PDB-4uhq: Crystal structure of the pyocin AP41 DNase

ID or keywords:

Entry

Database: PDB / ID: 4uhq

Title

Crystal structure of the pyocin AP41 DNase

Components

LARGE COMPONENT OF PYOCIN AP41

Keywords

HYDROLASE /

BACTERIOCIN /

DNASE /

PYOCIN

Function / homology

Function and homology information

cytolysis /

endonuclease activity / killing of cells of another organism / defense response to bacterium /

signaling receptor binding
Similarity search - Function

Biological species

PSEUDOMONAS AERUGINOSA (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.5 Å

Authors

Joshi, A. / Chen, S. / Wojdyla, J.A. / Kaminska, R. / Kleanthous, C.

Citation

Journal: J.Mol.Biol. / Year: 2015
Title: Structures of the Ultra-High Affinity Protein-Protein Complexes of Pyocins S2 and Ap41 and Their Cognate Immunity Proteins from Pseudomonas Aeruginosa
Authors: Joshi, A. / Grinter, R. / Josts, I. / Chen, S. / Wojdyla, J.A. / Lowe, E.D. / Kaminska, R. / Sharp, C. / Mccaughey, L. / Roszak, A.W. / Cogdell, R.J. / Byron, O. / Walker, D. / Kleanthous, C.

History

Deposition	Mar 25, 2015	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Aug 5, 2015	Provider: repository / Type: Initial release
Revision 1.1	Sep 2, 2015	Group: Database references
Revision 1.2	Jan 10, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	4uhq.cif.gz	122.8 KB	Display	PDBx/mmCIF format
PDB format	pdb4uhq.ent.gz	98 KB	Display	PDB format
PDBx/mmJSON format	4uhq.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/uh/4uhq ftp://data.pdbj.org/pub/pdb/validation_reports/uh/4uhq	HTTPS FTP

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Related structure data

Related structure data	4uhpC 1bx1S C: citing same article (ref.) S: Starting model for refinement
Similar structure data	2l30-d 6hs9-d 5jnr-d 6mta-3 6q9v-1 1iaq-1 5kqm-d 1f18-d 3kbf-d 1yso-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	#181 - Jan 2015 Cascade and CRISPR similarity (1)

Deposited unit

A: LARGE COMPONENT OF PYOCIN AP41

B: LARGE COMPONENT OF PYOCIN AP41

hetero molecules

31 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: LARGE COMPONENT OF PYOCIN AP41

hetero molecules

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

2

B: LARGE COMPONENT OF PYOCIN AP41

hetero molecules

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

Unit cell

Length a, b, c (Å)	100.575, 100.575, 71.532
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	92
Space group name H-M	P4₁2₁2

Components on special symmetry positions

ID	Model	Components
1	1	A-2041- HOH
2	1	A-2083- HOH

#1: Protein	LARGE COMPONENT OF PYOCIN AP41 / PYOCIN AP41 LARGE COMPONENT Mass: 15153.019 Da / Num. of mol.: 2 / Fragment: DNASE DOMAIN, RESIDUES 642-777 Source method: isolated from a genetically manipulated source Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Strain: PAO1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q51502
#2: Chemical	ChemComp-CIT / CITRIC ACID / Citric acid Mass: 192.124 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₆H₈O₇
#3: Chemical	ChemComp-NI / NICKEL (II) ION / Nickel Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 135 / 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: 2.98 Å³/Da / Density % sol: 59 % / Description: NONE
Crystal grow	Details: 0.1 M TRISODIUM CITRATE, 20% 2-PROPANOL, 20% PEG4000

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795
Detector	Type: DECTRIS PILATUS / Detector: PIXEL / Date: Oct 5, 2014
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9795 Å / Relative weight: 1
Reflection	Resolution: 1.5→44.98 Å / Num. obs: 59171 / % possible obs: 100 % / Observed criterion σ(I): 6 / Redundancy: 13 % / B_iso Wilson estimate: 21.92 Å² / R_merge(I) obs: 0.06 / Net I/σ(I): 22
Reflection shell	Resolution: 1.5→1.53 Å / Redundancy: 11.8 % / Mean I/σ(I) obs: 1.6 / % possible all: 99.3

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Processing

Software

Name	Version	Classification
PHENIX	(PHENIX.REFINE)	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BX1

1bx1

Resolution: 1.5→44.979 Å / SU ML: 0.16 / σ(F): 1.34 / Phase error: 18.26 / Stereochemistry target values: ML
Details: THE METAL WAS IDENTIFIED BY XRAY FLUORESCENCE OF THE CRYSTALLINE SAMPLE.

	R_factor	Num. reflection	% reflection
R_free	0.1913	2960	5 %
R_work	0.1738	-	-
obs	0.1747	59106	99.96 %

Solvent computation

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

Displacement parameters

B_iso mean: 30.04 Å²

Refinement step

Cycle: LAST / Resolution: 1.5→44.979 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2088	0	41	135	2264

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.013	2211
X-RAY DIFFRACTION	f_angle_d	1.462	3006
X-RAY DIFFRACTION	f_dihedral_angle_d	17.414	830
X-RAY DIFFRACTION	f_chiral_restr	0.065	306
X-RAY DIFFRACTION	f_plane_restr	0.009	404

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 (%)
1.5-1.5246	0.308	122	0.2764	2651	X-RAY DIFFRACTION	99
1.5246-1.5509	0.2671	155	0.2448	2596	X-RAY DIFFRACTION	100
1.5509-1.5791	0.2452	122	0.2397	2640	X-RAY DIFFRACTION	100
1.5791-1.6095	0.2686	135	0.2229	2632	X-RAY DIFFRACTION	100
1.6095-1.6423	0.2281	133	0.2026	2649	X-RAY DIFFRACTION	100
1.6423-1.678	0.2207	145	0.1938	2638	X-RAY DIFFRACTION	100
1.678-1.7171	0.2137	136	0.1843	2652	X-RAY DIFFRACTION	100
1.7171-1.76	0.1797	125	0.1759	2652	X-RAY DIFFRACTION	100
1.76-1.8076	0.1873	145	0.1672	2636	X-RAY DIFFRACTION	100
1.8076-1.8608	0.1953	140	0.1698	2664	X-RAY DIFFRACTION	100
1.8608-1.9208	0.1808	163	0.1721	2624	X-RAY DIFFRACTION	100
1.9208-1.9895	0.1776	173	0.166	2643	X-RAY DIFFRACTION	100
1.9895-2.0692	0.1967	144	0.1658	2627	X-RAY DIFFRACTION	100
2.0692-2.1633	0.2085	130	0.1735	2696	X-RAY DIFFRACTION	100
2.1633-2.2774	0.1622	146	0.1665	2664	X-RAY DIFFRACTION	100
2.2774-2.4201	0.1922	160	0.1711	2670	X-RAY DIFFRACTION	100
2.4201-2.6069	0.1698	133	0.175	2687	X-RAY DIFFRACTION	100
2.6069-2.8692	0.2152	114	0.1823	2739	X-RAY DIFFRACTION	100
2.8692-3.2843	0.2178	133	0.1943	2721	X-RAY DIFFRACTION	100
3.2843-4.1374	0.1795	162	0.1658	2749	X-RAY DIFFRACTION	100
4.1374-44.9987	0.1728	144	0.151	2916	X-RAY DIFFRACTION	100

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	3.0863	-4.2463	1.6223	6.0403	-2.026	2.1285	-0.118	0.8767	-0.2043	-0.1807	-0.2119	0.2074	0.4148	0.4299	0.4468	0.2999	-0.0743	0.0176	0.3096	-0.019	0.2729	23.5228	2.7889	-20.6433
2	3.5229	1.6346	-0.6731	6.6868	-0.2651	5.9987	-0.0139	-0.4322	-0.0954	0.3886	0.1155	-0.3295	0.3424	0.6716	-0.0501	0.201	0.0768	-0.0195	0.2697	-0.0277	0.2038	36.2578	9.7273	-10.0069
3	4.0363	-1.0728	0.8156	7.6572	-1.7832	6.5079	-0.1558	-0.0537	-0.4189	-0.1262	0.0749	0.5936	0.7202	-0.7745	0.0733	0.2106	-0.0673	0.0486	0.2221	-0.0653	0.2757	19.9218	3.9492	-14.9475
4	6.3496	0.517	2.0839	4.1559	-0.3823	8.5526	-0.1081	0.268	0.0152	-0.0708	-0.0445	0.3945	-0.2977	-0.5154	0.0595	0.1955	0.0023	0.0062	0.2022	-0.0551	0.2696	20.2095	12.5841	-13.7618
5	3.502	0.8719	-1.4338	3.1346	0.9881	4.2261	0.1425	-0.1182	0.0549	-0.0848	0.0103	-0.1847	-0.2084	0.1878	-0.1187	0.1437	0.0011	0.016	0.1379	-0.0471	0.1856	28.2046	20.088	-7.4411
6	2.5586	0.4948	0.6599	1.9588	1.8853	3.6589	-0.0055	0.1365	-0.057	-0.122	0.0501	-0.0146	-0.0001	0.0021	-0.0582	0.2274	-0.0015	0.0124	0.1854	-0.028	0.2029	30.4508	9.7844	-22.7777
7	4.4226	-1.2856	-1.997	4.4953	3.4024	3.3169	0.1604	0.5433	0.0406	-0.3125	0.2283	-0.3107	-0.097	0.3054	-0.4213	0.2015	-0.0346	0.0458	0.28	-0.0532	0.2369	40.7887	17.4927	-25.2014
8	5.4771	1.1677	-0.6156	3.9548	-2.676	2.7654	-0.1654	-0.185	0.2462	0.5048	0.0607	-0.1212	-0.3995	-0.0003	0.1307	0.3378	0.0793	-0.0204	0.2565	0.0326	0.2747	23.6813	50.0278	-10.3375
9	3.4824	-0.2379	1.0083	5.9401	0.1529	5.4987	-0.1834	-0.4864	0.6967	0.3607	0.0529	-0.4197	-0.6381	0.4806	0.1051	0.286	0.0256	-0.084	0.1362	0.0457	0.2548	27.4679	51.5384	-11.1486
10	4.952	0.5761	-0.7639	5.0217	-1.1906	8.7592	-0.0769	0.2484	0.2744	0.0457	-0.1667	-0.6698	0.2597	0.3334	0.1991	0.2321	0.0185	-0.0363	0.1875	0.088	0.3443	32.19	44.3661	-12.0254
11	1.2693	-0.4866	0.6394	3.1869	-2.6094	2.988	-0.0524	-0.0078	0.0498	-0.0089	0.0572	0.0391	-0.0907	-0.0736	0.0095	0.1945	0.0257	0.0142	0.1672	0.0075	0.1968	23.559	41	-10.5995
12	5.5286	-3.5923	4.2189	2.3838	-2.3887	7.775	-0.1023	0.1446	-0.0456	-0.7535	0.4582	1.0127	0.1676	-0.8332	-0.4252	0.3383	-0.0517	-0.1556	0.3834	0.1658	0.4601	9.7088	41.9149	-19.5496

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN 'A' AND (RESID 643 THROUGH 652 )
2	X-RAY DIFFRACTION	2	CHAIN 'A' AND (RESID 653 THROUGH 671 )
3	X-RAY DIFFRACTION	3	CHAIN 'A' AND (RESID 672 THROUGH 685 )
4	X-RAY DIFFRACTION	4	CHAIN 'A' AND (RESID 686 THROUGH 699 )
5	X-RAY DIFFRACTION	5	CHAIN 'A' AND (RESID 700 THROUGH 735 )
6	X-RAY DIFFRACTION	6	CHAIN 'A' AND (RESID 736 THROUGH 759 )
7	X-RAY DIFFRACTION	7	CHAIN 'A' AND (RESID 760 THROUGH 774 )
8	X-RAY DIFFRACTION	8	CHAIN 'B' AND (RESID 642 THROUGH 663 )
9	X-RAY DIFFRACTION	9	CHAIN 'B' AND (RESID 664 THROUGH 685 )
10	X-RAY DIFFRACTION	10	CHAIN 'B' AND (RESID 686 THROUGH 699 )
11	X-RAY DIFFRACTION	11	CHAIN 'B' AND (RESID 700 THROUGH 759 )
12	X-RAY DIFFRACTION	12	CHAIN 'B' AND (RESID 760 THROUGH 774 )

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