PDB-6hp3: ARBITRIUM PEPTIDE RECEPTOR FROM SPBETA PHAGE

ID or keywords:

Entry

Database: PDB / ID: 6hp3

Title

ARBITRIUM PEPTIDE RECEPTOR FROM SPBETA PHAGE

Components

SPBc2 prophage-derived uncharacterized protein YopK

Keywords

DNA BINDING PROTEIN / Arbitrium peptide receptor / SPbeta phage

Function / homology

: / AimR transcriptional regulator-like / SPbeta prophage-derived uncharacterized protein YopK

Function and homology information

Biological species

Bacillus subtilis subsp. subtilis str. 168 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.7 Å

Authors

Marina, A. / Gallego del Sol, F.

Citation

Journal: Mol.Cell / Year: 2019
Title: Deciphering the Molecular Mechanism Underpinning Phage Arbitrium Communication Systems.
Authors: Gallego Del Sol, F. / Penades, J.R. / Marina, A.

History

Deposition	Sep 19, 2018	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Feb 13, 2019	Provider: repository / Type: Initial release
Revision 1.1	Feb 20, 2019	Group: Data collection / Database references Category: citation / citation_author ...citation / citation_author / pdbx_database_proc / pdbx_seq_map_depositor_info Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 1.2	Apr 17, 2019	Group: Data collection / Database references Category: citation / database_PDB_rev ...citation / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc / pdbx_seq_map_depositor_info Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 1.3	Nov 13, 2024	Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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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PDBx/mmCIF format	6hp3.cif.gz	1.2 MB	Display	PDBx/mmCIF format
PDB format	pdb6hp3.ent.gz	1 MB	Display	PDB format
PDBx/mmJSON format	6hp3.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	6hp3_validation.pdf.gz	501.7 KB	Display	wwPDB validaton report
Full document	6hp3_full_validation.pdf.gz	589.4 KB	Display
Data in XML	6hp3_validation.xml.gz	107.9 KB	Display
Data in CIF	6hp3_validation.cif.gz	145.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/hp/6hp3 ftp://data.pdbj.org/pub/pdb/validation_reports/hp/6hp3	HTTPS FTP

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Related structure data

Related structure data	6hp5C 6hp7C C: citing same article (ref.)
Similar structure data	6hp5-d 6s7i-d 3wy9-d 6s7l-d 5d4v-d 2x1w-2 2x89-d 6lc1-2 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 - HomologyF&H Search

Related structure data

6hp5C

6hp7C

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: SPBc2 prophage-derived uncharacterized protein YopK

B: SPBc2 prophage-derived uncharacterized protein YopK

C: SPBc2 prophage-derived uncharacterized protein YopK

D: SPBc2 prophage-derived uncharacterized protein YopK

E: SPBc2 prophage-derived uncharacterized protein YopK

F: SPBc2 prophage-derived uncharacterized protein YopK

G: SPBc2 prophage-derived uncharacterized protein YopK

H: SPBc2 prophage-derived uncharacterized protein YopK

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

1

A: SPBc2 prophage-derived uncharacterized protein YopK

B: SPBc2 prophage-derived uncharacterized protein YopK

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

2

C: SPBc2 prophage-derived uncharacterized protein YopK

D: SPBc2 prophage-derived uncharacterized protein YopK

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

3

E: SPBc2 prophage-derived uncharacterized protein YopK

F: SPBc2 prophage-derived uncharacterized protein YopK

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

4

G: SPBc2 prophage-derived uncharacterized protein YopK

H: SPBc2 prophage-derived uncharacterized protein YopK

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

Unit cell

Length a, b, c (Å)	78.907, 251.202, 95.077
Angle α, β, γ (deg.)	90.00, 90.89, 90.00
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Component-ID: _ / Beg auth comp-ID: MSE / Beg label comp-ID: MSE / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: _ / Auth seq-ID: 1 - 386 / Label seq-ID: 1 - 386

NCS ensembles :

#1: Protein	SPBc2 prophage-derived uncharacterized protein YopK Mass: 46076.375 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis subsp. subtilis str. 168 (bacteria) Gene: yopK, BSU20860 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: O31927
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 211 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	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: 2.6 Å³/Da / Density % sol: 52.77 %
Crystal grow	Temperature: 294 K / Method: vapor diffusion, hanging drop / Details: PEG 3500, sodium chloride, hepes

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97925 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 12, 2017
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97925 Å / Relative weight: 1
Reflection	Resolution: 2.7→251.2 Å / Num. obs: 101076 / % possible obs: 100 % / Redundancy: 7.5 % / Net I/σ(I): 8.1
Reflection shell	Resolution: 2.7→2.85 Å

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0158	refinement
XDS		data reduction
SCALA		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.7→125.6 Å / Cor.coef. F_o:F_c: 0.936 / Cor.coef. F_o:F_c free: 0.922 / SU B: 36.162 / SU ML: 0.322 / Cross valid method: THROUGHOUT / ESU R Free: 0.354 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2497	4902	4.9 %	RANDOM
R_work	0.21866	-	-	-
obs	0.22019	96094	99.92 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 65.645 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	3.69 Å²	0 Å²	-0.35 Å²
2-	-	-3.26 Å²	0 Å²
3-	-	-	-0.42 Å²

Refinement step

Cycle: 1 / Resolution: 2.7→125.6 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	25464	0	0	211	25675

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.018	0.019	25926
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	2.168	1.981	34881
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.157	5	3082
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	41.776	25.482	1328
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	22.128	15	4712
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	31.429	15	104
X-RAY DIFFRACTION	r_chiral_restr	0.186	0.2	3833
X-RAY DIFFRACTION	r_gen_planes_refined	0.01	0.02	19308
X-RAY DIFFRACTION	r_gen_planes_other
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	3.519	5.249	12346
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	5.504	7.867	15419
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	4.486	5.438	13580
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined	9.144	69.958	38681
X-RAY DIFFRACTION	r_long_range_B_other
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	26320	0.08
1	2	B	26320	0.08
2	1	A	26212	0.08
2	2	C	26212	0.08
3	1	A	26204	0.08
3	2	D	26204	0.08
4	1	A	26156	0.08
4	2	E	26156	0.08
5	1	A	26172	0.08
5	2	F	26172	0.08
6	1	A	26182	0.08
6	2	G	26182	0.08
7	1	A	25952	0.09
7	2	H	25952	0.09
8	1	B	26194	0.08
8	2	C	26194	0.08
9	1	B	26338	0.08
9	2	D	26338	0.08
10	1	B	26180	0.08
10	2	E	26180	0.08
11	1	B	26170	0.08
11	2	F	26170	0.08
12	1	B	26208	0.08
12	2	G	26208	0.08
13	1	B	25860	0.09
13	2	H	25860	0.09
14	1	C	26202	0.08
14	2	D	26202	0.08
15	1	C	25944	0.08
15	2	E	25944	0.08
16	1	C	26096	0.08
16	2	F	26096	0.08
17	1	C	26196	0.08
17	2	G	26196	0.08
18	1	C	25904	0.09
18	2	H	25904	0.09
19	1	D	26262	0.07
19	2	E	26262	0.07
20	1	D	26180	0.08
20	2	F	26180	0.08
21	1	D	26272	0.08
21	2	G	26272	0.08
22	1	D	25654	0.09
22	2	H	25654	0.09
23	1	E	26184	0.07
23	2	F	26184	0.07
24	1	E	26238	0.08
24	2	G	26238	0.08
25	1	E	25670	0.09
25	2	H	25670	0.09
26	1	F	26096	0.08
26	2	G	26096	0.08
27	1	F	25828	0.09
27	2	H	25828	0.09
28	1	G	25762	0.09
28	2	H	25762	0.09

LS refinement shell

Resolution: 2.7→2.77 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.362	328	-
R_work	0.341	7109	-
obs	-	-	99.96 %

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	0.4403	-0.0542	0.076	0.3654	0.2885	0.2795	-0.033	-0.0266	0.0094	-0.0098	0.0122	0.0437	0.0325	0.0219	0.0208	0.1307	0.0302	-0.0388	0.0595	0.0428	0.0879	-8.117	36.3406	-26.7298
2	1.2727	-0.5077	-0.2163	0.594	0.3407	0.214	-0.1185	0.0576	-0.0898	0.0807	0.0956	0.0429	0.0329	0.0357	0.0229	0.0629	0.0294	-0.0163	0.1045	-0.0067	0.0594	-26.0831	71.6666	-14.3988
3	0.4487	-0.6163	-0.2503	1.0274	0.631	1.0999	0.067	0.0217	0.0079	-0.0395	0.0054	-0.0946	-0.0711	0.0081	-0.0724	0.1312	-0.0036	0.0056	0.0285	-0.0071	0.0797	28.5692	-26.5415	-9.3689
4	0.3622	-0.4189	-0.3319	0.516	0.2894	1.0035	0.0625	0.0506	0.0457	-0.0241	-0.03	-0.0537	0.0016	-0.0434	-0.0325	0.118	0.0493	0.0149	0.0848	0.0495	0.0652	15.8225	10.2233	-25.0684
5	0.5341	0.0216	-0.2846	0.1739	0.0112	0.2243	0.0296	-0.03	-0.0421	-0.0238	-0.0708	0.0365	0.0266	0.0509	0.0413	0.1929	0.0738	0.0564	0.0707	0.0215	0.0508	-8.7721	-12.6969	-58.909
6	0.6631	-0.0337	0.1919	0.9239	-0.079	0.0824	-0.0029	0.0196	0.1059	-0.1893	-0.0747	-0.0951	0.0433	0.018	0.0775	0.2199	0.045	0.0237	0.0127	0.0141	0.0768	-21.116	26.3907	-70.818
7	0.2433	0.058	-0.08	0.0736	-0.2481	1.5644	0.0686	0.0623	0.031	0.031	0.0625	-0.0074	0.0701	-0.1668	-0.131	0.1507	0.0281	-0.0349	0.0806	0.017	0.0729	32.9341	50.9464	-75.7946
8	0.294	-0.1	0.0762	0.8435	-0.2135	0.751	-0.0158	0.0213	0.1617	-0.0854	-0.0325	0.2137	0.0894	-0.0132	0.0483	0.0827	0.0096	-0.0762	0.0292	0.0181	0.2395	13.6305	87.2913	-62.483

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 386
2	X-RAY DIFFRACTION	2	B	1 - 386
3	X-RAY DIFFRACTION	3	C	1 - 386
4	X-RAY DIFFRACTION	4	D	1 - 386
5	X-RAY DIFFRACTION	5	E	1 - 386
6	X-RAY DIFFRACTION	6	F	1 - 386
7	X-RAY DIFFRACTION	7	G	1 - 386
8	X-RAY DIFFRACTION	8	H	1 - 386

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