PDB-6txd: Variant W229D/F290W-12 of the last common ancestor of Gram-negati...

ID or keywords:

Entry

Database: PDB / ID: 6txd

Title

Variant W229D/F290W-12 of the last common ancestor of Gram-negative bacteria beta-lactamase class A (GNCA4)

Components

Beta lactamase (GNCA4-12)

Keywords

HYDROLASE / ANTIBIOTIC RESISTANCE / ANCESTRAL RECONSTRUCTED

Function / homology

Beta-lactamase / DD-peptidase/beta-lactamase superfamily / 3-Layer(aba) Sandwich / Alpha Beta / ACETATE ION / FORMIC ACID

Function and homology information

Biological species

synthetic construct (others)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2 Å

Authors

Gavira, J.A. / Risso, V. / Sanchez-Ruiz, J.M. / Romero-Rivera, A. / Kamerlin, S.C.L.

Funding support

Spain,

United States, 3items

Organization	Grant number	Country
Spanish Ministry of Science, Innovation, and Universities	BIO2016-74875-P	Spain
Spanish Ministry of Economy and Competitiveness	BIO2015-66426-R	Spain
Human Frontier Science Program (HFSP)	RGP0041/2017	United States

Citation

Journal: Chem Sci / Year: 2020
Title: Enhancing ade novoenzyme activity by computationally-focused ultra-low-throughput screening.
Authors: Risso, V.A. / Romero-Rivera, A. / Gutierrez-Rus, L.I. / Ortega-Munoz, M. / Santoyo-Gonzalez, F. / Gavira, J.A. / Sanchez-Ruiz, J.M. / Kamerlin, S.C.L.

History

Deposition	Jan 14, 2020	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jun 3, 2020	Provider: repository / Type: Initial release
Revision 1.1	Sep 16, 2020	Group: Database references / Derived calculations Category: citation / citation_author ...citation / citation_author / pdbx_struct_conn_angle / struct_conn Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _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.ptnr2_auth_seq_id
Revision 1.2	Jan 24, 2024	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6txd.cif.gz	398 KB	Display	PDBx/mmCIF format
PDB format	pdb6txd.ent.gz	271.9 KB	Display	PDB format
PDBx/mmJSON format	6txd.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/tx/6txd ftp://data.pdbj.org/pub/pdb/validation_reports/tx/6txd	HTTPS FTP

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Related structure data

Related structure data	6twwC 6ty6C 5fqkS 5fqi S: Starting model for refinement C: citing same article (ref.)
Similar structure data	2pha-3 3gn0-1 3e6v-2 1t4p-d 3lp7-2 6ra2-d 1zpg-d 1t5f-d 3e8q-d 4gwd-2 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Beta lactamase (GNCA4-12)

B: Beta lactamase (GNCA4-12)

C: Beta lactamase (GNCA4-12)

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	77.314, 148.228, 245.962
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	23
Space group name H-M	I222
Space group name Hall	I22
Symmetry operation	#1: x,y,z #2: x,-y,-z #3: -x,y,-z #4: -x,-y,z #5: x+1/2,y+1/2,z+1/2 #6: x+1/2,-y+1/2,-z+1/2 #7: -x+1/2,y+1/2,-z+1/2 #8: -x+1/2,-y+1/2,z+1/2

Components on special symmetry positions

ID	Model	Components
1	1	C-608- HOH

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Protein , 1 types, 3 molecules ABC

#1: Protein	Beta lactamase (GNCA4-12) Mass: 28946.594 Da / Num. of mol.: 3 / Mutation: W229D, F290W Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Plasmid: pET-24b(+) Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)

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Non-polymers , 5 types, 438 molecules

#2: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₃H₈O₃
#3: Chemical	ChemComp-FMT / FORMIC ACID Mass: 46.025 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: CH₂O₂
#4: Chemical	ChemComp-ACT / ACETATE ION Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂H₃O₂
#5: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 422 / Source method: isolated from a natural source / Formula: H₂O

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Details

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: 3.9 Å³/Da / Density % sol: 68.8 %
Crystal grow	Temperature: 293 K / Method: counter-diffusion / pH: 4 / Details: 5.0 M Sodium formate, 100 mM AcNa pH 4.0

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.979 Å
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 14, 2019
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.979 Å / Relative weight: 1
Reflection	Resolution: 2→71.74 Å / Num. obs: 95172 / % possible obs: 98.99 % / Redundancy: 4.5 % / B_iso Wilson estimate: 28.62 Å² / CC_1/2: 0.993 / CC star: 0.998 / R_merge(I) obs: 0.103 / R_pim(I) all: 0.056 / R_rim(I) all: 0.118 / Net I/σ(I): 11.89
Reflection shell	Resolution: 2→2.07 Å / Redundancy: 4.5 % / R_merge(I) obs: 0.678 / Mean I/σ(I) obs: 2.63 / Num. unique obs: 9368 / CC_1/2: 0.81 / CC star: 0.946 / R_pim(I) all: 0.3612 / R_rim(I) all: 0.771 / % possible all: 98.87

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Processing

Software

Name	Version	Classification
PHENIX	1.15.2_3472	refinement
Coot		model building
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5FQK

5fqk

Resolution: 2→71.74 Å / SU ML: 0.2143 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.5341

	R_factor	Num. reflection	% reflection
R_free	0.2352	4769	5.04 %
R_work	0.2119	-	-
obs	0.213	94616	99 %

Solvent computation

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

Displacement parameters

B_iso mean: 38.25 Å²

Refinement step

Cycle: LAST / Resolution: 2→71.74 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6023	0	59	422	6504

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0024	6422
X-RAY DIFFRACTION	f_angle_d	0.5897	8753
X-RAY DIFFRACTION	f_chiral_restr	0.0374	1002
X-RAY DIFFRACTION	f_plane_restr	0.0034	1170
X-RAY DIFFRACTION	f_dihedral_angle_d	4.8421	5575

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 (%)
2-2.02	0.3218	164	0.2986	2966	X-RAY DIFFRACTION	98.93
2.02-2.05	0.3296	146	0.2855	2947	X-RAY DIFFRACTION	98.69
2.05-2.07	0.3284	160	0.2887	2968	X-RAY DIFFRACTION	99.02
2.07-2.1	0.2884	166	0.277	2983	X-RAY DIFFRACTION	99.21
2.1-2.13	0.2758	169	0.2658	2949	X-RAY DIFFRACTION	99.05
2.13-2.15	0.2894	152	0.2595	2946	X-RAY DIFFRACTION	98.41
2.15-2.19	0.3411	161	0.2634	2970	X-RAY DIFFRACTION	99.37
2.19-2.22	0.3218	170	0.2446	2981	X-RAY DIFFRACTION	99.28
2.22-2.25	0.2427	180	0.2504	2979	X-RAY DIFFRACTION	99.5
2.25-2.29	0.2793	147	0.2434	2952	X-RAY DIFFRACTION	99.26
2.29-2.33	0.2574	154	0.2367	2981	X-RAY DIFFRACTION	99.24
2.33-2.37	0.2696	165	0.2296	2952	X-RAY DIFFRACTION	99.43
2.37-2.42	0.2599	156	0.2254	3002	X-RAY DIFFRACTION	99.25
2.42-2.47	0.2405	141	0.2306	2993	X-RAY DIFFRACTION	99.37
2.47-2.52	0.2484	152	0.229	3031	X-RAY DIFFRACTION	99.59
2.52-2.58	0.2444	146	0.2252	3004	X-RAY DIFFRACTION	99.53
2.58-2.64	0.2278	179	0.2236	2950	X-RAY DIFFRACTION	99.4
2.64-2.71	0.2391	158	0.2242	3008	X-RAY DIFFRACTION	99.28
2.71-2.79	0.2633	168	0.227	2993	X-RAY DIFFRACTION	99.5
2.79-2.88	0.2348	169	0.2238	2978	X-RAY DIFFRACTION	99.24
2.88-2.99	0.2411	151	0.2152	3022	X-RAY DIFFRACTION	99.28
2.99-3.11	0.2324	164	0.2056	2995	X-RAY DIFFRACTION	99.56
3.11-3.25	0.2502	179	0.2107	2997	X-RAY DIFFRACTION	99.47
3.25-3.42	0.2345	148	0.2089	3021	X-RAY DIFFRACTION	99.28
3.42-3.63	0.2052	149	0.1822	3055	X-RAY DIFFRACTION	99.38
3.63-3.91	0.1715	139	0.1803	3028	X-RAY DIFFRACTION	98.97
3.91-4.31	0.1865	169	0.1662	3008	X-RAY DIFFRACTION	98.42
4.31-4.93	0.2119	149	0.1713	2999	X-RAY DIFFRACTION	97.07
4.93-6.21	0.2158	156	0.2071	3043	X-RAY DIFFRACTION	97.8
6.21-71.74	0.2188	162	0.2034	3146	X-RAY DIFFRACTION	96.53

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	3.69293687465	-0.447814773984	-1.37418190417	2.86347880028	-0.685928116673	3.4336753395	0.216571634093	0.121543521519	0.366845180191	-0.596771565146	-0.0527236277563	0.0322354801293	-0.359917840596	0.118059446316	-0.15564167354	0.568700545721	0.0518466481981	-0.0003046240947	0.243524988028	0.00263928815496	0.250711472206	-21.4546714478	4.6406552847	-84.2109011849
2	2.08235106416	-0.163530923312	-0.261697629143	3.47492576103	-0.228280345716	2.01651451875	0.0354566588212	-0.181670231384	0.0436175906809	0.169908768286	-0.0359021690562	-0.378207691551	0.0498449916134	0.111103244397	-0.00454043676345	0.211220732953	0.0388962175873	-0.0489717580736	0.204684989666	-0.0334924716102	0.1880224991	-15.9202101877	-20.4359905967	-64.8252136333
3	0.832674616351	-0.0469876875102	0.654725620244	2.45148058117	-0.389812997204	2.64889190251	0.00165127204279	0.0220600305652	0.0446364394525	-0.287933298807	-0.00903249083549	-0.230005493166	-0.0134227407894	0.0906666164724	0.00384016559285	0.254549564586	0.031028536374	0.00643723704889	0.217630282383	-0.0262583426041	0.240855344329	-19.6782523113	-15.0539544603	-76.1510523907
4	1.45868724962	1.19212154969	-0.235737464577	4.29260170627	-0.925559073537	2.53109294646	-0.052120200553	0.0874794004465	0.0904175219509	-0.0547469972158	0.0344230492288	-0.0525391191673	-0.312046132116	0.050826264923	0.00257638909125	0.227091220881	0.0213896281585	-0.0128081133517	0.190311071738	-0.0423829547431	0.189849055446	-21.1546908105	1.33976014696	-71.4423310401
5	2.4379009207	-1.49217739406	-1.63905709728	3.63124486263	-0.325065125043	1.7545482272	0.10201894835	-0.77253916096	0.164858072321	0.464887656504	0.103082737621	-0.749603740136	0.319373427436	0.863979405876	-0.0373931273002	0.357914296442	0.05328580131	-0.13127552142	0.383664263111	0.0432150369893	0.352126243722	-4.74723357787	-47.259590663	-53.2200716528
6	1.08284193908	1.21925036888	0.748483719131	2.67343769557	-0.480590724002	2.96035305695	0.0409870112784	-0.125263724112	0.00434781558273	0.248473387896	-0.0980955943891	-0.0058431915246	-0.153590583682	-0.141855037266	0.00707516290871	0.155410066926	0.0662340702069	-0.0482971573984	0.2504777328	0.00994364233202	0.253561228494	-15.8252891785	-41.0903367448	-59.0203973256
7	2.40980892891	-0.713861551427	-0.167659323455	1.71652407908	0.0508586758533	2.83940978775	-0.00745349184228	0.196383420828	-0.0831745300617	-0.377921651041	-0.115165086745	0.257797153804	0.204762657315	-0.213183214813	0.157844950488	0.451094960368	0.0102910637502	-0.0919301953929	0.181444900483	-0.00966766754396	0.258258781801	-28.2119257052	-44.7911740374	-83.264696778
8	3.66517649828	-0.430719738287	-1.34443853858	2.26163019119	-0.342656238488	2.67041453185	0.105005086614	0.352796398914	-0.295679932634	-0.426782461213	-0.121066732039	-0.112789505809	0.47145285182	0.116728402926	0.033669257832	0.726027664421	0.0943327475148	-0.0587685323923	0.241983474805	-0.0471747996832	0.319234361328	-18.9976794645	-52.9464264498	-87.618913724
9	1.55955660244	0.637840501623	0.293266753221	2.16580330298	-0.0376166944079	1.06795351575	0.0150455786123	0.00342693177354	-0.0323315487886	-0.233396450881	-0.00110031326957	0.0849636740767	0.123513019808	-0.0513183174462	-0.00944040154573	0.306210174859	0.0414926663369	-0.0340808220673	0.188256154813	-0.00596363616655	0.199999529435	-22.1936174408	-40.5618155224	-74.6230777419
10	2.16259907181	0.609379389531	0.0293281991906	3.69051077711	-1.32250491641	5.50954351084	0.150970634401	-0.123165660219	-0.27790897287	-0.750493218372	-0.000928758078947	-0.0165850195797	0.559589220222	-0.0535280749096	-0.209413159999	0.358384107152	0.0494447974786	-0.0539032484352	0.160176548441	-0.0102177856814	0.280524748912	-18.1397076317	-56.9906797301	-66.7753491274
11	3.01391296398	-0.48869583187	0.0467043758524	1.35180671525	0.411810983459	1.96961566132	-0.0818031767205	-0.129038170524	-0.188553656505	-0.125752070323	-0.0612499044341	-0.166720891322	0.252757594076	0.205853852506	0.0206599827677	0.0319089306184	0.0739264332218	0.043543966636	0.251544312079	0.0599976519949	0.376565846622	-15.071893781	-49.0164239401	-64.1810386203
12	6.51034590422	-0.238511396778	-2.86840725172	6.94448127762	0.771523734963	7.67108876925	-0.157663435405	-0.434818494915	-0.559382742354	0.853871885035	-0.0853883754435	0.131936509494	0.434693708134	0.228528689114	0.278688208266	0.278522718797	0.0220938527376	-0.0993164448146	0.18462200173	0.0427693422135	0.285333331094	-13.5971886004	-53.4988893113	-55.3435379408
13	6.12636558954	3.26653860398	2.61239655362	3.4909038552	3.13829337088	4.39424633039	0.0846771991532	0.96432003135	-0.746530827582	-0.318079050765	0.394994847687	-0.314274923666	0.783030400212	0.438074800696	-0.339220258137	1.09683581659	0.181669997272	-0.166792161041	0.531789500958	-0.133486125752	0.316808208752	-25.8297369239	-48.0296521443	-117.522302165
14	1.69758341141	-1.8743645198	-0.0442154994461	2.43028275587	0.599000424663	1.21630675896	0.242357517179	0.226101599021	-0.354381654713	-0.286958449471	0.0631225399683	0.120895174877	0.707602720967	0.0623889845366	-0.297370185169	0.859090846012	0.0600190009594	-0.136445408211	0.3041517446	-0.00790926281628	0.228121803109	-30.7726233321	-42.7361279925	-106.204095963
15	1.45538897158	0.575794883247	-0.627395076577	1.18525164751	0.738039657092	1.47523673441	0.0963134820622	0.0639767826583	0.107613626372	-0.243306564706	-0.126649982079	0.165324356979	-0.265628022146	-0.168627908594	0.0254907042284	0.612454168391	0.0760969972376	-0.127034197985	0.296409217701	0.00718418006516	0.244535386291	-31.9883255234	-17.7743325053	-94.6484218843
16	7.66370655814	-0.262277263006	0.851953307779	1.89204691932	-1.15049401532	5.62739582673	0.356870695842	0.465460526272	0.2656412663	-0.976661801353	-0.0957609542756	-0.232924202196	-0.45963444062	0.557128157384	-0.185506970103	0.820298008171	0.0257454026879	0.0605925562451	0.355451293515	0.0326166314706	0.318987106006	-20.0152197712	-9.76094428189	-102.635889004
17	0.716112244431	-0.0364663560947	-0.407600099665	1.71591410305	0.0403371539369	1.92771125242	-0.0303583424152	0.10998949573	0.00903732301272	-0.429525268499	0.0550068560959	0.082004891778	0.0131384055526	-0.0154760624717	-0.0369107892596	0.599400060838	0.051605407459	-0.0993783116593	0.280402527103	-0.0151051707352	0.22319912076	-26.5051134482	-27.4970008456	-97.4005639682
18	1.92585262554	-0.999534576004	-0.147534472439	0.523576142494	-0.124241014137	8.04067698902	-0.0220141999286	0.235909816154	0.0383595084957	-0.775569998747	-0.277064383142	0.430206380798	-0.208764410272	-0.814799293107	0.227722466609	0.572670731929	0.0681242567875	-0.172929832134	0.319785445174	-0.0504004402986	0.322453753908	-42.1252014691	-23.9989975761	-99.7521180738
19	4.10087176146	0.54372041715	4.15628841015	1.34199570914	0.862487963731	4.29158395087	-0.0754066118722	0.255545608697	0.0384562452705	-0.475862316455	0.0902038093745	0.00671989261591	-0.108546716235	-0.170683038479	-0.00143196338002	0.861568861861	0.0537722169829	-0.0921660642891	0.412189377185	0.0196087481227	0.237792745327	-33.2659574586	-27.9440928348	-114.763783349
20	3.99524274937	-0.756051551467	-0.192530927932	1.35693141577	-0.397238687394	1.86839808714	-0.033378898711	0.0290263337966	-0.0700138165006	-0.241858996462	0.107814579261	-0.0185291625666	0.158472368017	0.0472303321776	-0.0677289954012	0.861899829491	0.0407912164015	-0.0923437724153	0.347159282972	-0.0434442336373	0.20749498247	-29.9081977734	-34.7422614462	-110.835000102
21	5.56668301192	2.20382499537	-0.400651522608	1.92584722108	0.0334304742352	6.76273965343	0.297094138542	0.688830478994	-0.358427398982	-0.115222159019	0.195830224575	-0.047828388905	0.54878739077	-0.224774682495	-0.366681256053	1.07957587659	0.133171665311	-0.180263069124	0.408770772351	-0.0407067354424	0.274462767848	-32.8457145531	-39.7175780391	-118.322552299

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 27 through 68 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 69 through 118 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 119 through 195 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 196 through 295 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 27 through 40 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 41 through 68 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 69 through 98 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 99 through 131 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 132 through 212 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 213 through 238 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 240 through 271 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 272 through 295 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 27 through 40 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 41 through 68 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 69 through 98 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 99 through 118 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 119 through 195 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 196 through 212 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 213 through 238 )
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 240 through 271 )
21	X-RAY DIFFRACTION	21	chain 'C' and (resid 272 through 294 )

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