250316	0.26834384267	0.061244009644	0.0424656290799	0.274412141732	-0.0976210842854	0.38118015656	33.6531179311	-4.32712487863	11.9625321687
7	4.71026285269	2.61653322313	0.0474096933549	6.54826872907	-0.796456948394	2.53018265461	-0.131651593868	-0.432469787241	-1.29740723222	0.182385806099	-0.278924501401	-0.550272169345	0.796082700021	0.474951821651	0.418058343807	0.404993647723	0.155208512289	-0.00125893813306	0.373341539849	-0.0126471347084	0.601729427028	41.4173831837	-8.39720337222	14.8942483437
8	5.22860227759	0.155759730411	-2.27223257507	3.79669942589	-2.17197915596	7.20356496829	-0.0984896738182	0.0501002149504	-0.126902128609	0.308559140078	-0.183724377586	-0.445171716649	-0.0646202595583	0.767036540959	0.285838028024	0.238999853558	0.0320443334944	-0.0861723619548	0.325477871759	0.00769103616925	0.394670685423	51.6759044609	5.07790504244	14.5880806232
9	2.27067474861	-1.39880123028	0.174727195748	7.41024100867	4.81543825246	8.76282300141	-0.0981926759422	-0.328776675416	-0.697195751879	0.737623836464	-0.00126579145304	0.387414180996	0.965254752302	0.0804312745066	0.0790538156206	0.504535739471	0.0779623319409	0.0158434887278	0.371363886914	0.156857801032	0.678015989799	44.2321569372	-7.41322596143	25.8168297786
10	3.00077851298	0.0377012717371	-0.0493420935117	2.95858596267	-0.265397341426	2.40737549181	-0.0254667782385	0.0901043863934	-0.289317196465	0.0686090876591	-0.031962512184	-0.0249806898104	0.313184637158	0.150024818827	0.0510669678858	0.218199342071	0.0475898226651	0.00206892491531	0.202280321807	-0.0410463094043	0.237477154886	37.487067242	4.27611467738	10.4612682036
11	4.22022754828	-1.20007533066	-1.32988394052	6.00240615641	1.4678660019	4.1707758414	-0.357512106322	-0.41684602469	0.169188537804	0.723643933275	-0.0221758265135	-1.39564586678	-0.173262284826	1.124594776	0.382663746895	0.55493816668	-0.0531575910422	-0.137719971783	0.58488058554	0.215210699693	0.664936475279	43.5004040863	40.8499785335	-0.439503040016
12	1.1106329568	0.249811899351	0.559357404239	2.92315534859	-0.314834380974	2.26087025205	-0.123021020445	-0.208864155759	0.295107912673	0.569167496103	0.128336468581	0.676212785356	-0.421811296395	-0.513510332046	-0.0127739547852	0.489039469977	0.163559502626	0.0512138007031	0.354867573392	-0.0135808945453	0.379042833921	18.8438995376	25.0377775657	21.9235911006
13	1.96231339486	-0.638260405884	0.301093229887	2.90931278136	0.546590980945	2.40917948992	-0.216905390386	-0.2440150146	0.172316341612	0.46258963279	0.0235408496961	0.239402108382	-0.391742930653	-0.383096159944	0.187346137664	0.382864646079	0.0928768393745	0.020272473705	0.281139083899	-0.00329548315386	0.251498550302	23.4847496064	25.4364081184	23.3567069785
14	6.5773192072	1.80608068199	2.04409082514	7.61060729003	1.45614669228	7.88570213551	-0.30801327178	-0.920154259974	-0.137533566038	0.864107382832	0.238893202639	1.29746145554	-0.11965645883	-1.11635533583	0.0456022639975	0.496553843669	0.0604857283892	0.1450972337	0.368256860417	0.0915915965537	0.40865704385	20.0449931623	13.1494894813	26.7431749306
15	0.540224241679	0.287972638895	1.29834721618	0.986527781979	0.0202234141834	3.66571847274	-0.435931011076	1.02598225674	0.580078148674	-0.427516764144	0.0614310525581	-0.691454426793	-0.0923465824475	0.776377388539	0.332212456973	0.807204680035	-0.160202645456	0.274389016079	1.02208664907	-0.0271872687398	1.83580886475	95.2814434912	44.5450765913	-39.7847473173
16	2.76791727924	-2.56795089305	-1.02920145523	4.21157869808	2.52419694217	4.01950237056	-0.122713485677	0.325277470108	0.477852536851	-0.254337690808	0.323130153538	-0.916474903195	0.985542278786	0.00577532431238	-0.201209671715	0.824015106897	-0.088782711065	0.162890776284	0.679364754865	-0.028362002089	1.04967030567	80.7667989692	31.5530841386	-37.6161200248
17	2.6929368663	-0.121970017132	1.13669991907	3.65501518133	-2.93222114989	6.02305489138	0.388083747692	-0.539388298451	-0.641721063981	0.13754951894	-0.0273320239849	0.834959262146	0.663032725644	-0.165595088805	-0.353025786984	0.535046517352	-0.0734550114748	0.144573407423	0.561708593203	0.0141763402807	1.24622416756	72.6944219678	21.2094830757	-10.6413563008
18	3.17147524167	-1.72381254256	-0.0808006567826	5.64370754141	0.534473291039	4.75541753661	-0.0413370700023	0.599706299841	-0.898192444002	-1.2328379087	-0.0540363922097	0.812208901977	0.394159249734	-0.716850294011	0.103117037732	0.829081187706	-0.161750558777	-0.116201796893	0.814406651283	-0.213985448788	1.27489748184	60.8855013735	25.5511535578	-33.6928979952
19	0.319150955466	-1.39877953359	0.0923127371843	6.23199101319	-0.110354670512	2.18331683743	-0.156131368946	0.27225952458	-0.832428700969	-0.421618472856	0.00179753752564	-0.901177389633	0.606229989101	0.337475153631	0.15673465604	0.693566888503	0.00993912312206	0.111818228957	0.522699153387	-0.0810202887381	1.72113604973	77.4661859742	20.5067513579	-23.4994212415
20	1.38121863807	0.617812969925	-0.00453630159294	2.94061689756	-0.0799382059969	5.29299126659	-0.0330561059145	-0.168184966585	-0.403574472694	0.182896558777	0.0791551037774	0.399970611462	-0.10115784414	-0.488373977371	-0.0248173664397	0.422456322826	0.0286454289952	0.0211990745732	0.536531823512	0.0364702644306	0.922479004356	69.1723716085	35.5924752758	-9.70439553885
21	1.38459189969	1.10057418564	0.284903561515	2.9494262006	-0.412858451848	5.68956802079	-0.124950204645	-0.439257307597	-0.526519281651	-0.0848421589978	0.130289775499	0.85031400611	0.870624393669	-1.04623879051	-0.0121814286621	0.638755162112	-0.101415192937	0.0359596870463	0.715907612082	-0.0817889434227	1.26238053024	63.0170224186	27.084195919	-12.6695568567

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 383 through 421 )	A	A	383 - 421	1 - 39
2	2	chain 'A' and (resid 422 through 606 )	A	A	422 - 606	40 - 224
3	3	chain 'A' and (resid 607 through 627 )	A	A	607 - 627	225 - 245
4	4	chain 'B' and (resid 383 through 405 )	B	B	383 - 405	1 - 23
5	5	chain 'B' and (resid 406 through 421 )	B	B	406 - 421	24 - 39
6	6	chain 'B' and (resid 422 through 449 )	B	B	422 - 449	40 - 67
7	7	chain 'B' and (resid 450 through 472 )	B	B	450 - 472	68 - 90
8	8	chain 'B' and (resid 473 through 517 )	B	B	473 - 517	91 - 135
9	9	chain 'B' and (resid 518 through 534 )	B	B	518 - 534	136 - 152
10	10	chain 'B' and (resid 535 through 627 )	B	B	535 - 627	153 - 245
11	11	chain 'C' and (resid 383 through 405 )	C	C	383 - 405	1 - 23
12	12	chain 'C' and (resid 406 through 472 )	C	C	406 - 472	24 - 90
13	13	chain 'C' and (resid 473 through 606 )	C	C	473 - 606	91 - 224
14	14	chain 'C' and (resid 607 through 627 )	C	C	607 - 627	225 - 245
15	15	chain 'D' and (resid 383 through 405 )	D	D	383 - 405	1 - 23
16	16	chain 'D' and (resid 406 through 421 )	D	D	406 - 421	24 - 39
17	17	chain 'D' and (resid 422 through 472 )	D	D	422 - 472	40 - 90
18	18	chain 'D' and (resid 473 through 493 )	D	D	473 - 493	91 - 111
19	19	chain 'D' and (resid 494 through 574 )	D	D	494 - 574	112 - 192
20	20	chain 'D' and (resid 575 through 606 )	D	D	575 - 606	193 - 224
21	21	chain 'D' and (resid 607 through 627 )	D	D	607 - 627	225 - 245

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