PDB-6s3y: CBDP35 SeMet structure

ID or keywords:

Entry

Database: PDB / ID: 6s3y

Title

CBDP35 SeMet structure

Components

PlyP35

Keywords

HYDROLASE

Function / homology

PSA endolysin, cell wall binding domain / PSA endolysin C-terminal cell wall binding domain / Peptidase M15C /

D-alanyl-D-alanine carboxypeptidase / Hedgehog signalling/DD-peptidase zinc-binding domain superfamily /

peptidase activity / PlyP35

Function and homology information

Biological species

Listeria phage P35 (virus)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.043 Å

Authors

Hermoso, J.A. / Bartual, S.G.

Citation

Journal: To Be Published
Title: CBDP35 SeMet structure
Authors: Hermoso, J.A. / Bartual, S.G.

History

Deposition	Jun 26, 2019	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jul 15, 2020	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6s3y.cif.gz	371.4 KB	Display	PDBx/mmCIF format
PDB format	pdb6s3y.ent.gz	314.6 KB	Display	PDB format
PDBx/mmJSON format	6s3y.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/s3/6s3y ftp://data.pdbj.org/pub/pdb/validation_reports/s3/6s3y	HTTPS FTP

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Related structure data

Similar structure data	6thj-6 6s4s-8 6s4s-12 6s4s-2 6s4s-4 6thj-10 6s4s-9 6s4s-5 6s4s-6 6s4s-7 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) 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) 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

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#192 - Dec 2015 Vancomycin similarity (1)

Deposited unit

A: PlyP35

B: PlyP35

C: PlyP35

D: PlyP35

E: PlyP35

F: PlyP35

G: PlyP35

H: PlyP35

I: PlyP35

J: PlyP35

L: PlyP35

K: PlyP35

197 kDa, 12 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: PlyP35

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

2

B: PlyP35

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

3

C: PlyP35

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

4

D: PlyP35

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

5

E: PlyP35

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

6

F: PlyP35

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

7

G: PlyP35

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

8

H: PlyP35

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

9

I: PlyP35

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

10

J: PlyP35

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

11

L: PlyP35

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

12

K: PlyP35

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

Unit cell

Length a, b, c (Å)	335.878, 95.565, 84.408
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	A-437- HOH
2	1	B-406- HOH

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Dom-ID	Ens-ID	Auth asym-ID	Auth seq-ID
1	1	A	153 - 290
2	1	B	153 - 290
1	2	A	153 - 289
2	2	C	153 - 289
1	3	A	153 - 291
2	3	D	153 - 291
1	4	A	154 - 290
2	4	E	154 - 290
1	5	A	153 - 291
2	5	F	153 - 291
1	6	A	153 - 291
2	6	G	153 - 291
1	7	A	153 - 291
2	7	H	153 - 291
1	8	A	154 - 290
2	8	I	154 - 290
1	9	A	154 - 289
2	9	J	154 - 289
1	10	A	153 - 291
2	10	L	153 - 291
1	11	A	153 - 291
2	11	K	153 - 291
1	12	B	152 - 289
2	12	C	152 - 289
1	13	B	153 - 290
2	13	D	153 - 290
1	14	B	154 - 290
2	14	E	154 - 290
1	15	B	153 - 290
2	15	F	153 - 290
1	16	B	153 - 290
2	16	G	153 - 290
1	17	B	153 - 290
2	17	H	153 - 290
1	18	B	154 - 290
2	18	I	154 - 290
1	19	B	154 - 289
2	19	J	154 - 289
1	20	B	153 - 290
2	20	L	153 - 290
1	21	B	153 - 290
2	21	K	153 - 290
1	22	C	153 - 289
2	22	D	153 - 289
1	23	C	154 - 289
2	23	E	154 - 289
1	24	C	153 - 289
2	24	F	153 - 289
1	25	C	153 - 289
2	25	G	153 - 289
1	26	C	153 - 289
2	26	H	153 - 289
1	27	C	154 - 289
2	27	I	154 - 289
1	28	C	154 - 289
2	28	J	154 - 289
1	29	C	153 - 289
2	29	L	153 - 289
1	30	C	153 - 289
2	30	K	153 - 289
1	31	D	154 - 290
2	31	E	154 - 290
1	32	D	153 - 291
2	32	F	153 - 291
1	33	D	153 - 291
2	33	G	153 - 291
1	34	D	153 - 291
2	34	H	153 - 291
1	35	D	154 - 290
2	35	I	154 - 290
1	36	D	154 - 289
2	36	J	154 - 289
1	37	D	153 - 291
2	37	L	153 - 291
1	38	D	153 - 291
2	38	K	153 - 291
1	39	E	154 - 290
2	39	F	154 - 290
1	40	E	154 - 290
2	40	G	154 - 290
1	41	E	154 - 290
2	41	H	154 - 290
1	42	E	154 - 291
2	42	I	154 - 291
1	43	E	154 - 289
2	43	J	154 - 289
1	44	E	154 - 290
2	44	L	154 - 290
1	45	E	154 - 290
2	45	K	154 - 290
1	46	F	153 - 291
2	46	G	153 - 291
1	47	F	153 - 291
2	47	H	153 - 291
1	48	F	154 - 290
2	48	I	154 - 290
1	49	F	154 - 289
2	49	J	154 - 289
1	50	F	153 - 291
2	50	L	153 - 291
1	51	F	153 - 291
2	51	K	153 - 291
1	52	G	153 - 291
2	52	H	153 - 291
1	53	G	154 - 290
2	53	I	154 - 290
1	54	G	154 - 289
2	54	J	154 - 289
1	55	G	153 - 291
2	55	L	153 - 291
1	56	G	153 - 291
2	56	K	153 - 291
1	57	H	154 - 290
2	57	I	154 - 290
1	58	H	154 - 289
2	58	J	154 - 289
1	59	H	153 - 291
2	59	L	153 - 291
1	60	H	153 - 291
2	60	K	153 - 291
1	61	I	154 - 289
2	61	J	154 - 289
1	62	I	154 - 290
2	62	L	154 - 290
1	63	I	154 - 290
2	63	K	154 - 290
1	64	J	154 - 289
2	64	L	154 - 289
1	65	J	154 - 289
2	65	K	154 - 289
1	66	L	153 - 291
2	66	K	153 - 291

NCS ensembles :

#1: Protein	PlyP35 Mass: 16416.248 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Listeria phage P35 (virus) / Gene: ply Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: A8ATR6
#2: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 1512 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 3.48 Å³/Da / Density % sol: 64.64 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / Details: 4M Na Formate

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.8726 Å
Detector	Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 26, 2013
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.8726 Å / Relative weight: 1
Reflection	Resolution: 2.043→19.84 Å / Num. obs: 168452 / % possible obs: 99.58 % / Redundancy: 7.5 % / R_merge(I) obs: 0.121 / Net I/σ(I): 13.01
Reflection shell	Resolution: 2.043→2.116 Å / Redundancy: 7.5 % / R_merge(I) obs: 0.6468 / Mean I/σ(I) obs: 2.93 / Num. unique obs: 16483 / % possible all: 98.29

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0238	refinement
XDS		data reduction
Aimless		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

SAD / Resolution: 2.043→19.84 Å / Cor.coef. F_o:F_c: 0.946 / Cor.coef. F_o:F_c free: 0.933 / SU B: 4.252 / SU ML: 0.112 / Cross valid method: THROUGHOUT / ESU R: 0.165 / ESU R Free: 0.145 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.22591	8475	5 %	RANDOM
R_work	0.20274	-	-	-
obs	0.20393	160162	99.76 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å

Displacement parameters

B_iso mean: 28.62 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.96 Å²	0 Å²	0.58 Å²
2-	-	0.17 Å²	0 Å²
3-	-	-	1.79 Å²

Refinement step

Cycle: LAST / Resolution: 2.043→19.84 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	13598	0	0	1512	15110

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.01	0.013	14014
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.017	12853
X-RAY DIFFRACTION	r_angle_refined_deg	1.639	1.649	18827
X-RAY DIFFRACTION	r_angle_other_deg	1.284	1.594	29879
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.667	5	1659
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	30.426	22.23	713
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.916	15	2388
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	11.587	15	60
X-RAY DIFFRACTION	r_chiral_restr	0.077	0.2	1728
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.02	15465
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	3199
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	2.771	2.802	6663
X-RAY DIFFRACTION	r_mcbond_other	2.771	2.801	6662
X-RAY DIFFRACTION	r_mcangle_it	4.089	4.182	8313
X-RAY DIFFRACTION	r_mcangle_other	4.089	4.182	8314
X-RAY DIFFRACTION	r_scbond_it	3.578	3.074	7351
X-RAY DIFFRACTION	r_scbond_other	3.577	3.074	7352
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	5.406	4.434	10515
X-RAY DIFFRACTION	r_long_range_B_refined	7.949	32.064	15820
X-RAY DIFFRACTION	r_long_range_B_other	7.857	31.689	15462
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	4381	0.11
1	2	B	4381	0.11
2	1	A	4476	0.07
2	2	C	4476	0.07
3	1	A	4479	0.09
3	2	D	4479	0.09
4	1	A	4431	0.09
4	2	E	4431	0.09
5	1	A	4487	0.09
5	2	F	4487	0.09
6	1	A	4538	0.08
6	2	G	4538	0.08
7	1	A	4531	0.09
7	2	H	4531	0.09
8	1	A	4452	0.09
8	2	I	4452	0.09
9	1	A	4454	0.08
9	2	J	4454	0.08
10	1	A	4461	0.1
10	2	L	4461	0.1
11	1	A	4500	0.09
11	2	K	4500	0.09
12	1	B	4417	0.09
12	2	C	4417	0.09
13	1	B	4355	0.1
13	2	D	4355	0.1
14	1	B	4365	0.09
14	2	E	4365	0.09
15	1	B	4429	0.09
15	2	F	4429	0.09
16	1	B	4402	0.1
16	2	G	4402	0.1
17	1	B	4376	0.09
17	2	H	4376	0.09
18	1	B	4341	0.1
18	2	I	4341	0.1
19	1	B	4374	0.08
19	2	J	4374	0.08
20	1	B	4375	0.1
20	2	L	4375	0.1
21	1	B	4400	0.1
21	2	K	4400	0.1
22	1	C	4360	0.09
22	2	D	4360	0.09
23	1	C	4372	0.09
23	2	E	4372	0.09
24	1	C	4423	0.08
24	2	F	4423	0.08
25	1	C	4411	0.08
25	2	G	4411	0.08
26	1	C	4444	0.08
26	2	H	4444	0.08
27	1	C	4351	0.09
27	2	I	4351	0.09
28	1	C	4374	0.09
28	2	J	4374	0.09
29	1	C	4386	0.1
29	2	L	4386	0.1
30	1	C	4382	0.09
30	2	K	4382	0.09
31	1	D	4404	0.08
31	2	E	4404	0.08
32	1	D	4457	0.09
32	2	F	4457	0.09
33	1	D	4419	0.1
33	2	G	4419	0.1
34	1	D	4411	0.11
34	2	H	4411	0.11
35	1	D	4386	0.09
35	2	I	4386	0.09
36	1	D	4381	0.09
36	2	J	4381	0.09
37	1	D	4386	0.11
37	2	L	4386	0.11
38	1	D	4410	0.1
38	2	K	4410	0.1
39	1	E	4474	0.08
39	2	F	4474	0.08
40	1	E	4376	0.09
40	2	G	4376	0.09
41	1	E	4385	0.09
41	2	H	4385	0.09
42	1	E	4440	0.09
42	2	I	4440	0.09
43	1	E	4373	0.09
43	2	J	4373	0.09
44	1	E	4365	0.1
44	2	L	4365	0.1
45	1	E	4398	0.09
45	2	K	4398	0.09
46	1	F	4430	0.09
46	2	G	4430	0.09
47	1	F	4444	0.1
47	2	H	4444	0.1
48	1	F	4415	0.09
48	2	I	4415	0.09
49	1	F	4438	0.08
49	2	J	4438	0.08
50	1	F	4423	0.1
50	2	L	4423	0.1
51	1	F	4499	0.08
51	2	K	4499	0.08
52	1	G	4564	0.08
52	2	H	4564	0.08
53	1	G	4439	0.09
53	2	I	4439	0.09
54	1	G	4519	0.07
54	2	J	4519	0.07
55	1	G	4524	0.09
55	2	L	4524	0.09
56	1	G	4561	0.07
56	2	K	4561	0.07
57	1	H	4405	0.09
57	2	I	4405	0.09
58	1	H	4469	0.07
58	2	J	4469	0.07
59	1	H	4451	0.1
59	2	L	4451	0.1
60	1	H	4483	0.09
60	2	K	4483	0.09
61	1	I	4372	0.1
61	2	J	4372	0.1
62	1	I	4408	0.09
62	2	L	4408	0.09
63	1	I	4381	0.1
63	2	K	4381	0.1
64	1	J	4477	0.08
64	2	L	4477	0.08
65	1	J	4553	0.06
65	2	K	4553	0.06
66	1	L	4480	0.09
66	2	K	4480	0.09

LS refinement shell

Resolution: 2.043→2.096 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.293	589	-
R_work	0.274	11521	-
obs	-	-	97.71 %

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