PDB-7zb1: S580A with 18mer

ID or keywords:

Entry

Database: PDB / ID: 7zb1

Title

S580A with 18mer

Components

18mer
Prolyl endopeptidase

Keywords

LYASE / macrocyclase for omphalotin A biosynthesis

Function / homology

BICARBONATE ION

Function and homology information

Biological species

Omphalotus olearius (fungus)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 2 Å

Authors

Song, H. / Naismith, J.H.

Funding support

United Kingdom, 1items

Citation

Journal: Biorxiv / Year: 2022
Title: Molecular basis for the enzymatic macrocyclization of multiply backbone N-methylated peptides
Authors: Matabaro, E. / Song, H. / Gherlone, F. / Sonderegger, L. / Giltrap, A. / Liver, S. / Gossert, A. / Kunzler, M. / Naismith, J.H.

History

Deposition	Mar 23, 2022	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jul 6, 2022	Provider: repository / Type: Initial release
Revision 1.1	Jan 25, 2023	Group: 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.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2	Feb 7, 2024	Group: Data collection / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_conn / struct_ncs_dom_lim Item: _struct_conn.pdbx_leaving_atom_flag / _struct_ncs_dom_lim.beg_auth_comp_id ..._struct_conn.pdbx_leaving_atom_flag / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7zb1.cif.gz	1.1 MB	Display	PDBx/mmCIF format
PDB format	pdb7zb1.ent.gz	979.1 KB	Display	PDB format
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Validation report

Summary document	7zb1_validation.pdf.gz	527 KB	Display	wwPDB validaton report
Full document	7zb1_full_validation.pdf.gz	546.2 KB	Display
Data in XML	7zb1_validation.xml.gz	102.9 KB	Display
Data in CIF	7zb1_validation.cif.gz	145.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/zb/7zb1 ftp://data.pdbj.org/pub/pdb/validation_reports/zb/7zb1	HTTPS FTP

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Related structure data

Related structure data	7zazC 7zb0C 7zb2C 5n4cS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#244 - Apr 2020 Photosynthetic Supercomplexes similarity (1) #49 - Jan 2004 Carbonic Anhydrase similarity (1) #59 - Nov 2004 Photosystem II similarity (1)

Deposited unit

A: Prolyl endopeptidase

B: Prolyl endopeptidase

C: Prolyl endopeptidase

D: Prolyl endopeptidase

E: 18mer

F: 18mer

G: 18mer

H: 18mer

hetero molecules

347 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Prolyl endopeptidase

E: 18mer

hetero molecules

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

2

B: Prolyl endopeptidase

F: 18mer

hetero molecules

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

3

C: Prolyl endopeptidase

G: 18mer

hetero molecules

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

4

D: Prolyl endopeptidase

H: 18mer

hetero molecules

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

Unit cell

Length a, b, c (Å)	70.010, 104.610, 110.650
Angle α, β, γ (deg.)	115.810, 98.870, 93.790
Int Tables number	1
Space group name H-M	P1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
1	2	A
2	2	C
1	3	A
2	3	D
1	4	B
2	4	C
1	5	B
2	5	D
1	6	C
2	6	D

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	PHE	PHE	THR	THR	A	A	3 - 731	3 - 731
2	1	PHE	PHE	THR	THR	B	B	3 - 731	3 - 731
1	2	PRO	PRO	GLN	GLN	A	A	4 - 730	4 - 730
2	2	PRO	PRO	GLN	GLN	C	C	4 - 730	4 - 730
1	3	PRO	PRO	THR	THR	A	A	4 - 731	4 - 731
2	3	PRO	PRO	THR	THR	D	D	4 - 731	4 - 731
1	4	PRO	PRO	MET	MET	B	B	4 - 729	4 - 729
2	4	PRO	PRO	MET	MET	C	C	4 - 729	4 - 729
1	5	PRO	PRO	THR	THR	B	B	4 - 731	4 - 731
2	5	PRO	PRO	THR	THR	D	D	4 - 731	4 - 731
1	6	PRO	PRO	GLN	GLN	C	C	4 - 730	4 - 730
2	6	PRO	PRO	GLN	GLN	D	D	4 - 730	4 - 730

NCS ensembles :

ID
1
2
3
4
5
6

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Protein / Protein/peptide , 2 types, 8 molecules ABCDEFGH

#1: Protein	Prolyl endopeptidase / macrocyclase / OphP Mass: 84445.562 Da / Num. of mol.: 4 / Mutation: S580A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Omphalotus olearius (fungus) / Production host: Komagataella pastoris (fungus) / Strain (production host): GS115
#2: Protein/peptide	18mer Mass: 1985.473 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Omphalotus olearius (fungus) / Production host: Escherichia coli BL21(DE3) (bacteria)

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Non-polymers , 5 types, 707 molecules

#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Na
#5: Chemical	ChemComp-BCT / BICARBONATE ION Mass: 61.017 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CHO₃ / Comment: pH buffer*YM
#6: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 682 / Source method: isolated from a natural source / Formula: H₂O

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Details

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: 2.08 Å³/Da / Density % sol: 40.79 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.2 M sodium acetate, 0.1 M Bis-Tris propane (pH 6.0-6.5) and 28% PEG 3350

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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 EIGER X 16M / Detector: PIXEL / Date: Jun 28, 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: 2→55.84 Å / Num. obs: 182773 / % possible obs: 98 % / Redundancy: 3.3 % / CC_1/2: 0.996 / R_merge(I) obs: 0.09 / R_rim(I) all: 0.108 / Net I/σ(I): 15
Reflection shell	Resolution: 2→2.03 Å / Redundancy: 3.5 % / R_merge(I) obs: 1.234 / Mean I/σ(I) obs: 1 / Num. unique obs: 8886 / CC_1/2: 0.545 / R_rim(I) all: 1.46 / % possible all: 96.9

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Phasing

Phasing	Method: molecular replacement

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0267	refinement
APEX		data reduction
Aimless		data scaling
PHASER		phasing
PDB_EXTRACT	3.27	data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5N4C

5n4c

Resolution: 2→55.84 Å / Cor.coef. F_o:F_c: 0.962 / Cor.coef. F_o:F_c free: 0.945 / SU B: 17.769 / SU ML: 0.216 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.236 / ESU R Free: 0.182 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.238	9445	5.2 %	RANDOM
R_work	0.2053	-	-	-
obs	0.207	173300	97.93 %	-

Solvent computation

Ion probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å / Solvent model: MASK

Displacement parameters

B_iso max: 166.76 Å² / B_iso mean: 45.089 Å² / B_iso min: 22.36 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	3.19 Å²	1.21 Å²	0.6 Å²
2-	-	-0.25 Å²	-1.28 Å²
3-	-	-	-1.26 Å²

Refinement step

Cycle: final / Resolution: 2→55.84 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	23327	0	54	682	24063
B_iso mean	-	-	63.16	43.18	-
Num. residues	-	-	-	-	2916

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.013	24099
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.015	21787
X-RAY DIFFRACTION	r_angle_refined_deg	1.431	1.649	32683
X-RAY DIFFRACTION	r_angle_other_deg	1.216	1.577	50312
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.086	5	2900
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	31.162	21.935	1328
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.98	15	3831
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.634	15	152
X-RAY DIFFRACTION	r_chiral_restr	0.064	0.2	3007
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	27432
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	5808

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-ID	Dom-ID	Auth asym-ID	Number	Rms dev position (Å)
1	1	A	23592	0.07
1	2	B	23592	0.07
2	1	A	23581	0.07
2	2	C	23581	0.07
3	1	A	23439	0.08
3	2	D	23439	0.08
4	1	B	23756	0.07
4	2	C	23756	0.07
5	1	B	23672	0.08
5	2	D	23672	0.08
6	1	C	23762	0.07
6	2	D	23762	0.07

LS refinement shell

Resolution: 2→2.052 Å / R_factor R_free error: 0 / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.351	666	-
R_work	0.332	12735	-
all	-	13401	-
obs	-	-	96.86 %

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	1.4539	-0.3805	-0.3017	1.4395	0.6339	2.801	-0.1461	-0.2866	-0.3219	0.2167	0.4255	-0.1268	0.654	0.6382	-0.2794	0.1618	0.1737	-0.0865	0.5915	-0.1782	0.5648	4.4092	-5.6456	84.945
2	3.7293	1.3941	0.3061	0.8999	0.6513	0.8821	0.0191	-0.4094	-0.2226	0.1973	-0.0683	0.0045	0.2652	-0.0659	0.0492	0.1195	0.0448	0.0178	0.5167	-0.105	0.4665	-33.1708	-1.3342	97.9836
3	1.9554	0.3822	-2.4572	1.1577	0.0672	4.9648	-0.3166	-0.1482	-0.4464	0.1532	0.0101	0.0876	0.3092	0.0882	0.3065	0.1299	0.0402	0.099	0.3003	-0.0732	0.5067	-32.7522	-15.4603	83.9826
4	0.8007	0.0893	-0.642	0.8089	0.6779	1.5846	-0.0681	0.1303	-0.1009	-0.0928	-0.151	0.2098	-0.079	-0.4076	0.2192	0.0328	0.0285	-0.0643	0.5135	-0.2359	0.5205	-35.0577	2.0193	69.6698
5	1.0342	-0.2066	-0.3579	0.9604	0.6668	1.5635	-0.0061	-0.1918	0.0831	-0.0608	0.069	-0.0204	-0.1345	0.1878	-0.0629	0.0176	-0.0043	-0.0379	0.3543	-0.2087	0.4284	-12.8546	13.8787	83.3936
6	1.1681	0.2157	-0.4585	1.4558	1.054	2.8204	-0.1081	-0.3375	-0.0633	0.1414	0.2089	-0.0733	0.3655	0.4633	-0.1007	0.0651	0.0942	-0.0902	0.4888	-0.1855	0.4618	-4.2175	2.4073	92.4814
7	2.1988	0.3973	0.5886	1.1675	0.7913	3.0278	0.0555	0.3624	0.5675	-0.0921	0.0088	-0.0456	-0.2665	0.5716	-0.0642	0.0305	-0.0286	0.0249	0.669	-0.0077	0.9029	-10.7528	-43.6702	77.4283
8	3.3046	0.3578	-0.5459	1.5224	-0.0612	1.9011	0.0786	0.4352	0.0318	-0.1629	-0.1181	0.097	-0.163	-0.3737	0.0394	0.0392	0.0781	-0.0616	0.6937	-0.0216	0.5583	-49.5921	-46.4043	71.0727
9	1.6475	-0.1751	1.057	0.4153	0.3377	5.6576	0.0997	0.055	0.215	-0.0049	-0.0293	0.025	-0.4124	-0.2989	-0.0704	0.0812	0.1106	-0.0216	0.3794	-0.0447	0.5513	-45.7942	-35.1096	85.3231
10	1.3646	-0.4712	0.0314	1.35	0.2781	1.8045	-0.1207	-0.1143	-0.0949	0.1676	0.0883	0.2045	0.0739	-0.3739	0.0324	0.0266	-0.0097	0.0112	0.5254	-0.1345	0.5674	-45.2039	-52.5782	100.8628
11	1.2196	-0.2974	-0.2616	0.6062	0	1.5847	0.0258	0.2421	0.0619	-0.0257	-0.0641	0.0876	0.2972	-0.0552	0.0383	0.0611	0.0111	-0.0055	0.4087	-0.1721	0.5226	-30.1816	-63.3984	79.5144
12	1.587	0.1632	0.1976	0.8249	-0.0891	3.8459	0.0827	0.1889	0.3751	0.0246	-0.0629	-0.0537	0.0127	0.2816	-0.0198	0.0101	0.0484	0.0189	0.484	-0.0135	0.6183	-15.5265	-50.4355	77.1895
13	2.6117	-0.8138	0.5588	1.3593	-0.19	0.5222	-0.0773	-0.0749	0.1011	-0.1762	-0.0036	0.2298	-0.1655	-0.2398	0.0809	0.1204	0.0119	-0.0913	0.431	-0.1282	0.5083	-39.8516	-17.4939	127.5599
14	3.0306	-0.681	0.3521	2.3044	0.2975	3.5917	-0.184	0.0648	0.507	-0.2431	-0.0061	-0.0186	-0.2414	-0.0263	0.1901	0.0781	-0.0269	-0.1352	0.2732	-0.0393	0.5997	-2.8717	-11.1039	126.0786
15	1.7033	0.0552	1.1773	1.6812	0.1505	0.8963	-0.2083	0.58	0.0379	-0.2355	0.0351	-0.1247	-0.1703	0.2609	0.1732	0.0726	-0.0871	-0.0677	0.5467	-0.1418	0.5612	-9.2677	-24.9653	111.0593
16	2.2136	0.7041	-0.8585	1.1911	-1.3816	2.4043	-0.1616	0.2915	-0.477	-0.0651	0.1142	-0.0602	0.1495	0.08	0.0474	0.0191	-0.0087	0.017	0.3665	-0.2243	0.6431	-2.687	-43.6498	121.1066
17	2.0598	-0.4322	0.3238	0.5086	-0.0773	0.4817	-0.1724	-0.3977	-0.129	0.0447	0.1245	0.006	-0.0325	-0.0732	0.0479	0.0206	0.0386	-0.0429	0.4316	-0.1124	0.5094	-18.755	-28.9967	140.3077
18	2.6683	0.4731	0.4903	2.1477	1.6437	2.1564	-0.1838	-0.1852	0.1648	-0.2608	0.1541	-0.0068	-0.1311	0.1195	0.0297	0.0618	0.0032	-0.1007	0.3676	-0.1487	0.5495	-33.7906	-15.6797	132.7851
19	1.3892	-0.0852	-0.6708	2.4738	1.1578	1.3281	-0.0937	0.0757	-0.4774	0.2791	-0.254	0.5631	0.1946	-0.2406	0.3477	0.0471	-0.0475	0.0364	0.4956	-0.2403	0.6885	-27.1016	-36.899	41.4027
20	1.1304	-0.5432	-0.225	0.6399	0.8422	1.5741	-0.1229	-0.161	-0.2612	0.1739	0.1417	-0.0229	0.2488	0.0726	-0.0187	0.0517	0.0393	-0.0074	0.3526	-0.1428	0.5544	5.9749	-39.4758	50.5035
21	1.3127	-0.1591	-0.4496	0.7083	0.5386	1.368	-0.1575	-0.2026	0.0871	0.1379	0.2025	-0.1151	-0.0262	0.1998	-0.045	0.0715	0.0352	-0.0472	0.4305	-0.1969	0.5366	3.4609	-16.5979	56.5015
22	1.2181	-0.2795	0.0289	0.7648	0.4592	0.7951	0.015	0.2759	-0.0169	-0.1457	-0.0222	-0.0424	-0.124	0.0116	0.0072	0.0359	-0.0315	-0.0147	0.4529	-0.1792	0.4601	0.5489	-23.4037	27.4667
23	1.8162	0.2359	-0.0338	0.8513	0.7044	1.0193	-0.0113	0.2155	-0.1934	0.1362	-0.123	0.2451	0.029	-0.2136	0.1343	0.0657	-0.0325	-0.0085	0.4805	-0.2557	0.6108	-25.2596	-27.1015	37.4657
24	1.2435	-0.828	-1.5025	1.9819	3.8126	7.4071	-0.2617	0.0195	-0.5417	0.2308	0.2277	0.1202	0.4884	0.5224	0.034	0.1603	0.0016	-0.0003	0.4651	-0.2252	0.6552	-16.8487	-43.9878	30.4644

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	3 - 67
2	X-RAY DIFFRACTION	2	A	68 - 147
3	X-RAY DIFFRACTION	3	A	148 - 229
4	X-RAY DIFFRACTION	4	A	230 - 438
5	X-RAY DIFFRACTION	5	A	439 - 649
6	X-RAY DIFFRACTION	6	A	650 - 731
7	X-RAY DIFFRACTION	7	B	1 - 78
8	X-RAY DIFFRACTION	8	B	79 - 146
9	X-RAY DIFFRACTION	9	B	147 - 225
10	X-RAY DIFFRACTION	10	B	230 - 399
11	X-RAY DIFFRACTION	11	B	400 - 630
12	X-RAY DIFFRACTION	12	B	631 - 730
13	X-RAY DIFFRACTION	13	C	4 - 81
14	X-RAY DIFFRACTION	14	C	82 - 169
15	X-RAY DIFFRACTION	15	C	170 - 295
16	X-RAY DIFFRACTION	16	C	296 - 364
17	X-RAY DIFFRACTION	17	C	365 - 656
18	X-RAY DIFFRACTION	18	C	657 - 730
19	X-RAY DIFFRACTION	19	D	4 - 84
20	X-RAY DIFFRACTION	20	D	85 - 229
21	X-RAY DIFFRACTION	21	D	230 - 326
22	X-RAY DIFFRACTION	22	D	327 - 570
23	X-RAY DIFFRACTION	23	D	571 - 697
24	X-RAY DIFFRACTION	24	D	698 - 731

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Protein / Protein/peptide , 2 types, 8 molecules ABCDEFGH

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Non-polymers , 5 types, 707 molecules

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Protein / Protein/peptide , 2 types, 8 molecules ABCDEFGH

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Non-polymers , 5 types, 707 molecules

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