PDB-6w4u: Crystal structure of Triosephosphate isomerase from Stenotrophomo...

ID or keywords:

Entry

Database: PDB / ID: 6w4u

Title

Crystal structure of Triosephosphate isomerase from Stenotrophomonas maltophilia K279a

Components

Triosephosphate isomerase

Keywords

ISOMERASE / SSGCID / Stenotrophomonas maltophilia / Triosephosphate isomerase / tpiA / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease

Function / homology

Function and homology information

triose-phosphate isomerase / triose-phosphate isomerase activity / gluconeogenesis / glycolytic process / cytoplasm
Similarity search - Function

Biological species

Stenotrophomonas maltophilia (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.7 Å

Authors

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Citation

Journal: to be published
Title: Crystal structure of Triosephosphate isomerase from Stenotrophomonas maltophilia K279a
Authors: Abendroth, J. / Horanyi, P.S. / Lorimer, D.D. / Edwards, T.E.

History

Deposition	Mar 11, 2020	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 8, 2020	Provider: repository / Type: Initial release
Revision 1.1	Oct 18, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6w4u.cif.gz	253.4 KB	Display	PDBx/mmCIF format
PDB format	pdb6w4u.ent.gz	167.9 KB	Display	PDB format
PDBx/mmJSON format	6w4u.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	6w4u_validation.pdf.gz	429.6 KB	Display	wwPDB validaton report
Full document	6w4u_full_validation.pdf.gz	430.7 KB	Display
Data in XML	6w4u_validation.xml.gz	22.6 KB	Display
Data in CIF	6w4u_validation.cif.gz	33.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/w4/6w4u ftp://data.pdbj.org/pub/pdb/validation_reports/w4/6w4u	HTTPS FTP

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Related structure data

Related structure data	4iotS S: Starting model for refinement
Similar structure data	4unk-d 2bne-d 5v76-d 3mmg-d 5dxd-d 3vt0-3 3bjr-1 3mux-d 4a7x-2 6xhs-3 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search
Other databases	TargetTrack: StmaA.00317.a

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#50 - Feb 2004 Glycolytic Enzymes similarity (8)

Deposited unit

A: Triosephosphate isomerase

B: Triosephosphate isomerase

hetero molecules

54.6 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	43.500, 46.660, 66.830
Angle α, β, γ (deg.)	71.900, 71.086, 68.356
Int Tables number	1
Space group name H-M	P1
Space group name Hall	P1
Symmetry operation	#1: x,y,z

#1: Protein	Triosephosphate isomerase / TPI / Triose-phosphate isomerase Mass: 27247.775 Da / Num. of mol.: 2 / Fragment: StmaA.00317.a.B1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Stenotrophomonas maltophilia (strain K279a) (bacteria) Strain: K279a / Gene: tpiA, Smlt3407 / Plasmid: StmaA.00317.a.B1 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) Strain (production host): BL21(DE3) / References: UniProt: B2FNY1, triose-phosphate isomerase
#2: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 348 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N

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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: 42.5 %
Crystal grow	Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 8 Details: RigakuReagents JCSG+ screen, condition A9: 200mM Ammonium chloride, 20% (w/V) PEG 3350: StmaA.00317.a.B1.PW38736 at 25.5mg/ml + 5mM Glucose-3-phosphate : cryo: 20% EG + 5mM glucose-3- ...Details: RigakuReagents JCSG+ screen, condition A9: 200mM Ammonium chloride, 20% (w/V) PEG 3350: StmaA.00317.a.B1.PW38736 at 25.5mg/ml + 5mM Glucose-3-phosphate : cryo: 20% EG + 5mM glucose-3-phosphate, tray 313955a9: puck pzy9-10.

Crystal

Density Matthews: 2.14 Å³/Da / Density % sol: 42.5 %

Crystal grow

Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 8
Details: RigakuReagents JCSG+ screen, condition A9: 200mM Ammonium chloride, 20% (w/V) PEG 3350: StmaA.00317.a.B1.PW38736 at 25.5mg/ml + 5mM Glucose-3-phosphate : cryo: 20% EG + 5mM glucose-3- ...

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 21-ID-F / Wavelength: 0.97872 Å

Detector

Type: RAYONIX MX-300 / Detector: CCD / Date: Feb 13, 2020

Radiation

Monochromator: C111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.97872 Å / Relative weight: 1

Reflection

Resolution: 1.7→50 Å / Num. obs: 48225 / % possible obs: 97 % / Redundancy: 3.898 % / B_iso Wilson estimate: 34.952 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.037 / R_rim(I) all: 0.043 / Χ²: 1.048 / Net I/σ(I): 19.17

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. unique obs	CC_1/2	R_rim(I) all	% possible all
1.7-1.74	3.976	0.485	3.3	3573	0.876	0.561	95.6
1.74-1.79	3.982	0.397	4.16	3416	0.915	0.459	96.1
1.79-1.84	3.981	0.281	5.5	3293	0.958	0.325	95.8
1.84-1.9	3.977	0.219	7.04	3296	0.97	0.253	96.1
1.9-1.96	3.969	0.154	9.42	3179	0.986	0.179	96.6
1.96-2.03	3.96	0.111	12.57	3065	0.991	0.129	96.7
2.03-2.11	3.946	0.092	14.66	2954	0.993	0.106	96.7
2.11-2.19	3.92	0.072	18.04	2874	0.995	0.083	97
2.19-2.29	3.895	0.058	20.82	2737	0.996	0.067	97.2
2.29-2.4	3.885	0.049	23.84	2628	0.997	0.057	97.6
2.4-2.53	3.857	0.045	25.91	2518	0.997	0.052	97.9
2.53-2.69	3.837	0.04	28.44	2374	0.998	0.046	97.9
2.69-2.87	3.824	0.037	31.84	2233	0.998	0.042	98
2.87-3.1	3.808	0.034	34.06	2108	0.998	0.039	98.1
3.1-3.4	3.774	0.031	35.67	1902	0.998	0.036	98.5
3.4-3.8	3.776	0.029	37.34	1743	0.998	0.034	98.5
3.8-4.39	3.809	0.028	38.22	1549	0.999	0.032	98.5
4.39-5.38	3.83	0.024	38.75	1296	0.999	0.028	99.4
5.38-7.6	3.788	0.024	38.48	1019	0.999	0.028	98.8
7.6-50	3.274	0.024	35.54	468	0.998	0.028	84.5

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Processing

Software

Name	Version	Classification
XDS		data reduction
XSCALE		data scaling
PHENIX	1.18rc1	refinement
PDB_EXTRACT	3.25	data extraction
MoRDa		phasing
Coot		model building

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entry 4iot as per MORDA

4iot

Resolution: 1.7→39.28 Å / SU ML: 0.1921 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 23.6666

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2149	1964	4.07 %	0
R_work	0.1679	-	-	-
obs	0.1697	48219	97.13 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Displacement parameters

B_iso mean: 39.1 Å²

Refinement step

Cycle: LAST / Resolution: 1.7→39.28 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3684	0	4	348	4036

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0077	3800
X-RAY DIFFRACTION	f_angle_d	0.8788	5180
X-RAY DIFFRACTION	f_chiral_restr	0.0561	588
X-RAY DIFFRACTION	f_plane_restr	0.0057	696
X-RAY DIFFRACTION	f_dihedral_angle_d	19.2076	1340

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 (%)
1.7-1.74	0.2883	129	0.2475	3298	X-RAY DIFFRACTION	95.86
1.74-1.79	0.285	135	0.233	3267	X-RAY DIFFRACTION	95.97
1.79-1.84	0.2617	122	0.2229	3223	X-RAY DIFFRACTION	95.85
1.84-1.9	0.2642	143	0.2122	3310	X-RAY DIFFRACTION	96.4
1.9-1.97	0.2305	146	0.2107	3301	X-RAY DIFFRACTION	96.47
1.97-2.05	0.2396	159	0.1953	3248	X-RAY DIFFRACTION	96.93
2.05-2.14	0.2395	149	0.1903	3295	X-RAY DIFFRACTION	97.07
2.14-2.25	0.2351	137	0.1873	3305	X-RAY DIFFRACTION	97.26
2.25-2.4	0.2429	140	0.1847	3328	X-RAY DIFFRACTION	97.5
2.4-2.58	0.2471	161	0.1838	3319	X-RAY DIFFRACTION	98
2.58-2.84	0.2186	143	0.1803	3323	X-RAY DIFFRACTION	98.21
2.84-3.25	0.2081	161	0.1682	3324	X-RAY DIFFRACTION	98.45
3.25-4.1	0.1873	124	0.1485	3369	X-RAY DIFFRACTION	98.7
4.1-39.28	0.1745	115	0.1311	3345	X-RAY DIFFRACTION	97.14

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	4.76167110956	-1.17589898801	0.621252412726	6.11575596087	-2.78044610567	8.51031042828	0.383514706871	-0.680821447709	0.00973163483138	0.49804822696	-0.364744243347	-0.191255698152	0.272078725847	-0.00901568126421	0.04575785042	0.298332345881	-0.063422022466	-0.0863134721528	0.356277361274	-0.0122993510396	0.185076252344	-3.39513405006	23.2253955189	40.5751596274
2	6.33655509083	3.9441941825	-2.32761552666	4.49122086569	-4.2532289579	5.40776515399	0.18764214804	-0.340873155571	1.01157350585	0.0986437490349	0.0547039420115	-0.343814952612	-0.904162754535	-0.0947898216603	-0.154512874211	0.335456775885	0.039309233907	0.0246451047323	0.301929190912	-0.0643104617545	0.448716430703	2.13522744918	35.1192423694	37.1175393244
3	6.98020701374	0.0868223456567	0.463649721851	5.72653512495	0.552072546213	8.45831068022	-0.139728093962	-0.294727680167	0.686273662039	-0.40124139629	0.367786333708	-0.496991014717	-0.684274320671	0.816576603167	-0.169881410392	0.29474428986	-0.0141882740911	0.00534063590373	0.269692364725	-0.0953151930796	0.46309412612	7.90432542837	31.7901723997	27.7238108657
4	2.9477918248	-0.286430304005	0.762879898016	4.30760940178	0.0265007529282	4.81790840815	-0.136778868919	0.650731580957	-0.396383465083	0.0677660556915	0.269132157635	-0.821900700512	0.0568672206073	0.916446976786	-0.0508882521936	0.172259360113	-0.0139599244684	0.021731889747	0.37238763195	-0.0851841257051	0.367491632262	5.0859131469	-1.3821076702	2.52588806029
5	4.22251051333	0.259560515606	1.25220871284	2.11618952706	-0.410079416727	1.44076130353	-0.0446257301266	0.931602306213	-1.00892765263	0.426840555002	0.604534585413	-0.725674147526	0.236815583833	0.339886851002	-0.221633228989	0.306604838498	0.273970528822	-0.434944911638	0.626195040119	-0.339067896502	1.12950258247	15.2999641173	-1.47574018195	12.9702374492
6	5.32137147837	-4.85897981998	-1.68154902534	6.24285840521	3.15886508536	2.87934953797	0.0279245661365	1.47011976193	-0.0916151093469	-0.489496335773	0.712765953765	-1.33408126266	-0.0238876624081	0.708564955727	-0.621662520505	0.26573359215	-0.162127855999	0.157885274244	0.718976541188	-0.292167105289	0.594032468587	11.1949379	-0.333422951659	-0.213758291397
7	1.52847805896	-0.331706894957	0.33195635985	2.9356907904	1.79161614227	3.81350684571	-0.0248492383755	0.0564081357614	0.129128410615	-0.178208619008	0.277717252839	-0.572245186064	-0.381173186747	0.385044639629	-0.201529680563	0.219711644805	-0.0484981267132	0.0499651828435	0.191736084492	0.00170559989639	0.260903050347	3.23896246949	11.7484440238	7.57523434514
8	3.55710260327	0.773362847478	0.729407544847	4.65610143241	2.24712899415	4.20508014717	-0.0270943171156	-0.00893836432345	-0.0703139281923	0.00977296696964	-0.195230645969	0.370497415575	-0.0371297237432	-0.598787549274	0.161795717974	0.168709524077	0.00743496525029	0.0211554304383	0.225699537886	-0.00878036676894	0.152914712531	-11.6622492635	2.96398856977	2.16807119157
9	7.56104025225	6.68697427472	-0.0040088454792	9.14453319057	0.527794255713	4.48962713089	-0.445861186325	0.177595953683	0.0186974985742	-0.910093969062	0.198341647359	0.0483369235807	-0.659410216406	-0.735043812403	0.20972121224	0.297786131149	0.0785241437553	-0.0271836178313	0.327437296003	-0.0218436058743	0.155057196586	-15.161211378	3.79768530625	-6.70659425545
10	2.86296202335	-0.300249627457	0.638634487078	5.15965802682	-0.477529927047	5.76094443985	0.0647417849249	0.195214457827	-0.424898847242	0.000572503482588	0.0381797820817	0.0101408113922	0.224265994851	-0.268239359439	-0.104834041181	0.152605645865	-0.0479519165623	0.0563869375486	0.236002077393	-0.0418777325813	0.217489872552	-8.00216939579	-6.09343657795	-5.60847647384
11	4.27044403949	-0.290076076503	1.36768165631	7.7132841911	-4.20677421611	3.08078358693	0.108040380118	0.4847810361	-0.230468282975	-0.660186220584	0.0309142608644	-0.309153517872	0.264936582698	0.280941858826	-0.0878347001599	0.320273247861	-0.0139393829819	0.115128704245	0.29364745888	-0.0688341813272	0.242081557107	-2.26152852172	-2.51278908919	-9.52992064878
12	3.05472082274	0.300508569528	1.26289560376	4.90263345253	2.95737502275	7.74852673789	0.115667244263	0.375298839968	-0.547399554649	0.171237697222	0.231751323419	-0.639690782739	0.467412737023	0.363547619412	-0.370320319377	0.221105208528	-0.014268836354	0.0537872387308	0.255784500816	-0.0794919653223	0.422452311366	2.22937528005	-8.84120524538	-2.40822286665
13	4.35371519312	-1.96121861241	-3.01245733961	3.47760216383	2.01769227246	3.98581451387	-0.25317959977	0.56282529969	-0.409054313451	0.200863482887	0.45625136006	-0.812319023872	0.592319384034	0.544279659839	-0.10432031928	-0.58815988617	0.659141463305	0.496614581252	0.40635134561	-0.789607739143	0.637040653996	10.6560267773	-9.71524412302	-0.856740801533
14	2.5561229671	0.691330175335	0.208724613561	3.9864806426	1.67832084806	1.5840251425	0.0133841589331	-0.404056395877	0.0973133336163	0.229625018809	0.135669676677	-0.486223003746	-0.0743834290156	0.599373278071	-0.113017252135	0.172164839125	0.0342282525544	-0.0504712071806	0.314791838602	-0.0146671402351	0.318465610831	5.49808416741	24.8393902405	29.3960427092
15	2.0615113824	0.922690198986	1.43797878849	3.35289445663	0.53650590915	3.05264978871	-0.188343977385	-0.135406707057	0.0480309119648	-0.356979339842	0.495745228295	-0.841962176539	-0.205407392017	0.913877160671	-0.25768275207	0.224930025073	-0.0109602238708	0.0639206036549	0.406278382548	-0.13122480617	0.462262634443	12.7932918213	24.0376967101	22.6772962536
16	3.20674457072	-0.282531687569	0.241811727777	3.21854815911	1.08670180763	5.26885644836	0.0345693395102	-0.123112443967	-0.0115707073908	0.143717877697	0.352066582835	-0.889144310472	0.193588753864	0.833947752065	-0.364919849865	0.212235337055	0.0168615569853	-0.0393906569257	0.280628327901	-0.079625881742	0.362262477487	8.7843446463	15.6372255599	20.7698956975
17	0.450110582024	0.00623947697674	0.499168241943	1.40167383846	2.3069517841	5.33116470838	0.158588369649	-0.0913060404891	-0.146066268094	0.833321729717	-0.0187789018571	-0.404354303353	1.11850811613	-0.0685119079985	-0.17398732974	0.402958689841	0.0275005340446	-0.0826700101821	0.231996580347	0.0536956125747	0.277133240913	-1.12438823692	7.92844100736	22.7545074255
18	2.85360315544	0.349870140237	-0.173157234242	3.5414411387	2.97110409094	4.4735813897	0.164813447095	-0.139342188318	0.15916425789	0.0643846776992	-0.478121122986	0.338170930497	0.19787269964	-1.00742504592	0.273723201797	0.210889030487	0.00112246897191	-0.0110624624557	0.453884198385	-0.0337906184263	0.186083531045	-11.6307303517	19.4680323641	27.8832245135
19	5.74198545638	-3.37626980906	0.677003185708	7.381995772	2.37105389543	4.8830817647	0.0145777073062	-0.625706891242	0.129416468012	1.06459534784	-0.577787721676	0.360130913073	0.798339653314	-1.51020394202	0.315382012957	0.328180187698	-0.173961024422	0.0660650310359	0.693503388741	-0.0884906296455	0.216636810197	-15.044499309	18.5184995022	36.7290794101
20	4.1121126487	0.753912307499	0.443065310361	3.00334924748	2.42963311437	5.88040970407	0.220701430015	-0.312895764278	0.464686616959	-0.142315157438	-0.361313190583	0.15459614808	-0.223918137136	-0.720272529022	0.0382688420149	0.206042123105	0.059177895687	-0.00039442681065	0.39263629543	-0.0498233741549	0.22197187133	-8.01916057597	28.2802719284	35.9365586787

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 'B' and (resid 195 through 213 )	B	D	195 - 213	197 - 215
2	2	chain 'B' and (resid 214 through 227 )	B	D	214 - 227	216 - 229
3	3	chain 'B' and (resid 228 through 251 )	B	D	228 - 251	230 - 255
4	4	chain 'A' and (resid 0 through 15 )	A	A	0 - 15	1 - 18
5	5	chain 'A' and (resid 16 through 29 )	A	A	16 - 29	19 - 32
6	6	chain 'A' and (resid 30 through 42 )	A	A	30 - 42	33 - 47
7	7	chain 'A' and (resid 43 through 94 )	A	A	43 - 94	48 - 101
8	8	chain 'A' and (resid 95 through 137 )	A	A	95 - 137	102 - 144
9	9	chain 'A' and (resid 138 through 153 )	A	A	138 - 153	145 - 160
10	10	chain 'A' and (resid 154 through 194 )	A	A	154 - 194	161 - 203
11	11	chain 'A' and (resid 195 through 216 )	A	A	195 - 216	204 - 227
12	12	chain 'A' and (resid 217 through 237 )	A	A	217 - 237	228 - 248
13	13	chain 'A' and (resid 238 through 251 )	A	A	238 - 251	249 - 262
14	14	chain 'B' and (resid -1 through 15 )	B	D	-1 - 15	1 - 17
15	15	chain 'B' and (resid 16 through 42 )	B	D	16 - 42	18 - 44
16	16	chain 'B' and (resid 43 through 66 )	B	D	43 - 66	45 - 68
17	17	chain 'B' and (resid 67 through 94 )	B	D	67 - 94	69 - 96
18	18	chain 'B' and (resid 95 through 137 )	B	D	95 - 137	97 - 139
19	19	chain 'B' and (resid 138 through 153 )	B	D	138 - 153	140 - 155
20	20	chain 'B' and (resid 154 through 194 )	B	D	154 - 194	156 - 196

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