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

ID or keywords:

Entry

Database: PDB / ID: 8ack

Title

Structure of Pseudomonas aeruginosa aminopeptidase, PaAP

Components

Keratinase KP1
PCP

Keywords

HYDROLASE / WT / Truncation bound to ERWGHDFIK

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: 1.784 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
Revision 1.3	Nov 6, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	8ack.cif.gz	391.1 KB	Display	PDBx/mmCIF format
PDB format	pdb8ack.ent.gz	315.1 KB	Display	PDB format
PDBx/mmJSON format	8ack.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	8ack_validation.pdf.gz	340.6 KB	Display	wwPDB validaton report
Full document	8ack_full_validation.pdf.gz	341 KB	Display
Data in XML	8ack_validation.xml.gz	29.7 KB	Display
Data in CIF	8ack_validation.cif.gz	45.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ac/8ack ftp://data.pdbj.org/pub/pdb/validation_reports/ac/8ack	HTTPS FTP

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Related structure data

Related structure data	8ac7SC 8ac9C 8acgC 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) #133 - Jan 2011 Nitric Oxide Synthase similarity (1) #203 - Nov 2016 Aminopeptidase 1 and Autophagy similarity (1) #75 - Mar 2006 Tissue Factor similarity (1) #90 - Jun 2007 Fatty Acid Synthase similarity (1)

Deposited unit

B: Keratinase KP1

A: Keratinase KP1

P: PCP

C: PCP

hetero molecules

109 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

B: Keratinase KP1

P: PCP

hetero molecules

defined by author&software
Evidence: gel filtration
54.4 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

A: Keratinase KP1

C: PCP

hetero molecules

defined by author&software
54.3 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	63.292, 85.661, 98.097
Angle α, β, γ (deg.)	90.00, 93.85, 90.00
Int Tables number	4
Space group name H-M	P12₁1

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Protein / Protein/peptide , 2 types, 4 molecules BAPC

#1: Protein	Keratinase KP1 Mass: 52621.320 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
#2: Protein/peptide	PCP Mass: 1190.330 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Pseudomonas aeruginosa (bacteria)

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Non-polymers , 4 types, 808 molecules

#3: Chemical	ChemComp-CAC / CACODYLATE ION / dimethylarsinate Mass: 136.989 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₆AsO₂
#4: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Zn
#5: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Formula: Na
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 787 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	Y
Has protein modification	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.45 Å³/Da / Density % sol: 49.87 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.2 M zinc acetate, 0.1 M sodium cacodylate pH6.4, 11.7% 2-propanol

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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: Dec 12, 2021

Radiation

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

Radiation wavelength

Wavelength: 0.9795 Å / Relative weight: 1

Reflection

Resolution: 1.784→64.46 Å / Num. obs: 98441 / % possible obs: 99.1 % / Redundancy: 5.7 % / CC_1/2: 0.997 / R_merge(I) obs: 0.114 / R_pim(I) all: 0.052 / R_rim(I) all: 0.126 / Net I/σ(I): 5.5 / Num. measured all: 566021

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. measured all	Num. unique obs	CC_1/2	R_pim(I) all	R_rim(I) all	Net I/σ(I) obs	% possible all
1.784-1.815	5.8	2.604	28343	4868	0.362	1.167	2.861	0.7	98.7
4.843-64.46	5.5	0.051	27331	4928	0.998	0.023	0.056	13.2	96.7

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Processing

Software

Name	Version	Classification
PHENIX	1.14_3260	refinement
Aimless		data scaling
PDB_EXTRACT	3.27	data extraction
XDS		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 8AC7

8ac7

Resolution: 1.784→42.831 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 22.77 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2101	4754	4.85 %
R_work	0.1713	-	-
obs	0.1731	97971	98.65 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.784→42.831 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7058	0	197	787	8042

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	7398
X-RAY DIFFRACTION	f_angle_d	0.816	10052
X-RAY DIFFRACTION	f_dihedral_angle_d	7.58	4388
X-RAY DIFFRACTION	f_chiral_restr	0.052	1088
X-RAY DIFFRACTION	f_plane_restr	0.006	1338

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 (%)
1.7844-1.8047	0.3819	142	0.3433	2914	X-RAY DIFFRACTION	92
1.8047-1.8259	0.3282	152	0.3239	3014	X-RAY DIFFRACTION	96
1.8259-1.8482	0.3422	169	0.3057	3034	X-RAY DIFFRACTION	98
1.8482-1.8716	0.3097	170	0.2896	3061	X-RAY DIFFRACTION	98
1.8716-1.8962	0.3086	154	0.2749	3115	X-RAY DIFFRACTION	99
1.8962-1.9222	0.2771	146	0.2575	3128	X-RAY DIFFRACTION	98
1.9222-1.9496	0.3138	159	0.2535	3083	X-RAY DIFFRACTION	99
1.9496-1.9787	0.2935	162	0.2475	3136	X-RAY DIFFRACTION	99
1.9787-2.0097	0.2722	147	0.2405	3102	X-RAY DIFFRACTION	99
2.0097-2.0426	0.305	166	0.2276	3136	X-RAY DIFFRACTION	99
2.0426-2.0778	0.2547	172	0.2217	3063	X-RAY DIFFRACTION	100
2.0778-2.1156	0.2507	186	0.2047	3103	X-RAY DIFFRACTION	99
2.1156-2.1563	0.2578	163	0.206	3100	X-RAY DIFFRACTION	100
2.1563-2.2003	0.2468	184	0.1949	3116	X-RAY DIFFRACTION	99
2.2003-2.2481	0.2345	171	0.1911	3088	X-RAY DIFFRACTION	98
2.2481-2.3004	0.2242	162	0.1769	3064	X-RAY DIFFRACTION	99
2.3004-2.358	0.2027	180	0.1757	3146	X-RAY DIFFRACTION	100
2.358-2.4217	0.2532	174	0.1728	3113	X-RAY DIFFRACTION	100
2.4217-2.493	0.2327	176	0.1749	3112	X-RAY DIFFRACTION	100
2.493-2.5734	0.2141	151	0.1708	3142	X-RAY DIFFRACTION	100
2.5734-2.6654	0.1989	168	0.1616	3153	X-RAY DIFFRACTION	100
2.6654-2.7721	0.2182	153	0.1667	3147	X-RAY DIFFRACTION	100
2.7721-2.8982	0.2117	148	0.1599	3146	X-RAY DIFFRACTION	99
2.8982-3.051	0.2246	131	0.1592	3148	X-RAY DIFFRACTION	99
3.051-3.2421	0.1861	131	0.1611	3110	X-RAY DIFFRACTION	98
3.2421-3.4923	0.1719	130	0.1549	3143	X-RAY DIFFRACTION	99
3.4923-3.8435	0.1696	169	0.147	3137	X-RAY DIFFRACTION	99
3.8435-4.3992	0.1508	162	0.1269	3143	X-RAY DIFFRACTION	99
4.3992-5.5407	0.1617	128	0.1331	3176	X-RAY DIFFRACTION	98
5.5407-42.83	0.2158	148	0.1768	3144	X-RAY DIFFRACTION	96

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	1.9876	0.0686	1.4645	2.1484	-0.2915	4.928	-0.0737	-0.1976	0.1062	0.2646	-0.064	0.1392	-0.3679	-0.1704	0.1425	0.2506	0.0099	0.0344	0.1922	-0.0088	0.2249	10.5458	-8.8223	6.6876
2	7.5867	-0.2457	2.8881	0.1846	-0.0894	1.6284	0.0679	-0.7277	0.3408	0.0685	-0.0088	-0.0307	-0.0831	-0.1958	-0.0358	0.3073	-0.0105	0.0574	0.2533	-0.0521	0.3292	36.6732	-18.6467	19.7626
3	3.7527	0.7452	-1.0747	1.3603	-0.1734	2.5692	0.0964	-0.0326	0.1105	0.1052	-0.0212	0.0443	0.043	0.0175	-0.0715	0.2322	0.0043	0.0095	0.1562	0.0202	0.2236	49.5116	-26.3107	14.3981
4	8.6559	0.0104	3.3173	0.1051	-0.2763	2.2774	0.151	-0.8805	0.0956	0.0413	-0.1082	-0.0247	0.0127	-0.2313	-0.0356	0.3395	-0.0032	0.0077	0.2008	-0.0227	0.2651	35.3754	-23.5932	20.5062
5	1.2277	-0.0317	0.2789	1.7234	-0.7422	2.1273	0.0717	0.0826	-0.0542	-0.0989	-0.1993	-0.1835	0.0669	0.4741	0.1048	0.2032	0.0499	0.012	0.267	0.0395	0.2048	22.7056	-13.8129	-3.5083
6	2.5504	-0.728	1.2039	2.3512	0.091	4.2336	0.1307	0.3828	0.1724	-0.2185	-0.0709	-0.1685	-0.24	0.2954	-0.0447	0.2346	0.0045	0.0617	0.2603	0.012	0.2326	67.8884	-2.8043	-39.7269
7	7.6724	-0.3176	3.3517	0.3035	-0.1808	2.5126	-0.135	0.6594	0.2095	-0.0481	0.0526	0.0927	-0.1876	0.1328	0.0854	0.3835	0.018	-0.0086	0.2613	0.0266	0.2742	41.7631	-8.9806	-54.7625
8	3.3665	0.1249	-0.999	1.6892	-0.1436	3.9711	-0.0121	-0.0201	-0.0164	-0.0928	0.0025	-0.0468	-0.0944	-0.155	0.0093	0.2618	0.0123	-0.0019	0.2394	-0.0505	0.2301	28.9597	-17.7411	-51.5317
9	8.8034	-0.8728	3.4067	0.2655	0.1227	2.5004	0.0627	1.0126	-0.0295	-0.0193	-0.0491	0.0085	-0.0542	0.2509	-0.0145	0.4162	0.0218	-0.024	0.3719	0.0011	0.2795	43.0113	-13.6492	-56.8087
10	2.1924	-0.4699	0.0976	1.5893	0.2407	2.4098	0.111	0.0691	-0.1386	0.0846	-0.0718	0.1508	0.2302	-0.2612	-0.0359	0.2636	-0.03	-0.0148	0.216	-0.0142	0.1768	55.7181	-10.3005	-31.0794

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 511 )
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 511 )

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