PDB-5wdk: A processive dipeptidyl aminopeptidase secreted from an establish...

ID or keywords:

Entry

Database: PDB / ID: 5wdk

Title

A processive dipeptidyl aminopeptidase secreted from an established commensal bacterium P. distasonis

Components

Aminopeptidase C

Keywords

HYDROLASE /

Protease

Function / homology

Function and homology information

cysteine-type aminopeptidase activity /

proteolysis /

metal ion binding
Similarity search - Function

Biological species

Parabacteroides distasonis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.36 Å

Authors

Wolan, D.W. / Xu, J.H. / Solania, A. / Chatterjee, S. / Jiang, Z. / ODonoghue, A.J.

Citation

Journal: Acs Chem.Biol. / Year: 2018
Title: A Commensal Dipeptidyl Aminopeptidase with Specificity for N-Terminal Glycine Degrades Human-Produced Antimicrobial Peptides in Vitro.
Authors: Xu, J.H. / Jiang, Z. / Solania, A. / Chatterjee, S. / Suzuki, B. / Lietz, C.B. / Hook, V.Y.H. / O'Donoghue, A.J. / Wolan, D.W.

History

Deposition	Jul 5, 2017	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 11, 2018	Provider: repository / Type: Initial release
Revision 1.1	Jul 24, 2019	Group: Data collection / Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _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 / _citation.year
Revision 1.2	Oct 4, 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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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	5wdk.cif.gz	860.4 KB	Display	PDBx/mmCIF format
PDB format	pdb5wdk.ent.gz	712.5 KB	Display	PDB format
PDBx/mmJSON format	5wdk.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/wd/5wdk ftp://data.pdbj.org/pub/pdb/validation_reports/wd/5wdk	HTTPS FTP

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Related structure data

Related structure data	5wdlC 3pw3S S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6w4n-d 3pw3-d 5wdl-d 3134 5wa4-d 5wa3-3 6vrw-d 3jzm-d Search similar-shape structures by Omokage search (details) 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	#142 - Oct 2011 PDB Pioneers similarity (2)

Deposited unit

A: Aminopeptidase C

B: Aminopeptidase C

C: Aminopeptidase C

D: Aminopeptidase C

E: Aminopeptidase C

F: Aminopeptidase C

hetero molecules

278 kDa, 6 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)	103.912, 136.969, 208.235
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Aminopeptidase C Mass: 45895.367 Da / Num. of mol.: 6 / Fragment: UNP residues 23-405 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Parabacteroides distasonis (strain ATCC 8503 / DSM 20701 / CIP 104284 / JCM 5825 / NCTC 11152) (bacteria) Strain: ATCC 8503 / DSM 20701 / CIP 104284 / JCM 5825 / NCTC 11152 Gene: BDI_2249 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: A6LE66
#2: Chemical	ChemComp-K / POTASSIUM ION Mass: 39.098 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: K
#3: Chemical	ChemComp-T1O / 5-[(3aS,4R,6aR)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]-N-(2-oxopropyl)pentanamide Mass: 299.389 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₁₃H₂₁N₃O₃S / Feature type: SUBJECT OF INVESTIGATION
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 558 / 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: 2.9 Å³/Da / Density % sol: 57.58 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.25 M K/Na tartrate, 17.5% PEG3350, 1 mM ZnCl2

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 8, 2017 Details: Flat Si Rh coated M0, Kirkpatrick-Baez flat bent Si M1 & M2
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97946 Å / Relative weight: 1
Reflection	Resolution: 2.35→50.1 Å / Num. obs: 120727 / % possible obs: 99.9 % / Redundancy: 6.5 % / B_iso Wilson estimate: 46.08 Å² / R_merge(I) obs: 0.23 / R_pim(I) all: 0.06 / R_sym value: 0.14 / Net I/σ(I): 13.9
Reflection shell	Resolution: 2.35→2.39 Å / Redundancy: 6.8 % / R_merge(I) obs: 0.957 / Mean I/σ(I) obs: 2.11 / Num. unique obs: 5972 / CC_1/2: 0.744 / R_pim(I) all: 0.4 / R_sym value: 0.96 / Χ²: 0.683 / % possible all: 99.9

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Processing

Software

Name	Version	Classification
PHENIX	1.10.1_2155	refinement
PDB_EXTRACT	3.22	data extraction
HKL-2000		data reduction
HKL-2000		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3PW3

3pw3

Resolution: 2.36→50.1 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.26

	R_factor	Num. reflection	% reflection
R_free	0.2311	6066	5.03 %
R_work	0.1862	-	-
obs	0.1885	120638	98.99 %

Solvent computation

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

Displacement parameters

B_iso max: 162.08 Å² / B_iso mean: 60.7596 Å² / B_iso min: 26.9 Å²

Refinement step

Cycle: final / Resolution: 2.36→50.1 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	16703	0	131	558	17392
B_iso mean	-	-	82.41	47.82	-
Num. residues	-	-	-	-	2146

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	17293
X-RAY DIFFRACTION	f_angle_d	0.924	23496
X-RAY DIFFRACTION	f_chiral_restr	0.052	2497
X-RAY DIFFRACTION	f_plane_restr	0.006	3038
X-RAY DIFFRACTION	f_dihedral_angle_d	15.414	10035

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0 / Total num. of bins used: 30

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
2.3643-2.3912	0.3166	145	0.2482	2790	2935	73
2.3912-2.4193	0.3327	215	0.2467	3832	4047	100
2.4193-2.4488	0.2989	222	0.2341	3766	3988	100
2.4488-2.4798	0.3119	195	0.2441	3820	4015	100
2.4798-2.5125	0.2929	196	0.2404	3809	4005	100
2.5125-2.5469	0.3084	199	0.2362	3819	4018	100
2.5469-2.5833	0.2855	202	0.2318	3807	4009	100
2.5833-2.6218	0.2913	193	0.2166	3858	4051	100
2.6218-2.6628	0.2719	200	0.2262	3825	4025	100
2.6628-2.7064	0.3	214	0.2215	3793	4007	100
2.7064-2.7531	0.2763	201	0.2185	3821	4022	100
2.7531-2.8032	0.2518	197	0.2151	3820	4017	100
2.8032-2.8571	0.2964	205	0.2156	3790	3995	99
2.8571-2.9154	0.2793	194	0.2293	3853	4047	100
2.9154-2.9788	0.2972	205	0.2272	3842	4047	100
2.9788-3.0481	0.2971	204	0.2262	3834	4038	100
3.0481-3.1243	0.3093	207	0.2212	3840	4047	100
3.1243-3.2087	0.2755	196	0.2139	3819	4015	100
3.2087-3.3031	0.2449	206	0.2096	3844	4050	100
3.3031-3.4097	0.2554	204	0.1992	3864	4068	100
3.4097-3.5316	0.2323	209	0.1944	3836	4045	100
3.5316-3.6729	0.2345	183	0.1838	3867	4050	100
3.6729-3.84	0.2021	210	0.1725	3869	4079	100
3.84-4.0424	0.2159	218	0.1654	3847	4065	100
4.0424-4.2955	0.189	188	0.1501	3911	4099	100
4.2955-4.627	0.1762	231	0.1401	3854	4085	100
4.627-5.0922	0.1929	185	0.1349	3935	4120	100
5.0922-5.8281	0.201	214	0.1585	3902	4116	100
5.8281-7.3391	0.2032	188	0.1849	4003	4191	100
7.3391-50.1321	0.1799	240	0.1731	4102	4342	100

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	0.2265	-0.2198	-0.2055	0.6638	-0.0988	0.3899	-0.446	-0.3241	-0.346	0.3655	0.2517	0.2328	0.6235	0.4725	-0.0729	0.8342	0.3482	0.1002	0.6955	0.1886	0.5088	49.1168	-22.0524	-6.224
2	1.6185	-0.5436	-0.3206	0.7492	0.6351	1.4754	-0.1379	-0.3311	-0.1476	0.2897	0.0787	0.0408	0.393	0.4095	-0.0097	0.5093	0.1007	0.0112	0.5005	0.0668	0.3529	39.8739	-3.0911	-3.3791
3	1.4642	-0.4972	-1.3119	1.0377	-0.2418	2.5425	-0.4126	-0.3499	-0.3609	0.0435	0.2303	0.1087	0.8083	0.4539	-0.008	0.6682	0.26	0.0584	0.5883	0.0935	0.5231	55.3421	-20.1345	-19.8293
4	0.347	0.0796	0.2596	0.432	-0.0261	0.2052	-0.1305	0.0617	0.1036	0.1781	-0.0626	0.1211	-0.2404	-0.3419	0.0002	0.5756	0.1164	0.0278	0.5	-0.0693	0.6128	2.9541	27.127	-5.2814
5	0.958	-0.7778	-0.5075	1.2412	0.3225	1.3759	-0.06	-0.0021	-0.043	0.3073	-0.1058	0.2034	0.0231	-0.1136	-0.0007	0.4656	-0.0055	0.0811	0.4034	-0.0222	0.4427	12.8617	8.7183	-1.412
6	0.9534	-0.6364	0.6505	1.2449	0.6239	1.8693	0.0115	0.3191	0.0001	-0.1073	-0.2688	0.3324	-0.3484	-0.3319	-0.0002	0.4336	0.1223	0.0207	0.641	-0.1316	0.682	-5.7277	22.5012	-15.6695
7	0.3379	-0.3168	0.1817	0.527	-0.3512	0.2341	0.3582	-0.3749	-0.1389	0.3308	-0.3803	0.1883	0.8318	-0.5445	-0.0447	0.8992	-0.5306	0.1767	1.0293	-0.1827	0.6844	-7.2559	-26.5662	-21.3116
8	0.7366	0.0826	0.1939	0.6013	0.3405	1.5404	0.1288	-0.2115	0.0934	0.1808	-0.5216	0.5008	0.2508	-0.7516	-0.0671	0.3847	-0.062	0.0792	0.8968	-0.3064	0.697	-8.2733	-7.8865	-31.1873
9	0.7274	0.4663	0.3905	0.3207	0.2022	1.1855	0.428	-0.6115	-0.1474	0.4505	-0.4929	0.135	0.9982	-0.9813	-0.01	1.0333	-0.4964	0.1853	0.9425	-0.0494	0.6567	0.7041	-22.5356	-9.4273
10	0.2068	0.1543	0.066	0.3655	-0.1284	0.1428	-0.1393	0.2679	0.8406	-0.0967	-0.0351	0.3812	-0.4867	-0.1418	-0.1308	0.8664	0.1094	-0.3775	0.6041	0.2156	0.9411	7.5615	23.5604	-63.6892
11	1.7007	0.5319	-0.1483	1.0467	-0.1295	0.8357	-0.1824	0.1027	0.3367	-0.198	-0.0232	0.4945	-0.1687	-0.3037	-0.0138	0.4636	0.1126	-0.1796	0.5367	-0.0783	0.6119	1.9715	4.6491	-56.2166
12	2.4274	0.0936	-0.4101	0.796	-0.565	0.7783	-0.272	0.5538	1.0033	-0.3597	0.1752	0.3074	-0.3613	-0.1571	0.0073	0.7977	-0.0117	-0.271	0.615	0.2285	0.7689	22.4891	21.7636	-65.1808
13	0.7833	-0.0671	0.2353	0.4194	0.0799	0.1522	0.0573	-0.0027	-0.139	0.2542	-0.1178	0.0705	0.1325	0.1077	-0.0005	0.4812	0.0011	0.016	0.3539	-0.0374	0.4511	33.4342	-27.3615	-61.7457
14	0.4598	0.0088	0.1661	0.9709	0.9341	1.2786	-0.0064	0.0399	-0.0416	-0.1897	-0.001	-0.0341	-0.0656	0.0319	-0.0001	0.4313	0.011	0.0087	0.332	0.0255	0.377	40.3801	-7.3434	-58.976
15	1.7092	-0.5224	0.0345	1.1245	0.7099	0.607	-0.0516	-0.064	-0.3115	0.119	-0.0613	0.3002	0.0443	-0.1952	0.0003	0.4519	-0.0134	0.016	0.442	-0.0489	0.4941	19.4012	-24.2603	-61.9515
16	0.3003	0.1954	-0.3629	0.5044	0.0398	0.6375	-0.0094	-0.0396	0.0353	-0.2102	-0.0288	0.1597	-0.0601	-0.1159	-0.0003	0.4205	-0.0233	-0.0051	0.3371	0.0039	0.4252	54.8975	29.2646	-31.264
17	0.8842	0.6005	0.0897	1.3474	0.4807	0.3982	-0.0149	0.0569	0.0039	-0.1129	-0.0023	-0.1707	-0.057	0.0817	0	0.3777	0.0141	0.0122	0.3332	0.0287	0.3641	54.885	8.9814	-38.5051
18	0.3223	0.5376	-0.1281	1.2211	-0.1175	1.1068	0.0237	-0.1034	0.1324	0.1694	-0.0164	0.1546	-0.1323	-0.1332	0	0.4273	-0.01	-0.0031	0.423	-0.0144	0.4227	47.746	28.1299	-17.4684

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 33 through 71 )	A	33 - 71
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 72 through 216 )	A	72 - 216
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 217 through 405 )	A	217 - 405
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 33 through 71 )	B	33 - 71
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 72 through 216 )	B	72 - 216
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 217 through 405 )	B	217 - 405
7	X-RAY DIFFRACTION	7	chain 'C' and (resid 33 through 71 )	C	33 - 71
8	X-RAY DIFFRACTION	8	chain 'C' and (resid 72 through 216 )	C	72 - 216
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 217 through 404 )	C	217 - 404
10	X-RAY DIFFRACTION	10	chain 'D' and (resid 33 through 71 )	D	33 - 71
11	X-RAY DIFFRACTION	11	chain 'D' and (resid 72 through 216 )	D	72 - 216
12	X-RAY DIFFRACTION	12	chain 'D' and (resid 217 through 405 )	D	217 - 405
13	X-RAY DIFFRACTION	13	chain 'E' and (resid 32 through 71 )	E	32 - 71
14	X-RAY DIFFRACTION	14	chain 'E' and (resid 72 through 216 )	E	72 - 216
15	X-RAY DIFFRACTION	15	chain 'E' and (resid 217 through 405 )	E	217 - 405
16	X-RAY DIFFRACTION	16	chain 'F' and (resid 32 through 71 )	F	32 - 71
17	X-RAY DIFFRACTION	17	chain 'F' and (resid 72 through 216 )	F	72 - 216
18	X-RAY DIFFRACTION	18	chain 'F' and (resid 217 through 405 )	F	217 - 405

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