PDB-5n4b: Prolyl oligopeptidase B from Galerina marginata bound to 25mer ma...

ID or keywords:

Entry

Database: PDB / ID: 5n4b

Title

Prolyl oligopeptidase B from Galerina marginata bound to 25mer macrocyclization substrate - S577A mutant

Components

Alpha-amanitin proprotein
Prolyl oligopeptidase

Keywords

HYDROLASE / amanitin biosynthesis / prolyl oligopeptidase / macrocyclase / peptidase / beta-propeller / closed form

Function / homology

Function and homology information

prolyl oligopeptidase / oligopeptidase activity / toxin activity / serine-type endopeptidase activity / proteolysis / cytosol
Similarity search - Function

Biological species

Galerina marginata (funeral bell)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.44 Å

Authors

Czekster, C.M. / McMahon, S.A. / Ludewig, H. / Naismith, J.H.

Funding support

United Kingdom, 1items

Citation

Journal: Nat Commun / Year: 2017
Title: Characterization of a dual function macrocyclase enables design and use of efficient macrocyclization substrates.
Authors: Czekster, C.M. / Ludewig, H. / McMahon, S.A. / Naismith, J.H.

History

Deposition	Feb 10, 2017	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Nov 1, 2017	Provider: repository / Type: Initial release
Revision 1.1	Nov 8, 2017	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2	Oct 16, 2019	Group: Data collection / Category: reflns_shell
Revision 1.3	Jan 17, 2024	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	5n4b.cif.gz	625.1 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	5n4b_validation.pdf.gz	449.6 KB	Display	wwPDB validaton report
Full document	5n4b_full_validation.pdf.gz	461.4 KB	Display
Data in XML	5n4b_validation.xml.gz	71.5 KB	Display
Data in CIF	5n4b_validation.cif.gz	111.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/n4/5n4b ftp://data.pdbj.org/pub/pdb/validation_reports/n4/5n4b	HTTPS FTP

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Related structure data

Related structure data	5n4cC 5n4dC 5n4eC 5n4fC 1h2zS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5n4d-1 5n4e-2 2r9q-2 5n4d-2 5lmg-d 5n4c-3 7ne7-d 5n4e-1 2iwz-d 2xe4-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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	#202 - Oct 2016 Dipeptidyl Peptidase 4 similarity (4)

Deposited unit

A: Prolyl oligopeptidase

B: Prolyl oligopeptidase

D: Alpha-amanitin proprotein

C: Alpha-amanitin proprotein

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

1

A: Prolyl oligopeptidase

D: Alpha-amanitin proprotein

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

2

B: Prolyl oligopeptidase

C: Alpha-amanitin proprotein

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

Unit cell

Length a, b, c (Å)	99.084, 114.716, 141.265
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Prolyl oligopeptidase Mass: 81917.648 Da / Num. of mol.: 2 / Mutation: S577A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Galerina marginata (funeral bell) / Gene: POPB / Plasmid: pJ411 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: H2E7Q8
#2: Protein/peptide	Alpha-amanitin proprotein Mass: 2701.964 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Galerina marginata (funeral bell) / References: UniProt: H2E7Q5, UniProt: A0A067SLB9*PLUS
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1941 / 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: 2.37 Å³/Da / Density % sol: 48.14 % / Description: small tiles
Crystal grow	Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 9 Details: 28% PEG6000, 100 mM Bicine pH 9.0, 60 mM Magnesium formate, and 2.42% DMSO, 12.5mM Hexammine cobalt chloride, cryoprotected with 12% glycerol

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.961 Å
Detector	Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Sep 18, 2015
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.961 Å / Relative weight: 1
Reflection	Resolution: 1.44→100 Å / Num. obs: 288485 / % possible obs: 99.68 % / Redundancy: 6.6 % / R_merge(I) obs: 0.114 / Net I/σ(I): 9.26

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Processing

Software

Name	Version	Classification
PHENIX	(1.11rc2_2522: ???)	refinement
xia2		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1h2z

1h2z

Resolution: 1.44→43.561 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.57 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1814	14680	5.09 %
R_work	0.1553	-	-
obs	0.1566	288430	99.68 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.44→43.561 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	11716	0	0	1941	13657

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.013	12184
X-RAY DIFFRACTION	f_angle_d	1.216	16590
X-RAY DIFFRACTION	f_dihedral_angle_d	15.165	4409
X-RAY DIFFRACTION	f_chiral_restr	0.095	1752
X-RAY DIFFRACTION	f_plane_restr	0.009	2166

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 (%)
1.44-1.4564	0.2624	472	0.2379	8772	X-RAY DIFFRACTION	96
1.4564-1.4735	0.2308	510	0.2197	9012	X-RAY DIFFRACTION	100
1.4735-1.4915	0.2368	469	0.2049	9078	X-RAY DIFFRACTION	100
1.4915-1.5104	0.2281	496	0.1912	9066	X-RAY DIFFRACTION	100
1.5104-1.5302	0.2194	471	0.1822	9091	X-RAY DIFFRACTION	100
1.5302-1.5512	0.2195	461	0.1737	9128	X-RAY DIFFRACTION	100
1.5512-1.5734	0.207	463	0.1664	9096	X-RAY DIFFRACTION	100
1.5734-1.5968	0.1895	528	0.1616	9079	X-RAY DIFFRACTION	100
1.5968-1.6218	0.1884	466	0.1593	9093	X-RAY DIFFRACTION	100
1.6218-1.6484	0.188	473	0.1552	9088	X-RAY DIFFRACTION	100
1.6484-1.6768	0.1939	485	0.1541	9094	X-RAY DIFFRACTION	100
1.6768-1.7073	0.1834	462	0.1547	9176	X-RAY DIFFRACTION	100
1.7073-1.7401	0.1895	491	0.1565	9093	X-RAY DIFFRACTION	100
1.7401-1.7757	0.1891	476	0.1541	9052	X-RAY DIFFRACTION	100
1.7757-1.8143	0.1667	491	0.1532	9144	X-RAY DIFFRACTION	100
1.8143-1.8565	0.1896	509	0.1501	9103	X-RAY DIFFRACTION	100
1.8565-1.9029	0.176	477	0.1536	9098	X-RAY DIFFRACTION	100
1.9029-1.9544	0.1686	485	0.147	9119	X-RAY DIFFRACTION	100
1.9544-2.0119	0.1804	488	0.1428	9080	X-RAY DIFFRACTION	100
2.0119-2.0768	0.1546	499	0.143	9084	X-RAY DIFFRACTION	99
2.0768-2.151	0.1787	496	0.1464	9096	X-RAY DIFFRACTION	100
2.151-2.2372	0.1695	464	0.1404	9099	X-RAY DIFFRACTION	99
2.2372-2.339	0.1621	467	0.1395	9199	X-RAY DIFFRACTION	100
2.339-2.4623	0.1672	502	0.1409	8993	X-RAY DIFFRACTION	98
2.4623-2.6165	0.1796	477	0.1516	9234	X-RAY DIFFRACTION	100
2.6165-2.8185	0.1888	533	0.1544	9144	X-RAY DIFFRACTION	100
2.8185-3.1021	0.194	540	0.1569	9211	X-RAY DIFFRACTION	100
3.1021-3.5508	0.1714	500	0.1522	9275	X-RAY DIFFRACTION	100
3.5508-4.4729	0.1547	491	0.139	9368	X-RAY DIFFRACTION	100
4.4729-43.5812	0.1872	538	0.1762	9585	X-RAY DIFFRACTION	99

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	0.2667	-0.1308	-0.0252	-0.0112	0.15	0.2096	0.0282	0.0161	-0.0498	0.0158	-0.0519	-0.0187	0.0144	0.089	-0.0233	0.0565	0.0167	0.0067	0.0384	-0.0028	0.0601	18.8161	75.6285	19.5001
2	0.384	0.0041	0.0222	0.3382	0.004	0.2406	0.0199	-0.0229	-0.06	0.0028	0.0023	0.0002	0.0118	-0.0015	0.1082	0.0418	-0.0059	0.0015	0.0353	0.0086	0.0437	3.3717	68.7912	42.0732
3	0.2885	-0.0307	-0.0107	0.1078	0.1286	0.1876	0.002	0.0395	0.0055	0.0069	-0.021	0.0167	0.0146	0.0043	-0.0671	0.0541	0.0035	0.0039	0.0408	0.0085	0.0416	6.0148	81.827	18.0305
4	0.2292	-0.0792	0.0827	-0.0024	0.0183	0.2324	0.01	-0.0188	0.0227	0.0032	-0.0342	0.0095	-0.0279	-0.0692	-0.0179	0.0571	-0.0024	-0.0045	0.0561	-0.0019	0.0494	30.7555	34.8559	27.7264
5	0.2557	-0.0344	-0.048	0.3089	0.0555	0.218	-0.0151	-0.0276	0.0924	-0.0151	0.0122	0.0073	-0.0411	-0.0526	-0.0003	0.0735	0.0061	-0.0096	0.0677	-0.0056	0.0749	41.4212	50.9108	41.9785
6	0.0388	-0.0125	-0.0007	0.024	-0.0127	0.026	0.027	-0.0105	0.0923	0.001	0.0071	-0.0761	-0.0434	0.0686	0	0.0567	-0.0072	-0.0134	0.0519	-0.0272	0.0901	63.7361	42.7821	42.4497
7	0.2123	0.0236	0.0612	0.0898	0.1085	0.1899	0.0062	-0.0236	-0.0366	0.0121	-0.0037	-0.0287	0.0217	-0.0005	-0.0248	0.0527	-0.0015	-0.0098	0.0523	-0.0029	0.0631	51.2812	22.3257	32.9474
8	0.2452	-0.0067	0.0841	0.3434	-0.074	0.2404	0.0008	0.0552	0.0281	0.0416	-0.02	-0.0381	-0.0467	-0.017	-0.0467	0.0669	0.0059	-0.0062	0.0517	-0.0001	0.0474	41.7227	35.5258	11.655
9	0.0095	-0.001	0.0001	0.0036	-0.0001	0.0028	0.0045	0.0064	-0.0074	-0.0225	0.0086	0.0233	-0.0062	0.0029	-0	0.4009	0.0218	0.0035	0.3359	0.0196	0.4688	10.1474	80.8116	24.7975
10	0.0036	0.0011	0.0012	0.0164	0.0117	0.0051	-0.0219	-0.0714	-0.0333	-0.0915	0.0493	0.1112	0.0073	-0.0342	0	0.1231	-0.0174	-0.0182	0.089	0.0182	0.11	9.8367	80.9158	39.0362
11	0.0172	-0.0008	-0.0008	0.0017	0.0001	0.0036	0.0076	0.0129	0.0106	-0.0221	0.0058	-0.0063	0.0048	0.0004	-0	0.3801	0.0065	-0.0159	0.334	0.0128	0.4408	39.3897	30.5526	25.0252
12	0.0092	-0.0093	0.0014	0.0218	-0.0116	0.0051	-0.0883	-0.0357	0.0435	-0.0751	0.0425	-0.158	0.0025	-0.0328	0	0.1208	-0.0181	0.014	0.1087	-0.0248	0.1183	39.709	30.2869	39.1933

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 6 through 112 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 113 through 403 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 404 through 727 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 6 through 163 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 164 through 313 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 314 through 348 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 349 through 518 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 519 through 727 )
9	X-RAY DIFFRACTION	9	chain 'D' and (resid 9 through 13 )
10	X-RAY DIFFRACTION	10	chain 'D' and (resid 14 through 25 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 9 through 13 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 14 through 25 )

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