PDB-8ac7: Structure of Pseudomonas aeruginosa aminopeptidase, PaAP

ID or keywords:

Entry

Database: PDB / ID: 8ac7

Title

Structure of Pseudomonas aeruginosa aminopeptidase, PaAP

Components

Keratinase KP1

Keywords

HYDROLASE / WT / Full-length

Function / homology

Function and homology information

metalloexopeptidase activity / aminopeptidase activity / proteolysis
Similarity search - Function

Biological species

Pseudomonas aeruginosa (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.4 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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Download

PDBx/mmCIF format	8ac7.cif.gz	406.1 KB	Display	PDBx/mmCIF format
PDB format	pdb8ac7.ent.gz	325 KB	Display	PDB format
PDBx/mmJSON format	8ac7.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8ac7_validation.pdf.gz	459.9 KB	Display	wwPDB validaton report
Full document	8ac7_full_validation.pdf.gz	465.4 KB	Display
Data in XML	8ac7_validation.xml.gz	48.3 KB	Display
Data in CIF	8ac7_validation.cif.gz	75.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ac/8ac7 ftp://data.pdbj.org/pub/pdb/validation_reports/ac/8ac7	HTTPS FTP

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Related structure data

Related structure data	8ac9C 8acgC 8ackC 8acrC 1tkjS 5ib9S 6hc6S 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) #70 - Oct 2005 Designer Proteins similarity (1)

Deposited unit

B: Keratinase KP1

A: Keratinase KP1

hetero molecules

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

1

B: Keratinase KP1

hetero molecules

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

2

A: Keratinase KP1

hetero molecules

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

Unit cell

Length a, b, c (Å)	62.952, 85.953, 98.216
Angle α, β, γ (deg.)	90.00, 93.56, 90.00
Int Tables number	4
Space group name H-M	P12₁1

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Protein , 1 types, 2 molecules BA

#1: Protein	Keratinase KP1 Mass: 54973.910 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: E3ULB5

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Non-polymers , 5 types, 1346 molecules

#2: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#3: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Na
#4: Chemical	ChemComp-ACT / ACETATE ION Mass: 59.044 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₂H₃O₂
#5: Chemical	ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL Mass: 60.095 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₃H₈O / Comment: alkaloid*YM
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1318 / 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: 2.41 Å³/Da / Density % sol: 49.01 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.1 M sodium acetate pH 4.5, 0.2 M zinc acetate, 10 % PEG3000, 20 % 2-propanol

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762 Å
Detector	Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Nov 18, 2021
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9762 Å / Relative weight: 1
Reflection	Resolution: 1.4→85.95 Å / Num. obs: 203540 / % possible obs: 99.4 % / Redundancy: 6.8 % / CC_1/2: 0.998 / R_merge(I) obs: 0.057 / R_pim(I) all: 0.023 / R_rim(I) all: 0.061 / Net I/σ(I): 20.6 / Num. measured all: 1375192
Reflection shell	Resolution: 1.4→1.42 Å / % possible obs: 87.7 % / Redundancy: 5.2 % / R_merge(I) obs: 0.66 / Num. measured all: 45920 / Num. unique obs: 8909 / CC_1/2: 0.82 / R_pim(I) all: 0.316 / R_rim(I) all: 0.736 / Net I/σ(I) obs: 1.1

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Processing

Software

Name	Version	Classification
PHENIX	1.14_3260	refinement
xia2	3.6.1	data scaling
PDB_EXTRACT	3.27	data extraction
xia2		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 6HC6, 5IB9, 1TKJ

6hc6

5ib9

1tkj

Resolution: 1.4→64.627 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 17.39 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1749	10041	4.94 %
R_work	0.1558	-	-
obs	0.1567	203411	99.33 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.4→64.627 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7226	0	61	1318	8605

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.005	7470
X-RAY DIFFRACTION	f_angle_d	0.774	10144
X-RAY DIFFRACTION	f_dihedral_angle_d	6.861	4253
X-RAY DIFFRACTION	f_chiral_restr	0.076	1097
X-RAY DIFFRACTION	f_plane_restr	0.005	1357

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 (%)
1.4002-1.4161	0.3383	288	0.298	5509	X-RAY DIFFRACTION	85
1.4161-1.4328	0.2627	321	0.2638	6196	X-RAY DIFFRACTION	96
1.4328-1.4502	0.2581	352	0.2422	6417	X-RAY DIFFRACTION	100
1.4502-1.4686	0.218	342	0.2128	6454	X-RAY DIFFRACTION	100
1.4686-1.4879	0.2366	329	0.203	6465	X-RAY DIFFRACTION	100
1.4879-1.5083	0.2175	353	0.1922	6461	X-RAY DIFFRACTION	100
1.5083-1.5299	0.2178	347	0.1886	6420	X-RAY DIFFRACTION	100
1.5299-1.5527	0.2139	368	0.1787	6467	X-RAY DIFFRACTION	100
1.5527-1.577	0.2102	281	0.1729	6499	X-RAY DIFFRACTION	100
1.577-1.6028	0.1944	344	0.1655	6420	X-RAY DIFFRACTION	100
1.6028-1.6305	0.1871	329	0.1652	6495	X-RAY DIFFRACTION	100
1.6305-1.6601	0.2053	302	0.1651	6532	X-RAY DIFFRACTION	100
1.6601-1.6921	0.1843	328	0.1669	6514	X-RAY DIFFRACTION	100
1.6921-1.7266	0.1904	336	0.169	6400	X-RAY DIFFRACTION	100
1.7266-1.7641	0.187	355	0.1681	6449	X-RAY DIFFRACTION	100
1.7641-1.8052	0.1884	331	0.175	6519	X-RAY DIFFRACTION	100
1.8052-1.8503	0.1873	351	0.1713	6468	X-RAY DIFFRACTION	100
1.8503-1.9004	0.1911	358	0.1669	6447	X-RAY DIFFRACTION	100
1.9004-1.9563	0.17	340	0.1619	6489	X-RAY DIFFRACTION	100
1.9563-2.0194	0.1873	358	0.1595	6442	X-RAY DIFFRACTION	100
2.0194-2.0916	0.1828	323	0.1578	6527	X-RAY DIFFRACTION	100
2.0916-2.1754	0.1756	332	0.1531	6500	X-RAY DIFFRACTION	100
2.1754-2.2744	0.1682	374	0.1484	6431	X-RAY DIFFRACTION	100
2.2744-2.3943	0.1768	333	0.1496	6484	X-RAY DIFFRACTION	100
2.3943-2.5443	0.1747	322	0.1498	6535	X-RAY DIFFRACTION	100
2.5443-2.7407	0.1728	310	0.1477	6554	X-RAY DIFFRACTION	100
2.7407-3.0165	0.1827	324	0.1506	6516	X-RAY DIFFRACTION	100
3.0165-3.453	0.1486	315	0.1429	6576	X-RAY DIFFRACTION	100
3.453-4.3503	0.1452	336	0.1324	6541	X-RAY DIFFRACTION	100
4.3503-64.625	0.1521	359	0.1444	6643	X-RAY DIFFRACTION	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	1.6996	-0.6924	1.0131	1.3173	-0.2084	2.9752	0.0195	0.1687	0.1236	-0.0581	-0.0177	-0.1525	-0.152	0.1783	0.0276	0.1209	-0.0206	0.0315	0.1327	0.013	0.1345	4.3956	24.9441	-39.7413
2	7.1934	-0.5988	2.3479	0.4797	-0.3053	1.2589	0.078	0.4294	0.1806	-0.093	-0.0444	0.096	0.0001	0.116	-0.0263	0.171	-0.0089	0.0137	0.1188	0.018	0.1243	-21.8586	19.0566	-54.8775
3	2.3107	0.3568	-0.5349	1.1213	0.0781	2.3149	-0.0035	-0.0597	-0.0602	-0.0193	0.0021	-0.0309	0.0653	-0.0456	0.0014	0.0846	0.0024	0.0009	0.0777	-0.0145	0.0952	-34.4159	10.0941	-51.6081
4	6.2351	-0.6172	2.4039	0.1526	-0.0784	2.0316	0.0891	0.7159	-0.017	-0.0266	-0.0563	-0.0111	0.0235	0.2392	-0.0387	0.1502	-0.004	0.0029	0.0904	-0.0063	0.1191	-20.487	14.3316	-56.9375
5	1.1674	-0.4684	0.07	0.9463	-0.1637	1.0345	0.0065	0.0326	-0.0614	0.0236	0.0263	0.1015	0.0075	-0.0916	-0.0337	0.1101	-0.0038	-0.0015	0.1062	-0.0028	0.1024	-8.6925	18.1425	-32.5776
6	1.4407	0.137	1.307	1.0727	-0.2238	3.8957	-0.0398	-0.1185	0.0864	0.1062	-0.0033	0.1056	-0.2091	-0.1486	0.0444	0.12	0.0242	0.0268	0.0935	-0.013	0.1252	-52.494	18.9037	6.6611
7	6.3975	0.176	1.9407	0.1838	0.0647	1.1249	0.0348	-0.4628	0.2999	0.0495	-0.0106	-0.0431	-0.0231	-0.0428	-0.0135	0.1688	0.0023	0.0256	0.1441	-0.0455	0.1784	-26.9026	9.1118	19.5252
8	3	0.2419	-0.7227	1.1035	-0.0333	2.1384	0.025	-0.0186	0.0565	0.0249	-0.0017	0.0058	0.0948	0.0552	-0.0285	0.1009	0.0002	0.0001	0.082	0.0071	0.101	-13.7286	1.3972	14.4247
9	6.8912	0.0536	2.96	0.0611	-0.2213	2.3004	0.1727	-0.6537	-0.0294	0.0236	-0.0657	-0.0149	0.0807	-0.1572	-0.106	0.1503	0.0058	0.0109	0.0893	-0.0181	0.1407	-27.7595	4.213	20.5042
10	0.8101	0.113	0.1401	0.7653	-0.2027	0.9346	-0.0017	0.0262	0.0025	-0.0062	-0.0388	-0.0897	-0.0421	0.1728	0.0384	0.1061	0.0093	-0.0001	0.1215	0.0132	0.1137	-39.5102	14.1485	-2.1413
11	1.6029	-0.3276	0.9597	0.8666	-0.2722	1.3916	0.0308	0.0994	0.0014	-0.0532	-0.0488	-0.0881	-0.0225	0.1208	0.0054	0.1076	-0.0025	0.0328	0.1336	0.0217	0.111	-40.0482	12.333	-7.2081
12	1.4529	-0.0407	0.6994	0.5772	0.1113	1.3902	0.0201	-0.0737	-0.1248	0.0505	0.0298	0.0972	0.0539	-0.1191	-0.0605	0.1255	0.0077	0.0189	0.124	0.001	0.1164	-8.3018	14.5251	-27.9129

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'B' and (resid 44 through 105 )
2	X-RAY DIFFRACTION	2	chain 'B' and (resid 106 through 143 )
3	X-RAY DIFFRACTION	3	chain 'B' and (resid 144 through 256 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 257 through 281 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 282 through 477 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 44 through 105 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 106 through 143 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 144 through 256 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 257 through 281 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 282 through 477 )
11	X-RAY DIFFRACTION	11	chain 'A' and (resid 478 through 536 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 478 through 536 )

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