PDB-8acg: Structure of Pseudomonas aeruginosa aminopeptidase, PaAP_T E340A ...

ID or keywords:

Entry

Database: PDB / ID: 8acg

Title

Structure of Pseudomonas aeruginosa aminopeptidase, PaAP_T E340A mutant

Components

Keratinase KP1

Keywords

HYDROLASE / E340A mutant /

truncation

Function / homology

Function and homology information

metalloexopeptidase activity /

aminopeptidase activity /

Biological species

Pseudomonas aeruginosa (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.84 Å

Authors

Harding, C.J. / Czekster, C.M.

Funding support

United Kingdom, 1items

Citation

Journal: Nat.Chem.Biol. / Year: 2023
Title: An anti-biofilm cyclic peptide targets a secreted aminopeptidase from P. aeruginosa.
Authors: Harding, C.J. / Bischoff, M. / Bergkessel, M. / Czekster, C.M.

History

Deposition	Jul 5, 2022	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jul 12, 2023	Provider: repository / Type: Initial release
Revision 1.1	Sep 6, 2023	Group: Data collection / Database references Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author / diffrn_source Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _diffrn_source.pdbx_synchrotron_site
Revision 1.2	Feb 7, 2024	Group: Refinement description / Category: pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	8acg.cif.gz	1 MB	Display	PDBx/mmCIF format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ac/8acg ftp://data.pdbj.org/pub/pdb/validation_reports/ac/8acg	HTTPS FTP

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Related structure data

Related structure data	8ac7SC 8ac9C 8ackC 8acrC 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	#35 - Nov 2002 Ferritin and Transferrin similarity (4)

Deposited unit

F: Keratinase KP1

D: Keratinase KP1

A: Keratinase KP1

E: Keratinase KP1

B: Keratinase KP1

C: Keratinase KP1

hetero molecules

317 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

F: Keratinase KP1

hetero molecules

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

2

D: Keratinase KP1

hetero molecules

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

3

A: Keratinase KP1

hetero molecules

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

4

E: Keratinase KP1

hetero molecules

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

5

B: Keratinase KP1

hetero molecules

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

6

C: Keratinase KP1

hetero molecules

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

Unit cell

Length a, b, c (Å)	186.740, 186.740, 84.730
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	143
Space group name H-M	P3

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	(chain A and resid 47 through 509)
2	1	(chain B and resid 47 through 509)
3	1	(chain C and resid 47 through 509)
4	1	(chain D and resid 47 through 509)
5	1	(chain E and resid 47 through 509)
6	1	(chain F and resid 47 through 509)

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: ALA / End label comp-ID: ALA / Auth seq-ID: 47 - 509 / Label seq-ID: 21 - 483

Dom-ID	Selection details	Auth asym-ID	Label asym-ID
1	(chain A and resid 47 through 509)	A	C
2	(chain B and resid 47 through 509)	B	E
3	(chain C and resid 47 through 509)	C	F
4	(chain D and resid 47 through 509)	D	B
5	(chain E and resid 47 through 509)	E	D
6	(chain F and resid 47 through 509)	F	A

#1: Protein	Keratinase KP1 Mass: 52563.285 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Details: E314A mutation / Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: E3ULB5
#2: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: Zn
#3: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 9 / 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: 2.7 Å³/Da / Density % sol: 54.47 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.1 M magnesium acetate tetrahydrate, 0.1 M potassium chloride, 0.1 M MES pH 6.2, 12 % v/v PEG Smear High

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

Diamond

/ Beamline: I04 / Wavelength: 0.9795 Å

Detector

Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: May 31, 2022

Radiation

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

Radiation wavelength

Wavelength: 0.9795 Å / Relative weight: 1

Reflection

Resolution: 2.84→61.13 Å / Num. obs: 77841 / % possible obs: 99.8 % / Redundancy: 5.2 % / B_iso Wilson estimate: 89.97 Å² / R_pim(I) all: 0.027 / R_rim(I) all: 0.062 / Net I/σ(I): 15.2 / Num. measured all: 406620

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	Mean I/σ(I) obs	Num. measured all	Num. unique obs	R_pim(I) all	R_rim(I) all	% possible all
2.84-2.89	3.8	0.8	14467	3761	0.791	1.606	97.3
7.7-61.14	5.1	53.8	19950	3877	0.01	0.022	99.5

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Processing

Software

Name	Version	Classification
PHENIX	1.14_3260	refinement
xia2	3.10.dev0	data scaling
PDB_EXTRACT	3.27	data extraction
xia2		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 8AC7

8ac7

Resolution: 2.84→49.572 Å / SU ML: 0.44 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 27.29 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2389	3812	4.9 %
R_work	0.1907	73967	-
obs	0.1928	77779	99.76 %

Solvent computation

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

Displacement parameters

B_iso max: 210.01 Å² / B_iso mean: 104.6791 Å² / B_iso min: 67.53 Å²

Refinement step

Cycle: final / Resolution: 2.84→49.572 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	21270	0	21	9	21300
B_iso mean	-	-	101	81.88	-
Num. residues	-	-	-	-	2820

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Number	Refine-ID	Rms	Type
1	1	A	13014	X-RAY DIFFRACTION	6.865	TORSIONAL
1	2	B	13014	X-RAY DIFFRACTION	6.865	TORSIONAL
1	3	C	13014	X-RAY DIFFRACTION	6.865	TORSIONAL
1	4	D	13014	X-RAY DIFFRACTION	6.865	TORSIONAL
1	5	E	13014	X-RAY DIFFRACTION	6.865	TORSIONAL
1	6	F	13014	X-RAY DIFFRACTION	6.865	TORSIONAL

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	% reflection obs (%)
2.8402-2.8761	0.383	146	0.3323	2623	96
2.8761-2.9139	0.3466	163	0.3237	2716	99
2.9139-2.9539	0.329	154	0.316	2710	100
2.9539-2.9961	0.392	166	0.3294	2693	100
2.9961-3.0408	0.2905	104	0.3045	2828	100
3.0408-3.0883	0.3475	155	0.2945	2702	100
3.0883-3.1389	0.2953	146	0.2719	2755	100
3.1389-3.193	0.3356	148	0.2774	2755	100
3.193-3.2511	0.3031	164	0.253	2730	100
3.2511-3.3136	0.3087	148	0.2407	2740	100
3.3136-3.3812	0.286	130	0.2277	2760	100
3.3812-3.4547	0.257	154	0.2376	2716	100
3.4547-3.535	0.2788	104	0.2405	2791	100
3.535-3.6234	0.288	120	0.2204	2708	100
3.6234-3.7214	0.2621	130	0.2045	2832	100
3.7214-3.8308	0.2752	120	0.2031	2738	100
3.8308-3.9544	0.2483	128	0.1857	2770	100
3.9544-4.0957	0.2134	156	0.1779	2737	100
4.0957-4.2596	0.2036	164	0.1713	2734	100
4.2596-4.4533	0.1984	146	0.1571	2750	100
4.4533-4.688	0.2255	122	0.1589	2750	100
4.688-4.9814	0.2203	138	0.1556	2742	100
4.9814-5.3656	0.2041	152	0.1655	2731	100
5.3656-5.9048	0.2662	122	0.177	2752	100
5.9048-6.7574	0.2272	132	0.1787	2763	100
6.7574-8.5066	0.1967	157	0.1762	2756	100
8.5066-49.57	0.2264	143	0.1717	2685	98

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	1.235	1.1862	-0.8285	1.4253	-0.019	4.8046	0.0962	0.3272	0.237	-0.4705	-0.2817	-0.2032	-0.9464	-0.1204	0.1396	1.1081	0.3371	-0.0046	1.0271	0.0466	0.9231	6.6986	41.0455	-30.9499
2	4.6794	-6.5497	-5.4639	9.3102	7.0368	6.7877	0.4192	0.3511	-0.2188	-1.1143	-0.2316	0.4948	-1.0406	-0.2379	-0.2344	0.9304	-0.0347	0.045	1.0041	-0.0019	0.9143	29.1594	26.6764	-39.7973
3	7.4037	-0.6799	-0.87	8.7566	-0.205	6.5759	0.1722	-0.4257	-0.6006	0.9316	-0.2652	0.2979	0.5142	-0.0889	0.088	0.8251	-0.0609	0.0078	0.8112	0.0343	0.6487	46.018	7.2265	-40.1272
4	6.97	-7.2937	-7.2926	8.1011	7.7731	9.2159	0.7129	0.6104	0.7603	-0.4665	-0.2205	-0.8854	-0.5142	-0.5711	-0.5359	0.9175	-0.0288	0.1231	0.9537	-0.0736	0.891	37.1173	22.4308	-40.8885
5	4.4179	-0.7288	-1.5619	2.3245	-0.4268	3.6322	-0.0641	0.1781	-0.3185	-0.0888	0.1046	-0.1876	-0.0232	-0.0366	-0.0427	0.7758	0.1336	0.0466	0.8864	-0.041	0.7397	12.326	27.0523	-23.0081
6	2.0522	-0.4039	-1.3881	4.5396	3.1206	5.9102	0.003	-0.4424	0.0138	0.6432	0.0693	0.1877	0.3911	-0.2317	0.1897	0.7736	0.2251	0.0894	0.9159	-0.0999	0.6361	8.1116	32.0489	-12.1745
7	5.0094	-0.3427	1.0314	0.892	-2.2945	6.0432	-0.0158	-0.635	-0.0587	0.6493	0.2435	-0.5915	1.3652	1.5089	-0.3405	0.6441	0.1488	-0.0429	0.6838	0.0094	0.6846	41.6431	-5.8651	3.6543
8	5.347	-3.5857	-1.3993	5.207	1.784	5.5181	-0.2581	-0.7078	1.1816	0.7298	0.4657	-0.9869	-0.7623	0.8827	-0.2455	0.8905	-0.0993	-0.0113	0.7821	-0.1896	0.8211	42.6149	14.0059	5.9957
9	2.954	-2.8519	-2.808	5.1052	3.3552	4.9766	0.3242	0.457	0.3268	-0.144	-0.3429	-0.0542	-1.1049	-1.1459	-0.0068	1.285	0.2455	-0.025	1.0816	-0.0811	0.8805	21.8903	39.0664	14.8435
10	2.2134	0.7384	0.0487	3.7364	0.0729	5.8912	0.0391	-0.0644	0.391	0.0445	-0.072	0.278	-0.3284	-0.5443	0.0108	0.6794	0.0605	0.0483	0.686	-0.0836	0.7561	30.3568	3.6463	-5.9061
11	3.1365	0.9479	0.3255	4.342	0.9702	3.0073	0.5222	0.5185	-0.7268	-0.0314	0.1066	-0.1039	0.8179	0.462	-0.641	1.0266	0.1459	-0.1914	0.9586	-0.153	1.0248	20.3786	71.0265	2.1516
12	7.7723	-1.1342	0.779	5.8362	-1.102	7.6969	-0.3611	-0.5321	0.9535	0.0766	0.5486	0.3365	-0.8835	-1.4233	-0.2197	1.1178	0.0971	-0.1445	0.7273	0.0655	0.8928	-21.4758	67.7927	-8.095
13	4.1082	2.0765	2.4201	1.4405	1.5077	2.8911	0.4959	0.0002	-0.1546	0.2836	-0.0611	0.0657	0.6863	0.0799	-0.502	1.1944	-0.0424	-0.1585	0.7627	0.0617	0.9793	10.6611	73.8738	9.0236
14	3.936	2.1359	1.2106	4.0778	3.3374	3.23	-0.0066	0.1052	0.2834	-0.0378	-0.0572	0.3625	-0.0793	-0.0773	0.0632	0.7978	-0.0605	-0.0851	0.7157	0.02	0.9813	14.8315	87.4744	11.6878
15	2.6232	-1.0222	0.6633	4.3445	-0.791	4.2961	0.1613	-0.8551	-1.2357	0.6437	0.615	0.6118	0.8771	-0.9529	-0.7396	1.1149	-0.0618	-0.2599	1.0792	0.3172	1.2524	-21.1464	71.4589	39.5491
16	9.3284	1.8493	1.0358	5.0382	0.9647	7.4697	-0.5032	0.373	0.382	-0.7678	0.0627	-0.3992	-1.1432	0.6126	0.4089	1.2421	-0.0019	-0.1112	0.8529	0.1589	1.0518	20.1608	67.9083	48.7257
17	0.4773	-0.968	1.4448	1.9102	-2.7698	4.1811	0.3284	-0.3133	-0.629	-0.1956	0.0158	0.4906	0.2607	0.0067	-0.3897	0.851	0.1747	-0.2145	0.7751	-0.1559	0.8195	4.8883	64.4641	48.0767
18	4.0063	-1.6029	1.4225	3.6973	-1.8653	6.8931	0.168	-0.2603	-0.3252	0.2054	0.2984	-0.385	0.3598	0.1263	-0.4536	0.6959	0.0511	-0.1928	0.6113	-0.0259	0.8684	-14.5821	81.4917	29.9683
19	2.7357	-1.3014	-0.3658	4.8569	-0.8934	6.2149	0.2034	0.4481	-0.0718	-0.8832	0.2279	0.1993	0.2514	-0.5906	-0.4087	0.8506	0.0166	-0.1862	0.8094	0.1139	0.9868	-21.2566	82.0874	19.2764
20	5.6463	-1.7993	0.7788	2.1499	1.5448	2.1559	0.1787	0.4661	0.078	-0.8082	-0.128	0.6982	0.0666	-0.6112	-0.1236	1.1331	-0.2926	-0.2468	0.9106	0.1143	0.7598	52.9524	47.2573	28.5224
21	0.7211	0.9989	-0.8612	1.7875	-0.8229	2.5084	0.0787	0.4957	0.4402	-0.2801	0.2642	0.8629	-0.1061	-1.1675	-0.3689	1.0857	0.1693	-0.1328	1.4485	0.2415	1.1556	48.4024	62.5756	29.6936
22	6.2255	1.7065	0.5764	7.632	0.2654	3.4156	0.4284	-0.0918	0.3694	-0.1391	0.027	-0.4164	-0.334	0.5354	-0.4541	0.915	0.0751	0.1819	1.1284	0.0751	0.9395	69.0547	92.1867	18.5695
23	0.2446	0.337	0.3282	4.7968	-2.9861	2.824	0.1981	0.1119	0.095	-0.0716	0.405	0.6214	-0.114	-0.7042	-0.6294	0.9644	0.0596	0.1126	1.0828	0.1379	0.937	56.547	61.4519	34.7853
24	1.1076	-0.3526	-0.1854	4.2981	0.2105	1.7471	0.1139	0.1833	0.3593	-0.3832	-0.0464	-0.4678	-0.1502	0.0682	-0.0677	0.8891	0.0224	0.0672	0.8815	0.1301	0.876	70.9511	52.67	37.5128
25	3.1708	-0.1748	-0.3571	4.1653	-0.3818	4.8493	0.2069	-0.4211	-0.5481	0.1192	-0.0551	0.5458	0.8667	0.1384	-0.1549	0.9559	-0.0162	-0.0213	0.7613	0.1663	0.7663	60.7327	46.0027	45.6358
26	5.5123	0.6668	-1.6711	2.8069	-1.4716	3.2766	0.0565	-0.5497	0.3632	0.7538	0.211	0.5611	-0.4316	-0.6156	-0.2376	0.9158	0.0813	0.1642	0.9957	0.119	0.7984	70.6737	90.4351	65.2505
27	4.5796	3.7902	-2.8851	4.8057	-3.8269	6.0322	-0.0678	0.0245	-0.3635	-0.1926	0.4214	0.4121	1.6225	-1.2605	-0.3282	1.4468	-0.2715	0.064	1.3755	0.2332	0.9326	48.3961	57.9788	75.9799
28	3.0167	0.4056	0.0519	2.4081	-0.4485	3.1136	-0.087	-0.4422	-0.4828	0.2337	0.2558	0.2678	0.2583	-0.3722	-0.1809	0.7461	0.0636	0.0883	0.83	0.146	0.7267	76.8876	79.3947	56.4716
29	2.1262	-0.1788	-0.1361	3.1622	0.1419	2.665	0.1496	0.3779	-0.0627	-0.5978	-0.026	0.178	0.0084	0.4078	-0.0105	0.8164	0.013	0.1082	0.9158	0.081	0.7309	80.6159	85.1724	45.7769

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'F' and (resid 46 through 81 )	F	46 - 81
2	X-RAY DIFFRACTION	2	chain 'F' and (resid 82 through 143 )	F	82 - 143
3	X-RAY DIFFRACTION	3	chain 'F' and (resid 144 through 256 )	F	144 - 256
4	X-RAY DIFFRACTION	4	chain 'F' and (resid 257 through 281 )	F	257 - 281
5	X-RAY DIFFRACTION	5	chain 'F' and (resid 282 through 477 )	F	282 - 477
6	X-RAY DIFFRACTION	6	chain 'F' and (resid 478 through 516 )	F	478 - 516
7	X-RAY DIFFRACTION	7	chain 'D' and (resid 43 through 81 )	D	43 - 81
8	X-RAY DIFFRACTION	8	chain 'D' and (resid 82 through 122 )	D	82 - 122
9	X-RAY DIFFRACTION	9	chain 'D' and (resid 123 through 281 )	D	123 - 281
10	X-RAY DIFFRACTION	10	chain 'D' and (resid 282 through 516 )	D	282 - 516
11	X-RAY DIFFRACTION	11	chain 'A' and (resid 46 through 122 )	A	46 - 122
12	X-RAY DIFFRACTION	12	chain 'A' and (resid 123 through 255 )	A	123 - 255
13	X-RAY DIFFRACTION	13	chain 'A' and (resid 256 through 395 )	A	256 - 395
14	X-RAY DIFFRACTION	14	chain 'A' and (resid 396 through 511 )	A	396 - 511
15	X-RAY DIFFRACTION	15	chain 'E' and (resid 48 through 122 )	E	48 - 122
16	X-RAY DIFFRACTION	16	chain 'E' and (resid 123 through 255 )	E	123 - 255
17	X-RAY DIFFRACTION	17	chain 'E' and (resid 256 through 281 )	E	256 - 281
18	X-RAY DIFFRACTION	18	chain 'E' and (resid 282 through 477 )	E	282 - 477
19	X-RAY DIFFRACTION	19	chain 'E' and (resid 478 through 516 )	E	478 - 516
20	X-RAY DIFFRACTION	20	chain 'B' and (resid 45 through 89 )	B	45 - 89
21	X-RAY DIFFRACTION	21	chain 'B' and (resid 90 through 122 )	B	90 - 122
22	X-RAY DIFFRACTION	22	chain 'B' and (resid 123 through 255 )	B	123 - 255
23	X-RAY DIFFRACTION	23	chain 'B' and (resid 256 through 381 )	B	256 - 381
24	X-RAY DIFFRACTION	24	chain 'B' and (resid 382 through 477 )	B	382 - 477
25	X-RAY DIFFRACTION	25	chain 'B' and (resid 478 through 509 )	B	478 - 509
26	X-RAY DIFFRACTION	26	chain 'C' and (resid 45 through 122 )	C	45 - 122
27	X-RAY DIFFRACTION	27	chain 'C' and (resid 123 through 281 )	C	123 - 281
28	X-RAY DIFFRACTION	28	chain 'C' and (resid 282 through 477 )	C	282 - 477
29	X-RAY DIFFRACTION	29	chain 'C' and (resid 478 through 516 )	C	478 - 516

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