PDB-7nlk: LasB, N-aryl-2-butylmercaptoacetamide

ID or keywords:

Entry

Database: PDB / ID: 7nlk

Title

LasB, N-aryl-2-butylmercaptoacetamide

Components

Pro-elastase

Keywords

HYDROLASE / LasB / N-aryl-2-butylmercaptoacetamide inhibitor complex

Function / homology

Function and homology information

pseudolysin / metalloendopeptidase activity / proteolysis / extracellular region / metal ion binding
Similarity search - Function

Biological species

Pseudomonas aeruginosa (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.7 Å

Authors

Koehnke, J. / Sikandar, A.

Funding support

Germany, 1items

Citation

Journal: to be published
Title: LasB, N-aryl-2-butylmercaptoacetamide inhibitor complex
Authors: Koehnke, J. / Sikandar, A.

History

Deposition	Feb 22, 2021	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Sep 7, 2022	Provider: repository / Type: Initial release
Revision 1.1	Jan 31, 2024	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	7nlk.cif.gz	251.3 KB	Display	PDBx/mmCIF format
PDB format	pdb7nlk.ent.gz	200.3 KB	Display	PDB format
PDBx/mmJSON format	7nlk.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	7nlk_validation.pdf.gz	998.4 KB	Display	wwPDB validaton report
Full document	7nlk_full_validation.pdf.gz	1002.4 KB	Display
Data in XML	7nlk_validation.xml.gz	28.4 KB	Display
Data in CIF	7nlk_validation.cif.gz	42.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/nl/7nlk ftp://data.pdbj.org/pub/pdb/validation_reports/nl/7nlk	HTTPS FTP

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Related structure data

Related structure data	7nlmC 1ezmS 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

Deposited unit

A: Pro-elastase

B: Pro-elastase

hetero molecules

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

1

A: Pro-elastase

hetero molecules

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

2

B: Pro-elastase

hetero molecules

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

Unit cell

Length a, b, c (Å)	43.771, 91.977, 67.088
Angle α, β, γ (deg.)	90.00, 92.80, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Pro-elastase Mass: 33059.324 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (strain UCBPP-PA14) (bacteria) Strain: UCBPP-PA14 / Gene: lasB, PA14_16250 Production host: Pseudomonas aeruginosa UCBPP-PA14 (bacteria) References: UniProt: Q02RJ6
#2: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical	ChemComp-UHK / (S)-2-mercapto-4-methyl-N-(p-tolyl)pentanamide / (2~{S})-4-methyl-~{N}-(4-methylphenyl)-2-sulfanyl-pentanamide Mass: 237.361 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C₁₃H₁₉NOS / Feature type: SUBJECT OF INVESTIGATION
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 498 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	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: 2.06 Å³/Da / Density % sol: 40.2 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.2 M Ammonium iodide, and 20% (w/v) PEG 3350

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0332 Å
Detector	Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 5, 2020
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.0332 Å / Relative weight: 1
Reflection	Resolution: 1.7→45.99 Å / Num. obs: 58319 / % possible obs: 99.7 % / Redundancy: 4.7 % / CC_1/2: 0.99 / R_merge(I) obs: 0.05 / Net I/σ(I): 8.7
Reflection shell	Resolution: 1.7→1.73 Å / R_merge(I) obs: 0.2 / Num. unique obs: 5778 / CC_1/2: 0.88

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Processing

Software

Name	Version	Classification
PHENIX	(1.18.2_3874: ???)	refinement
XDS		data reduction
SCALA		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1ezm

1ezm

Resolution: 1.7→45.99 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.89 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1909	2807	4.84 %
R_work	0.1627	-	-
obs	0.164	58022	99.5 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.7→45.99 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4618	0	36	498	5152

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.011	4788
X-RAY DIFFRACTION	f_angle_d	1.324	6490
X-RAY DIFFRACTION	f_dihedral_angle_d	14.952	672
X-RAY DIFFRACTION	f_chiral_restr	0.06	650
X-RAY DIFFRACTION	f_plane_restr	0.009	864

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 (%)
1.7-1.73	0.2685	150	0.2251	2718	X-RAY DIFFRACTION	99
1.73-1.76	0.2199	143	0.2025	2767	X-RAY DIFFRACTION	100
1.76-1.79	0.2216	157	0.1931	2716	X-RAY DIFFRACTION	100
1.79-1.83	0.2347	141	0.1973	2796	X-RAY DIFFRACTION	100
1.83-1.87	0.2352	160	0.1853	2712	X-RAY DIFFRACTION	100
1.87-1.91	0.2202	120	0.1752	2818	X-RAY DIFFRACTION	100
1.91-1.96	0.1822	135	0.1711	2735	X-RAY DIFFRACTION	100
1.96-2.02	0.2101	132	0.1626	2774	X-RAY DIFFRACTION	100
2.02-2.07	0.2059	153	0.1641	2753	X-RAY DIFFRACTION	100
2.07-2.14	0.1995	165	0.1545	2705	X-RAY DIFFRACTION	100
2.14-2.22	0.1813	161	0.1528	2743	X-RAY DIFFRACTION	100
2.22-2.31	0.1793	171	0.1438	2761	X-RAY DIFFRACTION	100
2.31-2.41	0.1964	125	0.1448	2769	X-RAY DIFFRACTION	100
2.41-2.54	0.1492	98	0.1515	2793	X-RAY DIFFRACTION	100
2.54-2.7	0.1645	144	0.1558	2784	X-RAY DIFFRACTION	100
2.7-2.91	0.1913	155	0.1546	2759	X-RAY DIFFRACTION	100
2.91-3.2	0.1793	125	0.1579	2774	X-RAY DIFFRACTION	100
3.2-3.66	0.1614	151	0.1471	2782	X-RAY DIFFRACTION	100
3.66-4.61	0.1371	115	0.142	2788	X-RAY DIFFRACTION	100
4.61-45.99	0.2485	106	0.1902	2768	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	2.0978	-0.0222	0.1935	1.9614	0.2125	1.5466	-0.0093	0.0665	0.5133	-0.0523	0.0383	-0.0646	-0.3324	-0.1006	-0.0066	0.126	0.0224	0.0174	0.0908	0.0469	0.1668	1.0689	16.622	-32.3872
2	2.3046	0.5034	-0.4702	1.6151	-0.1866	1.5992	0.0264	0.0211	0.1297	0.0331	-0.0296	0.0393	-0.0035	0.0616	-0.0064	0.0597	0.0035	-0.0076	0.0766	0.0041	0.0494	-7.5893	3.1709	-25.6338
3	1.9152	-0.0567	-0.8146	1.7265	-0.2541	1.7738	-0.0956	0.0842	-0.2961	-0.0459	0.0074	0.1518	0.2489	-0.1509	0.0027	0.0615	-0.0163	0.0016	0.0726	-0.0235	0.1168	-16.1226	-6.3826	-25.2184
4	3.2038	-0.3398	1.1641	3.9379	-3.4813	7.4244	0.1581	0.1663	0.1077	-0.2932	-0.1372	-0.2349	-0.0264	0.3646	0.0195	0.0869	0.021	0.0213	0.072	0.0145	0.0893	30.5844	10.2876	-0.8007
5	1.2025	-0.5467	0.1776	1.9058	0.0705	0.4143	0.3869	0.3884	0.7085	-0.1836	0.0542	-0.1573	-0.5207	-0.2207	-0.1872	0.3923	0.1145	0.1746	0.072	0.1556	0.3547	22.2492	21.7062	-4.598
6	2.0342	0.4203	0.0119	2.1309	-0.0215	1.3039	0.0793	0.1257	0.3784	0.0118	0.0157	0.0061	-0.2748	-0.1846	-0.0095	0.1247	0.0506	0.0354	0.1012	0.0417	0.1285	18.4985	14.1207	0.6668
7	2.3641	-1.0404	1.7139	2.991	0.5357	2.0502	0.0692	-0.409	0.0551	0.2094	0.169	0.2267	-0.2876	-0.2454	-0.1441	0.1536	0.0068	0.0836	0.1719	0.0296	0.1719	18.4833	15.2899	10.0967
8	4.8916	-0.5796	0.8368	2.1805	-0.2515	2.8879	0.1385	0.1831	0.5175	-0.0266	0.02	0.4112	-0.1842	-0.2256	-0.0338	0.0763	0.0268	-0.0076	0.0732	0.0362	0.1785	5.3071	8.3964	6.1303
9	3.1671	-0.5696	-2.7104	2.1079	0.0323	5.4661	0.0222	-0.0186	0.0612	-0.0567	-0.0393	0.0632	0.0649	0.1535	0.0125	0.052	0.0107	-0.0261	0.0689	0.0015	0.061	11.0804	1.4586	5.3634
10	3.3564	1.2164	0.9909	3.7414	0.0966	1.6164	0.087	-0.2145	-0.0722	0.1099	-0.1789	-0.2348	-0.0492	0.1252	0.0436	0.0603	0.005	-0.0212	0.1214	0.0232	0.0901	20.9949	-0.1077	11.7913
11	1.9449	0.0259	-0.5627	1.843	-0.462	1.9496	-0.0104	0.0876	-0.2457	-0.1386	0.0229	0.2473	0.2305	-0.187	0.0154	0.0677	-0.0196	-0.0278	0.0724	-0.0129	0.1293	4.2046	-6.4296	8.6508

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 134 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 135 through 202 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 203 through 298 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 1 through 17 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 18 through 61 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 62 through 112 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 113 through 134 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 135 through 156 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 157 through 179 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 180 through 202 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 203 through 298 )

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