PDB-7ptj: C54S mutant of choline-sulfatase from E. meliloti CECT4857 bound ...

ID or keywords:

Entry

Database: PDB / ID: 7ptj

Title

C54S mutant of choline-sulfatase from E. meliloti CECT4857 bound to HEPES

Components

Choline sulfatase

Keywords

HYDROLASE / choline / sulfatase / sulfate

Function / homology

Function and homology information

choline-sulfatase / choline-sulfatase activity / metal ion binding / cytoplasm
Similarity search - Function

Biological species

Rhizobium meliloti (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.1 Å

Authors

Gavira, J.A. / Martinez-Rodriguez, S.

Funding support

Spain, 1items

Citation

Journal: Acta Crystallogr D Struct Biol / Year: 2022
Title: Structural insights into choline-O-sulfatase reveal the molecular determinants for ligand binding.
Authors: Gavira, J.A. / Camara-Artigas, A. / Neira, J.L. / Torres de Pinedo, J.M. / Sanchez, P. / Ortega, E. / Martinez-Rodriguez, S.

History

Deposition	Sep 27, 2021	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Aug 3, 2022	Provider: repository / Type: Initial release
Revision 1.1	Jan 31, 2024	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7ptj.cif.gz	907.3 KB	Display	PDBx/mmCIF format
PDB format	pdb7ptj.ent.gz	718.7 KB	Display	PDB format
PDBx/mmJSON format	7ptj.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/pt/7ptj ftp://data.pdbj.org/pub/pdb/validation_reports/pt/7ptj	HTTPS FTP

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Related structure data

Related structure data	6g5zC 6g60SC 7pthC S: Starting model for refinement 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	#50 - Feb 2004 Glycolytic Enzymes similarity (1)

Deposited unit

A: Choline sulfatase

B: Choline sulfatase

C: Choline sulfatase

D: Choline sulfatase

hetero molecules

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

1

Idetical with deposited unit
defined by author
Evidence: gel filtration, also confirmed by DLS

Unit cell

Length a, b, c (Å)	128.521, 207.007, 116.833
Angle α, β, γ (deg.)	90.000, 110.290, 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	C-1000- HOH

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Protein , 1 types, 4 molecules ABCD

#1: Protein	Choline sulfatase Mass: 59495.551 Da / Num. of mol.: 4 / Mutation: C54S Source method: isolated from a genetically manipulated source Details: C54S mutant / Source: (gene. exp.) Rhizobium meliloti (bacteria) / Plasmid: pET22b+ / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A410NSD4, choline-sulfatase

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Non-polymers , 5 types, 1866 molecules

#2: Chemical	ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES Mass: 238.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₈H₁₈N₂O₄S / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: SO₄
#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C₃H₈O₃
#5: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1827 / Source method: isolated from a natural source / Formula: H₂O

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Details

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: 3.15 Å³/Da / Density % sol: 61 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1M hepes pH7.5, 1.5M LiSO4

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

ESRF

/ Beamline: ID30B / Wavelength: 0.9762 Å

Detector

Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 15, 2018

Radiation

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

Radiation wavelength

Wavelength: 0.9762 Å / Relative weight: 1

Reflection

Resolution: 2.1→109.58 Å / Num. obs: 157660 / % possible obs: 95 % / Redundancy: 1.9 % / CC_1/2: 0.994 / R_merge(I) obs: 0.068 / R_pim(I) all: 0.062 / R_rim(I) all: 0.092 / Net I/σ(I): 5.5 / Num. measured all: 306519 / Scaling rejects: 6

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. measured all	Num. unique obs	CC_1/2	R_pim(I) all	R_rim(I) all	Net I/σ(I) obs	% possible all
1.8-1.83	1.9	1.606	23433	12276	0.124	1.485	2.193	0.5	94.9
9.86-109.58	1.8	0.043	2775	1528	0.991	0.039	0.059	18.4	92.8

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Processing

Software

Name	Version	Classification
XDS		data reduction
Aimless	0.7.7	data scaling
PHENIX	1.19-4092	refinement
REFMAC	5	refinement
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 6G60

6g60

Resolution: 2.1→75.25 Å / SU ML: 0.2634 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 20.8288
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.1998	7963	5.05 %
R_work	0.162	149667	-
obs	0.1639	157630	94.9 %

Solvent computation

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

Displacement parameters

B_iso mean: 34.14 Å²

Refinement step

Cycle: LAST / Resolution: 2.1→75.25 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	16446	0	246	1833	18525

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0076	17422
X-RAY DIFFRACTION	f_angle_d	0.8892	23735
X-RAY DIFFRACTION	f_chiral_restr	0.0505	2452
X-RAY DIFFRACTION	f_plane_restr	0.0084	3125
X-RAY DIFFRACTION	f_dihedral_angle_d	15.5957	6515

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 (%)
2.1-2.12	0.3704	260	0.3286	4866	X-RAY DIFFRACTION	92.93
2.12-2.15	0.3221	250	0.3091	4879	X-RAY DIFFRACTION	93.1
2.15-2.18	0.3137	253	0.2964	4894	X-RAY DIFFRACTION	92.92
2.18-2.2	0.3546	256	0.2678	4864	X-RAY DIFFRACTION	92.82
2.2-2.23	0.276	273	0.2483	4722	X-RAY DIFFRACTION	90.64
2.23-2.26	0.294	249	0.2204	4682	X-RAY DIFFRACTION	88.85
2.26-2.29	0.252	285	0.21	4950	X-RAY DIFFRACTION	94.29
2.29-2.33	0.2548	274	0.2058	4912	X-RAY DIFFRACTION	94.62
2.33-2.37	0.2247	251	0.2045	4919	X-RAY DIFFRACTION	94.22
2.37-2.4	0.2554	232	0.1994	5053	X-RAY DIFFRACTION	95.07
2.4-2.45	0.2593	280	0.206	5017	X-RAY DIFFRACTION	96.01
2.45-2.49	0.2459	260	0.2024	5058	X-RAY DIFFRACTION	95.89
2.49-2.54	0.2345	262	0.1838	5033	X-RAY DIFFRACTION	95.66
2.54-2.59	0.2299	256	0.1835	5061	X-RAY DIFFRACTION	95.77
2.59-2.65	0.2342	296	0.1817	5032	X-RAY DIFFRACTION	96.59
2.65-2.71	0.2166	254	0.1815	5073	X-RAY DIFFRACTION	96.26
2.71-2.78	0.2241	243	0.1775	5111	X-RAY DIFFRACTION	96.61
2.78-2.85	0.2288	265	0.1711	5013	X-RAY DIFFRACTION	96.03
2.85-2.93	0.2304	278	0.1713	4989	X-RAY DIFFRACTION	95.18
2.93-3.03	0.1979	252	0.1642	5064	X-RAY DIFFRACTION	96.39
3.03-3.14	0.2082	242	0.1671	5059	X-RAY DIFFRACTION	95.44
3.14-3.26	0.1851	285	0.1653	5069	X-RAY DIFFRACTION	96.54
3.26-3.41	0.1922	250	0.151	5085	X-RAY DIFFRACTION	96.56
3.41-3.59	0.1716	249	0.1444	5128	X-RAY DIFFRACTION	96.74
3.59-3.82	0.1587	297	0.137	5066	X-RAY DIFFRACTION	96.74
3.82-4.11	0.1631	299	0.124	4995	X-RAY DIFFRACTION	95.46
4.11-4.52	0.1463	277	0.1276	5009	X-RAY DIFFRACTION	95.33
4.52-5.18	0.1629	288	0.1311	5029	X-RAY DIFFRACTION	95.91
5.18-6.52	0.1945	284	0.1604	5070	X-RAY DIFFRACTION	95.86
6.52-75.25	0.1676	263	0.1648	4965	X-RAY DIFFRACTION	92.76

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	1.99867611661	0.374468025779	0.755337767508	1.53992639283	-0.0930019828534	1.27235614706	-0.00954328704756	-0.213293190424	-0.0092971167368	0.0639280746424	-0.0189645901059	0.114561230997	0.219945585374	-0.238460462256	0.0455789263253	0.268588474205	-0.000540223054514	0.00632641293446	0.201074152498	0.0106517929272	0.140072512428	24.1335496207	-8.32522594872	60.3333846573
2	0.78264868638	-0.131640185831	-0.162855427261	0.926089889631	0.219254533519	0.312061966734	-0.0815643891865	0.00102383124391	0.0430058620209	-0.00106892732021	0.0656277479044	0.0431491196676	0.0657682705115	-0.0297287777381	0.0143479106634	0.227247618621	-0.00497946548679	-0.0196055496333	0.201822615175	0.0117215121714	0.145301706505	26.0919371499	3.82972328602	55.6686429263
3	1.02747177215	-0.632985058259	-0.312393878928	1.24867832106	0.29337849829	0.424298910878	0.0416039611507	0.315605795573	-0.114290305023	-0.393391574245	-0.122600786476	0.24305701279	0.0534546104242	-0.124085310476	0.0899362518531	0.409677512313	-0.0710467097789	-0.0740685319	0.42242880805	-0.0500710182412	0.287481177614	11.7277572771	-7.06250882142	36.5890473613
4	0.884000089582	-0.30762649602	-0.0631692652189	0.691185419542	-0.0466478838476	0.604611870103	-0.0906457089224	-0.0549311105109	-0.086152056943	0.062214360773	0.0593557900501	0.161048367811	0.132050499163	-0.107317407733	0.0296411534264	0.256096749968	-0.0394179868954	0.0151702357545	0.220760273059	0.0111824694779	0.194698368447	14.4223723494	-4.6762539264	57.6269017569
5	1.39971377237	0.713378542212	0.0626206154108	1.71207576342	0.0253955402411	0.736817421404	-0.0911398503326	0.121082044427	0.105479788054	0.116751845053	0.00101515172191	0.298067777148	-0.0171981790366	-0.320534712998	0.1169499197	0.205537374736	0.00943942811664	-0.0167058224409	0.296754152801	-0.041382097426	0.248858813546	3.00882303204	11.9423586089	52.1998493695
6	0.240343987904	-0.0248664890903	-0.209223418716	0.29370592874	0.116918803604	0.185740777062	-0.0536130062393	-0.208297872625	-0.00189053335723	0.164228453713	0.043376288288	-0.051856791172	0.0581142346004	0.00353996496023	0.00496396167357	0.312466889378	0.00132236746255	-0.0319319092992	0.282723732433	-0.0132699182703	0.201550731934	46.941029089	10.7722261694	63.7846792575
7	0.825702413362	-0.130066304685	-0.189457064767	0.990499430374	0.249026705291	0.443939317686	-0.0167421599195	-0.0513666858187	0.18885609436	0.0827969616168	0.0754868209967	0.0712164441721	-0.0194394367348	-0.00130449777765	-0.0529306238116	0.185735974693	0.0286385874544	-0.0160279187225	0.212775792649	-7.35029100552E-5	0.276029913349	22.7935015392	41.1922658597	60.9924700018
8	1.1955180795	0.0794169321627	-0.233750169254	1.04303336931	0.433672515896	0.483188951152	-0.0323958889925	0.0789925679485	0.254754136245	-0.0369107780064	0.104347639292	-0.0426861173316	-0.103932480314	0.0574246410214	-0.0545249498287	0.137695913343	0.00427469420646	-0.0156749846604	0.163478118669	0.0217490443385	0.277070119162	35.2926273761	47.4292537262	54.9765520766
9	1.09981436459	0.187614528647	-0.511906473668	0.852944155497	0.0520468620093	0.608122614052	0.080827858396	-0.170442125546	0.347833458213	0.215500249351	0.00228173618065	0.0350791569216	-0.152274232903	0.0120937994911	-0.0924955400335	0.245201400145	0.0337837741279	-0.0134701575818	0.24016394413	-0.0574907909423	0.380276972194	24.073122206	52.9682119655	69.2316970585
10	0.254943378954	-0.119932729979	-0.0170617914787	0.542028942211	-0.245536987049	0.559407318342	0.00692723935017	0.0949790582154	0.10367751076	-0.0350014667137	0.00214278193271	0.117796956171	-0.0129851356278	-0.0743679601751	-0.025341612217	0.221939855026	0.0379232745202	-0.0220595713045	0.249688269749	0.0317939087775	0.375115479236	11.2516740034	45.7523386966	53.2600670191
11	0.688754200696	-0.301277657493	-0.391892044902	0.730713868098	0.404302541714	0.550389199644	-0.0757616441023	-0.0500130784183	0.147972750802	0.142537118616	0.0880415583054	0.151551633064	-0.0180190765019	-0.0604193460905	-0.0115188043181	0.247828400256	0.0312117960061	0.0236583007538	0.252401188479	-0.00357652945243	0.357161511447	3.23350399548	41.954437255	70.5215423544
12	0.612454246937	-0.0713728982731	0.0580491342712	0.705901129456	0.269488938207	0.141074989262	-0.106711936135	0.179863222796	0.295811428834	-0.198763126795	0.171012450062	-0.148959441082	0.0467215286876	-0.0849620637709	-0.0689845092764	0.241163439791	-0.0251074015376	-0.0471161996678	0.289226690728	0.0280444056223	0.328024925011	44.3781569098	34.4032357094	44.6679173256
13	0.373795349736	-0.135825602622	-0.26500177542	0.693012745922	-0.0748904506258	1.10582371833	-0.00836498218509	-0.0707882223662	0.00837398462396	0.0339608939923	0.0390516878854	-0.04384413999	0.00290867217092	0.049169567901	-0.0284278534624	0.135109556898	0.015008579936	-0.0147102859597	0.1982814333	-0.0274164536239	0.142721066506	37.7874952293	-36.6074046693	92.4296715028
14	0.0117981369467	-0.0802589589116	0.0267557451136	-0.0227620702377	-0.0740432022277	0.188713614073	0.0188755848737	-0.079080802021	-0.242372724067	0.0724581612356	0.0621079246439	0.261713329965	0.307499795459	-0.274252664698	-0.0976730178511	0.306566711745	-0.0385003756062	-0.0143627559273	0.318327891694	0.0239986578879	0.352978689964	19.9952696856	-42.1386467989	81.7528799706
15	0.824803029386	-0.390354268993	-0.000984813281632	1.25894002693	-0.0597912020209	1.14201607139	-0.0188836028838	-0.197978086975	0.0541333553692	0.131090763573	-0.000785050106236	-0.0347735496392	0.0307718397198	-0.0340857192764	0.030542751099	0.191650779172	-0.00519207139858	0.0232835529761	0.289734438145	-0.0256449688795	0.163927316135	29.7178332793	-31.9925695168	103.028962177
16	0.629359162325	-0.0391595845037	-0.230563983065	0.425538554929	0.0432724189641	1.64644257602	0.0696935155371	0.0199842132906	0.0903626551742	-0.0191314261867	-0.00524119135637	0.0819898631044	-0.119579856632	-0.238868636	-0.082189435469	0.169012147311	0.0123378906624	0.0223688803252	0.235745544614	0.0101972915197	0.194570973021	25.5483398315	-27.1739435678	83.7831653783
17	0.6654436059	-0.140153497588	0.13682301404	0.458644905438	-0.431388820606	1.76193173114	0.0628787043263	-0.022490825865	-0.0297290067202	-0.0296646142729	0.0264806647518	-0.0882478417506	0.108225088387	0.221400994845	-0.0813389820948	0.161738178243	0.0122301591663	0.00846556846597	0.216291853438	-0.0337347864414	0.220421888651	42.8168381109	-35.3495462029	76.752304333
18	0.328891115683	-0.16062665325	-0.319612108272	0.959728014505	-0.0370593537264	0.233565376452	-0.0757323503052	-0.139430883509	-0.00491215786228	0.287730524146	0.307420824839	-0.0481840413221	-0.0328497416932	0.44922792141	-0.236719468812	0.368998873326	0.026175596388	0.0285320812757	0.4861113324	-0.0744905683972	0.505102503403	30.6174811051	-44.863478345	115.886976171
19	0.864779506849	-0.243109426165	-0.124267667781	1.2669624401	-0.22435123322	0.679679842714	-0.0462980854056	-0.0906836464727	-0.103250288203	-0.193770410711	0.0589593617125	-0.0349374386848	0.151472131906	-0.00518061453255	-0.0229320814596	0.255012480756	0.0104972434216	0.0464284522728	0.189503899072	0.0190310773897	0.229708873186	35.6243408243	-75.0033790555	90.5034674905
20	1.37540683167	0.152881344929	-0.432216778186	1.57586661672	-0.407469328398	1.28469404512	-0.0353557578183	-0.220805146779	-0.180379768596	0.049128468541	-0.0821708499889	-0.122867538463	0.246706929732	0.209223070819	0.113091174809	0.336749406312	0.0370153033226	0.0447243028486	0.26430743267	0.024147190383	0.306167220062	41.9184725957	-81.7371971445	100.834485436
21	0.905450984825	0.601824887521	-0.339845756235	0.958123393944	-0.0560412415898	0.671097131309	-0.194749502563	0.0402712538141	-0.2698696142	-0.299169508322	0.0785002289081	-0.151181281326	0.265885940883	0.0714382743919	0.114673977055	0.375677811861	0.0309919560278	0.0899489143933	0.191029857682	0.00572288455961	0.308225060975	42.8199081459	-83.1719888643	83.6856366923
22	-0.0395712878777	0.00223617499588	-0.156573867424	0.620129931495	0.0399044188993	0.528353033397	0.0170045985358	-0.0503746891143	0.0330552386483	0.129144411858	0.0135873788616	0.151223305709	0.0831000184833	-0.177524309251	-0.026643858813	0.305228527089	0.0261513722747	-0.00941503594161	0.346688547744	0.0244300656599	0.286602160711	26.9057159042	-64.684516983	100.495340834

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 31 )	A	A	2 - 31	1 - 30
2	2	chain 'A' and (resid 32 through 214 )	A	A	32 - 214	31 - 213
3	3	chain 'A' and (resid 215 through 251 )	A	A	215 - 251	214 - 250
4	4	chain 'A' and (resid 252 through 431 )	A	A	252 - 431	251 - 430
5	5	chain 'A' and (resid 432 through 472 )	A	A	432 - 472	431 - 471
6	6	chain 'A' and (resid 473 through 514 )	A	A	473 - 514	472 - 513
7	7	chain 'B' and (resid 4 through 159 )	B	E	4 - 159	1 - 156
8	8	chain 'B' and (resid 160 through 214 )	B	E	160 - 214	157 - 211
9	9	chain 'B' and (resid 215 through 313 )	B	E	215 - 313	212 - 310
10	10	chain 'B' and (resid 314 through 391 )	B	E	314 - 391	311 - 388
11	11	chain 'B' and (resid 392 through 472 )	B	E	392 - 472	389 - 469
12	12	chain 'B' and (resid 473 through 515 )	B	E	473 - 515	470 - 512
13	13	chain 'C' and (resid 4 through 121 )	C	G	4 - 121	1 - 118
14	14	chain 'C' and (resid 122 through 159 )	C	G	122 - 159	119 - 156
15	15	chain 'C' and (resid 160 through 214 )	C	G	160 - 214	157 - 211
16	16	chain 'C' and (resid 215 through 313 )	C	G	215 - 313	212 - 310
17	17	chain 'C' and (resid 314 through 472 )	C	G	314 - 472	311 - 469
18	18	chain 'C' and (resid 473 through 514 )	C	G	473 - 514	470 - 511
19	19	chain 'D' and (resid 4 through 135 )	D	I	4 - 135	1 - 132
20	20	chain 'D' and (resid 136 through 251 )	D	I	136 - 251	133 - 248
21	21	chain 'D' and (resid 252 through 450 )	D	I	252 - 450	249 - 447
22	22	chain 'D' and (resid 451 through 512 )	D	I	451 - 512	448 - 509

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