PDB-5o3w: Structural characterization of the fast and promiscuous macrocycl...

ID or keywords:

Entry

Database: PDB / ID: 5o3w

Title

Structural characterization of the fast and promiscuous macrocyclase from plant - PCY1-S562A bound to Presegetalin A1

Components

Peptide cyclase 1
Presegetalin A1

Keywords

HYDROLASE / segetalin biosynthesis /

prolyl oligopeptidase / macrocyclase /

peptidase /

beta-propeller / closed form

Function / homology

Function and homology information

Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / serine-type endopeptidase activity /

Biological species

Vaccaria hispanica (bladder-soapwort)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2 Å

Authors

Ludewig, H. / Czekster, C.M. / Bent, A.F. / Naismith, J.H.

Funding support

United Kingdom, 2items

Citation

Journal: ACS Chem. Biol. / Year: 2018
Title: Characterization of the Fast and Promiscuous Macrocyclase from Plant PCY1 Enables the Use of Simple Substrates.
Authors: Ludewig, H. / Czekster, C.M. / Oueis, E. / Munday, E.S. / Arshad, M. / Synowsky, S.A. / Bent, A.F. / Naismith, J.H.

History

Deposition	May 25, 2017	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Feb 7, 2018	Provider: repository / Type: Initial release
Revision 1.1	Mar 28, 2018	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2	Oct 16, 2019	Group: Data collection / Category: reflns_shell
Revision 1.3	Nov 27, 2019	Group: Derived calculations Category: pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	5o3w.cif.gz	1.1 MB	Display	PDBx/mmCIF format
PDB format	pdb5o3w.ent.gz	980.9 KB	Display	PDB format
PDBx/mmJSON format	5o3w.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/o3/5o3w ftp://data.pdbj.org/pub/pdb/validation_reports/o3/5o3w	HTTPS FTP

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Related structure data

Related structure data	5o3uC 5o3vC 5o3xC C: citing same article (ref.)
Similar structure data	5uw3-3 5uw5-3 5uzw-3 5uzw-1 5uw5-1 5uw5-4 5uw3-2 5uw5-2 5uzw-2 5uw6-3 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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

Related structure data

5o3uC

5o3vC

5o3xC

C: citing same article (ref.)

Similar structure data

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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: Peptide cyclase 1

B: Peptide cyclase 1

C: Peptide cyclase 1

D: Peptide cyclase 1

W: Presegetalin A1

X: Presegetalin A1

Y: Presegetalin A1

Z: Presegetalin A1

hetero molecules

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

1

A: Peptide cyclase 1

W: Presegetalin A1

defined by author&software
Evidence: gel filtration, PCY1-S562A is a monomer according to size exclusion chromatography
85.9 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Peptide cyclase 1

X: Presegetalin A1

hetero molecules

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

3

C: Peptide cyclase 1

Y: Presegetalin A1

hetero molecules

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

4

D: Peptide cyclase 1

Z: Presegetalin A1

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

Unit cell

Length a, b, c (Å)	60.080, 88.600, 144.950
Angle α, β, γ (deg.)	93.00, 99.32, 90.05
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:

Dom-ID	Ens-ID	Auth asym-ID	Auth seq-ID
1	1	A	6 - 724
2	1	B	6 - 724
1	2	A	6 - 724
2	2	C	6 - 724
1	3	A	6 - 724
2	3	D	6 - 724
1	4	B	6 - 724
2	4	C	6 - 724
1	5	B	6 - 724
2	5	D	6 - 724
1	6	C	6 - 724
2	6	D	6 - 724

NCS ensembles :

ID
1
2
3
4
5
6

#1: Protein	Peptide cyclase 1 Mass: 82483.266 Da / Num. of mol.: 4 / Mutation: S562A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vaccaria hispanica (bladder-soapwort) / Gene: Pcy1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: R4P353
#2: Protein/peptide	Presegetalin A1 Mass: 3404.907 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vaccaria hispanica (bladder-soapwort) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: F6LNL5
#3: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical	ChemComp-SO4 / SULFATE ION / Sulfate Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO₄
#5: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 844 / 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: 2.21 Å³/Da / Density % sol: 44.42 %
Crystal grow	Temperature: 293.15 K / Method: vapor diffusion, hanging drop Details: PCY1-S562A complex with PresegA1 was crystallized at 13.3 mg/mL with 0.163 mM PresegA1 in 28% (w/v) PEG 5000 MME, 140 mM Mg acetate tetrahydrate and 0.1 M Tris pH 7.5. For cryo protection 7% ...Details: PCY1-S562A complex with PresegA1 was crystallized at 13.3 mg/mL with 0.163 mM PresegA1 in 28% (w/v) PEG 5000 MME, 140 mM Mg acetate tetrahydrate and 0.1 M Tris pH 7.5. For cryo protection 7% (v/v) glycerol were added to reservoir solution.

Crystal

Density Matthews: 2.21 Å³/Da / Density % sol: 44.42 %

Crystal grow

Temperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: PCY1-S562A complex with PresegA1 was crystallized at 13.3 mg/mL with 0.163 mM PresegA1 in 28% (w/v) PEG 5000 MME, 140 mM Mg acetate tetrahydrate and 0.1 M Tris pH 7.5. For cryo protection 7% ...

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å
Detector	Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 1, 2016
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.92 Å / Relative weight: 1
Reflection	Resolution: 2→77.07 Å / Num. obs: 183511 / % possible obs: 97 % / Redundancy: 1.8 % / Net I/σ(I): 4.8

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0158	refinement
xia2		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: apo PCY1

Resolution: 2→77.07 Å / Cor.coef. F_o:F_c: 0.942 / Cor.coef. F_o:F_c free: 0.919 / SU B: 15.12 / SU ML: 0.193 / Cross valid method: THROUGHOUT / ESU R: 0.237 / ESU R Free: 0.19 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.25625	9515	4.9 %	RANDOM
R_work	0.22126	-	-	-
obs	0.22296	183511	96.97 %	-

Solvent computation

Ion probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.2 Å

Displacement parameters

B_iso mean: 38.259 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.5 Å²	-0.22 Å²	-0.38 Å²
2-	-	-0.96 Å²	-0.01 Å²
3-	-	-	-0.38 Å²

Refinement step

Cycle: 1 / Resolution: 2→77.07 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	23045	0	12	844	23901

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.013	0.019	23675
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	21482
X-RAY DIFFRACTION	r_angle_refined_deg	1.64	1.953	32074
X-RAY DIFFRACTION	r_angle_other_deg	2.073	3	49925
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.883	5	2867
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.387	24.017	1180
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.936	15	3976
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.007	15	149
X-RAY DIFFRACTION	r_chiral_restr	0.104	0.2	3404
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.021	26464
X-RAY DIFFRACTION	r_gen_planes_other	0.006	0.02	5033
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	1.835	1.304	11480
X-RAY DIFFRACTION	r_mcbond_other	1.835	1.304	11479
X-RAY DIFFRACTION	r_mcangle_it	2.871	1.943	14325
X-RAY DIFFRACTION	r_mcangle_other	2.871	1.943	14326
X-RAY DIFFRACTION	r_scbond_it	1.92	1.478	12195
X-RAY DIFFRACTION	r_scbond_other	1.92	1.476	12187
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	2.985	2.142	17731
X-RAY DIFFRACTION	r_long_range_B_refined	5.91	15.04	24679
X-RAY DIFFRACTION	r_long_range_B_other	5.911	14.992	24653
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

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	44302	0.07
1	2	B	44302	0.07
2	1	A	44206	0.08
2	2	C	44206	0.08
3	1	A	44802	0.06
3	2	D	44802	0.06
4	1	B	46394	0.06
4	2	C	46394	0.06
5	1	B	43940	0.08
5	2	D	43940	0.08
6	1	C	43836	0.08
6	2	D	43836	0.08

LS refinement shell

Resolution: 2→2.052 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.344	689	-
R_work	0.331	13441	-
obs	-	-	95.78 %

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	0.4845	0.0569	-0.0161	1.0449	-0.1854	2.4993	0.0052	-0.0376	0.0769	0.3027	-0.0071	0.0852	-0.0514	-0.1747	0.0019	0.2359	0.0327	0.0747	0.0278	0.0425	0.3649	2.013	-55.921	-294.943
2	3.7528	1.893	2.3727	3.2162	0.4332	4.1517	-0.0789	0.2458	0.3286	-0.472	0.0614	-0.1546	-0.2344	-0.0113	0.0175	0.346	0.0865	0.0516	0.1936	0.1446	0.4878	8.339	-52.193	-325.912
3	1.8835	-0.385	-0.3259	1.977	-0.3623	2.2144	0.1246	-0.1895	0.0062	-0.1485	-0.0852	0.3037	0.1647	-0.2224	-0.0394	0.2064	-0.0187	0.0072	0.0919	0.0374	0.3205	-12.533	-64.033	-323.27
4	1.0545	0.0549	0.9323	1.0654	0.1106	2.1906	0.1299	0.1077	-0.0467	-0.1547	-0.0315	-0.0283	0.5346	0.2182	-0.0984	0.3959	0.0991	0.0389	0.0352	0.0321	0.257	7.565	-80.571	-321.263
5	1.0247	0.0546	-0.0915	1.4066	0.1736	1.7943	-0.006	0.0459	0.098	0.2907	0.048	0.0141	0.3306	-0.061	-0.042	0.3381	0.0132	0.0365	0.0242	0.0713	0.242	7.926	-68.786	-292.278
6	1.6231	0.0275	0.2485	1.6319	0.5816	1.544	0.0573	-0.2323	-0.1377	0.1614	-0.0379	0.0513	0.2596	0.0816	-0.0194	0.0928	0.0235	0.0462	0.0888	0.1315	0.3262	29.964	-33.832	-299.324
7	1.232	-0.0409	-0.4601	1.907	0.1681	1.532	0.0696	0.0232	-0.0888	-0.3203	0.0096	-0.0817	-0.0863	0.0434	-0.0792	0.2005	0.0515	0.0568	0.0265	0.0376	0.3019	39.945	-34.278	-323.975
8	1.8104	0.1539	-0.6829	1.1191	0.4593	1.6842	0.0734	0.2226	0.0154	-0.5375	-0.0662	0.0858	-0.3075	-0.1271	-0.0072	0.4306	0.0943	0.0129	0.0741	0.0959	0.2858	28.952	-15.47	-329.54
9	1.6457	-0.1334	-0.1109	1.6521	0.1766	1.3044	0.016	-0.1262	0.0269	0.06	-0.0034	0.1256	-0.0927	-0.0465	-0.0125	0.0572	0.0198	0.0514	0.0281	0.0588	0.258	25.723	-17.744	-299.425
10	0.9827	-0.0524	-0.2498	1.952	1.2257	2.3394	-0.0182	-0.2242	-0.1932	0.2254	0.0318	0.1162	0.0826	-0.0383	-0.0136	0.1301	0.0076	0.068	0.0749	0.1144	0.3157	22.834	-32.38	-293.745
11	2.0391	-0.3166	-0.29	1.9005	0.8768	2.0161	0.0088	0.2558	0.1162	-0.175	-0.0162	0.0064	-0.2291	0.0884	0.0074	0.113	-0.0365	0.0258	0.0855	0.1136	0.3182	-6.67	-28.838	-388.353
12	1.1648	0.3244	0.4194	2.1037	0.3398	1.5783	0.0318	0.0276	0.0366	0.4683	0.03	-0.2041	0.142	0.0374	-0.0618	0.222	-0.039	-0.0208	0.0333	0.0485	0.3464	3.005	-27.841	-363.684
13	2.0227	-0.2624	0.8101	1.4287	0.3635	1.7382	0.0832	-0.2097	-0.0094	0.7405	-0.0669	-0.0656	0.4105	-0.1657	-0.0163	0.5277	-0.0785	-0.0117	0.0697	0.1062	0.2963	-7.637	-47.277	-358.201
14	1.7068	-0.0201	0.2213	1.7429	0.2657	1.3371	0.0317	0.1148	-0.0272	-0.0475	0.0108	0.0721	0.1408	-0.0116	-0.0425	0.0802	-0.0306	0.0214	0.0389	0.0518	0.2793	-10.903	-44.985	-388.237
15	0.7959	-0.0555	0.1986	2.2752	1.1344	2.6314	-0.0608	0.1985	0.1689	-0.215	0.0439	0.1097	0.0042	0.0167	0.0169	0.1121	-0.0378	0.0171	0.0683	0.0972	0.3231	-13.631	-30.502	-394.302
16	0.5523	-0.0979	0.2361	1.006	-0.4899	3.0213	-0.034	0.0394	-0.0516	-0.2424	0.0048	0.085	-0.0462	-0.1996	0.0292	0.2328	-0.043	-0.0144	0.0391	0.0316	0.388	25.408	-95.442	-392.802
17	1.4701	0.4093	-0.0289	1.8981	-0.297	1.9372	0.091	0.1613	-0.0518	0.1674	-0.0615	0.1856	-0.1956	-0.179	-0.0295	0.2351	0.0177	0.0357	0.0969	0.0387	0.2968	12.885	-87.32	-364.584
18	1.1907	-0.0268	-0.9393	1.2042	0.1984	2.2973	0.0919	-0.1138	-0.0013	0.2482	-0.0249	-0.0751	-0.578	0.2294	-0.067	0.4558	-0.1212	-0.0091	0.0476	0.0437	0.2616	32.656	-71.196	-365.985
19	1.0079	-0.1257	0.1471	1.3562	0.0789	2.0286	0.0333	-0.0402	-0.0871	-0.2607	0.008	0.0154	-0.4326	-0.1252	-0.0412	0.3661	-0.0277	-0.0005	0.036	0.0691	0.2598	30.609	-81.188	-395.893
20	4.7323	-0.2696	0.7882	2.9617	-0.3124	4.6436	0.0081	-0.2108	-0.1451	-0.1528	0.0813	0.017	-0.1139	-0.0041	-0.0894	0.2073	-0.0391	0.0284	0.0229	0.0428	0.3154	37.428	-96.847	-395.491

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	4 - 107
2	X-RAY DIFFRACTION	2	A	108 - 134
3	X-RAY DIFFRACTION	3	A	135 - 290
4	X-RAY DIFFRACTION	4	A	291 - 420
5	X-RAY DIFFRACTION	5	A	421 - 724
6	X-RAY DIFFRACTION	6	B	6 - 110
7	X-RAY DIFFRACTION	7	B	111 - 266
8	X-RAY DIFFRACTION	8	B	267 - 416
9	X-RAY DIFFRACTION	9	B	417 - 679
10	X-RAY DIFFRACTION	10	B	680 - 724
11	X-RAY DIFFRACTION	11	C	6 - 110
12	X-RAY DIFFRACTION	12	C	111 - 262
13	X-RAY DIFFRACTION	13	C	263 - 416
14	X-RAY DIFFRACTION	14	C	417 - 678
15	X-RAY DIFFRACTION	15	C	679 - 724
16	X-RAY DIFFRACTION	16	D	6 - 107
17	X-RAY DIFFRACTION	17	D	108 - 300
18	X-RAY DIFFRACTION	18	D	301 - 422
19	X-RAY DIFFRACTION	19	D	423 - 691
20	X-RAY DIFFRACTION	20	D	692 - 724

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+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi