PDB-7bk8: X-ray crystal structure of Pseudomonas aeruginosa MagC

ID or keywords:

Entry

Database: PDB / ID: 7bk8

Title

X-ray crystal structure of Pseudomonas aeruginosa MagC

Components

MagC

Keywords

HYDROLASE / alpha-2-macroglobulin / peptidoglycan / NlpC/P60 / endopeptidase / MagC

Function / homology

Protein of unknown function DUF1175 / Protein of unknown function (DUF1175) / PHOSPHATE ION / Uncharacterized protein PA4490

Function and homology information

Biological species

Pseudomonas aeruginosa (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON / AB INITIO PHASING / Resolution: 1.74 Å

Authors

Zouhir, S. / Contreras-Martel, C. / Maragno Trindade, D. / Attree, I. / Dessen, A. / Macheboeuf, P.

Funding support

Brazil,

France, 3items

Organization	Grant number	Country
Sao Paulo Research Foundation (FAPESP)	2011/52067-6	Brazil
Sao Paulo Research Foundation (FAPESP)	2017/12436-9	Brazil
French Infrastructure for Integrated Structural Biology (FRISBI)	ANR-10-INBS-0005-02	France

Citation

Journal: Febs Lett. / Year: 2021
Title: MagC is a NplC/P60-like member of the alpha-2-macroglobulin Mag complex of Pseudomonas aeruginosa that interacts with peptidoglycan.
Authors: Zouhir, S. / Contreras-Martel, C. / Maragno Trindade, D. / Attree, I. / Dessen, A. / Macheboeuf, P.

History

Deposition	Jan 15, 2021	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jul 21, 2021	Provider: repository / Type: Initial release
Revision 1.1	Aug 18, 2021	Group: Database references / Category: citation / database_2 Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2	Jun 19, 2024	Group: Data collection / Derived calculations / Category: atom_type / chem_comp_atom / chem_comp_bond / Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	7bk8.cif.gz	89.1 KB	Display	PDBx/mmCIF format
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PDBx/mmJSON format	7bk8.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/bk/7bk8 ftp://data.pdbj.org/pub/pdb/validation_reports/bk/7bk8	HTTPS FTP

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Related structure data

Similar structure data	4wko-d 5kb3-d 3u1i-1 3nm6-d 3zi5-1 3dlt-d 3mqz-d 3vm8-2 3dyi-d 3l15-1 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: MagC

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration, isothermal titration calorimetry

Unit cell

Length a, b, c (Å)	110.737, 110.737, 41.110
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	146
Space group name H-M	H3

Components on special symmetry positions

ID	Model	Components
1	1	A-300- PO4
2	1	A-300- PO4

#1: Protein	MagC / MagC Mass: 24028.264 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: N-terminal signal peptide was replaced by a hexa-histidine tag Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria) Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1 Gene: PA4490 / Plasmid: pET28a (Novagen) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Start / References: UniProt: Q9HVT1
#2: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO₄
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 82 / 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: 2.02 Å³/Da / Density % sol: 39.12 % / Description: Tiny baguettes
Crystal grow	Temperature: 293 K / Method: vapor diffusion / pH: 6.5 / Details: 30% w/v PEG6000, 100 mM Citrate pH 6.5

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.45868 Å
Detector	Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 29, 2016
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.45868 Å / Relative weight: 1
Reflection	Resolution: 1.74→37.79 Å / Num. obs: 18977 / % possible obs: 98.4 % / Observed criterion σ(I): -3 / Redundancy: 6.6 % / B_iso Wilson estimate: 31.783 Å² / CC_1/2: 1 / R_sym value: 0.045 / Net I/σ(I): 26.91
Reflection shell	Resolution: 1.74→1.85 Å / Redundancy: 4.9 % / Mean I/σ(I) obs: 3 / Num. unique obs: 3021 / CC_1/2: 0.889 / R_sym value: 0.569 / % possible all: 93.7

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0258	refinement
XDS		data reduction
XSCALE		data scaling
Arcimboldo		phasing

Refinement

Method to determine structure: AB INITIO PHASING / Resolution: 1.74→37.785 Å / Cor.coef. F_o:F_c: 0.959 / Cor.coef. F_o:F_c free: 0.947 / SU B: 6.076 / SU ML: 0.093 / Cross valid method: FREE R-VALUE / ESU R: 0.137 / ESU R Free: 0.124
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2219	1868	9.843 %
R_work	0.1932	17109	-
all	0.196	-	-
obs	-	18977	98.403 %

Solvent computation

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

Displacement parameters

B_iso mean: 39.74 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.416 Å²	0.208 Å²	-0 Å²
2-	-	0.416 Å²	-0 Å²
3-	-	-	-1.349 Å²

Refinement step

Cycle: LAST / Resolution: 1.74→37.785 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1545	0	5	82	1632

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.013	1590
X-RAY DIFFRACTION	r_bond_other_d	0	0.017	1410
X-RAY DIFFRACTION	r_angle_refined_deg	1.267	1.64	2159
X-RAY DIFFRACTION	r_angle_other_deg	1.271	1.574	3267
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.44	5	191
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	31.329	21.471	102
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.833	15	256
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	15.832	15	16
X-RAY DIFFRACTION	r_chiral_restr	0.058	0.2	189
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	1816
X-RAY DIFFRACTION	r_gen_planes_other	0	0.02	364
X-RAY DIFFRACTION	r_nbd_refined	0.209	0.2	319
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.212	0.2	1338
X-RAY DIFFRACTION	r_nbtor_refined	0.171	0.2	754
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.076	0.2	704
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.14	0.2	58
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.188	0.2	8
X-RAY DIFFRACTION	r_nbd_other	0.197	0.2	33
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.197	0.2	9
X-RAY DIFFRACTION	r_mcbond_it	2.352	2.426	767
X-RAY DIFFRACTION	r_mcbond_other	2.346	2.422	766
X-RAY DIFFRACTION	r_mcangle_it	3.426	3.629	957
X-RAY DIFFRACTION	r_mcangle_other	3.424	3.633	958
X-RAY DIFFRACTION	r_scbond_it	3.093	2.752	823
X-RAY DIFFRACTION	r_scbond_other	3.044	2.713	817
X-RAY DIFFRACTION	r_scangle_it	4.656	3.992	1202
X-RAY DIFFRACTION	r_scangle_other	4.661	3.947	1196
X-RAY DIFFRACTION	r_lrange_it	7.374	28.06	1784
X-RAY DIFFRACTION	r_lrange_other	7.371	27.882	1776

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
1.74-1.785	0.393	128	0.407	1160	0.406	1440	0.716	0.719	89.4444	0.408
1.785-1.834	0.351	138	0.348	1201	0.349	1377	0.795	0.799	97.2404	0.346
1.834-1.887	0.362	131	0.29	1197	0.296	1354	0.799	0.851	98.0798	0.274
1.887-1.945	0.276	112	0.288	1174	0.287	1307	0.882	0.862	98.3933	0.277
1.945-2.009	0.256	119	0.227	1120	0.23	1249	0.9	0.913	99.1994	0.188
2.009-2.079	0.234	111	0.208	1116	0.211	1234	0.919	0.934	99.4327	0.18
2.079-2.157	0.264	119	0.204	1087	0.209	1208	0.904	0.923	99.8344	0.175
2.157-2.245	0.233	117	0.191	1009	0.195	1133	0.921	0.937	99.3822	0.167
2.245-2.345	0.2	103	0.174	993	0.177	1102	0.948	0.949	99.4555	0.155
2.345-2.458	0.23	107	0.19	936	0.195	1047	0.93	0.944	99.618	0.164
2.458-2.591	0.232	92	0.178	898	0.182	992	0.933	0.949	99.7984	0.16
2.591-2.747	0.238	92	0.177	850	0.183	944	0.939	0.952	99.7881	0.156
2.747-2.936	0.223	100	0.179	781	0.184	883	0.935	0.951	99.7735	0.163
2.936-3.169	0.197	76	0.192	744	0.193	822	0.932	0.931	99.7567	0.183
3.169-3.469	0.218	87	0.181	673	0.185	765	0.938	0.946	99.3464	0.18
3.469-3.875	0.193	60	0.17	617	0.172	679	0.955	0.954	99.7055	0.177
3.875-4.467	0.202	57	0.149	545	0.154	608	0.962	0.971	99.0132	0.167
4.467-5.451	0.177	63	0.163	446	0.164	510	0.97	0.971	99.8039	0.182
5.451-7.63	0.207	33	0.194	361	0.195	400	0.926	0.936	98.5	0.211
7.63-37.785	0.147	23	0.181	201	0.177	230	0.967	0.95	97.3913	0.212

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	4.5458	-0.1847	0.0108	4.7305	-0.6901	4.2265	0.0696	0.3058	0.0451	-0.2504	-0.0904	0.0271	0.0717	0.0034	0.0208	0.1928	-0.0121	-0.0332	0.1716	-0.0009	0.2841	14.8262	11.9841	24.7502
2	0.6248	0.7004	-0.0152	5.5866	-0.3135	0.5138	-0.0463	0.1364	-0.2075	-0.5178	0.0501	0.1337	0.1685	0.0419	-0.0038	0.1111	0.0086	-0.0126	0.0477	-0.0264	0.1521	11.9362	8.4552	19.83
3	2.6115	-0.1247	0.8955	0.2814	0.1462	0.9552	-0.049	-0.0672	0.0874	0.0101	0.0447	-0.0434	0.0477	0.0071	0.0043	0.0803	0.001	-0.0061	0.0497	-0.0028	0.1582	20.1452	20.7234	29.8126
4	5.2285	-2.3436	4.4362	3.4294	-3.6035	14.3816	-0.0936	0.3255	-0.0945	0.0482	0.0053	0.0291	-0.1055	0.2932	0.0883	0.1479	0.0082	-0.0067	0.1426	-0.0139	0.1072	29.1392	13.0336	16.3716
5	4.0481	0.0429	0.8755	2.0808	0.1661	1.911	0.0234	0.0121	-0.2877	-0.0531	-0.0062	-0.2286	0.2769	0.2543	-0.0173	0.1322	0.0256	-0.009	0.0689	0.0028	0.1555	33.3782	15.9827	30.4736

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	ALL	A	21 - 57
2	X-RAY DIFFRACTION	2	ALL	A	58 - 94
3	X-RAY DIFFRACTION	3	ALL	A	95 - 159
4	X-RAY DIFFRACTION	4	ALL	A	160 - 180
5	X-RAY DIFFRACTION	5	ALL	A	181 - 212

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