PDB-6zm0: Crystal structure of MreC from Pseudomonas aeruginosa

ID or keywords:

Entry

Database: PDB / ID: 6zm0

Title

Crystal structure of MreC from Pseudomonas aeruginosa

Components

Cell shape-determining protein MreC

Keywords

STRUCTURAL PROTEIN / Rod-Shape Bacteria / Peptidoglycan / elongasome / cytoskeletal

Function / homology

Cell/Rod shape-determining protein MreC, domain 1 / Rod shape-determining protein MreC / Cell/Rod shape-determining protein MreC, domain 2 / rod shape-determining protein MreC / regulation of cell shape / plasma membrane / Cell shape-determining protein MreC

Function and homology information

Biological species

Pseudomonas aeruginosa PAO1 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON / AB INITIO PHASING / Resolution: 1.471 Å

Authors

Contreras-Martel, C. / Dessen, A. / Trindade, D.M.

Funding support

France,

Brazil, 3items

Organization	Grant number	Country
French National Research Agency	ANR-18-CE11-0019	France
Sao Paulo Research Foundation (FAPESP)	FAPESP 2011/52067-6	Brazil
Sao Paulo Research Foundation (FAPESP)	FAPESP 2017/12436-9	Brazil

Citation

Journal: Nat Commun / Year: 2021
Title: Self-association of MreC as a regulatory signal in bacterial cell wall elongation.
Authors: Alexandre Martins / Carlos Contreras-Martel / Manon Janet-Maitre / Mayara M Miyachiro / Leandro F Estrozi / Daniel Maragno Trindade / Caíque C Malospirito / Fernanda Rodrigues-Costa / ...
Abstract: The elongasome, or Rod system, is a protein complex that controls cell wall formation in rod-shaped bacteria. MreC is a membrane-associated elongasome component that co-localizes with the ...

History

Deposition	Jul 1, 2020	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Mar 17, 2021	Provider: repository / Type: Initial release
Revision 1.1	Jun 2, 2021	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2	Sep 29, 2021	Group: Database references / Category: database_2 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3	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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Download

PDBx/mmCIF format	6zm0.cif.gz	74.2 KB	Display	PDBx/mmCIF format
PDB format	pdb6zm0.ent.gz		Display	PDB format
PDBx/mmJSON format	6zm0.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	6zm0_validation.pdf.gz	425.5 KB	Display	wwPDB validaton report
Full document	6zm0_full_validation.pdf.gz	426.2 KB	Display
Data in XML	6zm0_validation.xml.gz	8.7 KB	Display
Data in CIF	6zm0_validation.cif.gz	11.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/zm/6zm0 ftp://data.pdbj.org/pub/pdb/validation_reports/zm/6zm0	HTTPS FTP

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Related structure data

Related structure data	11275C 6zlvC C: citing same article (ref.)
Similar structure data	2guz-3 5eic-2 6maq-d 6v0q-1 3lv9-d 5h46-d 2mpe-d 2rnw-d 5s8c-d 6thj-3 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

Deposited unit

AAA: Cell shape-determining protein MreC

hetero molecules

17.9 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

Unit cell

Length a, b, c (Å)	49.000, 49.000, 116.241
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	152
Space group name H-M	P3₁21

Components on special symmetry positions

ID	Model	Components
1	1	AAA-460- HOH

#1: Protein	Cell shape-determining protein MreC / Cell shape protein MreC Mass: 17692.201 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Gene: mreC, PA4480 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9HVU1
#2: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 66 / 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: 2.29 Å³/Da / Density % sol: 46.4 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: protein 10-11 mg/ml, 20 mM HEPES pH 8, 200 mM NaCl. reservoir 100 mM imidazole pH 6.5, 1.5 M NaCl, 15 % w/v PEG 3350, 100 mM MgCl2. Cryoprotection Parabar 10312 (Hampton Research) PH range: 5.5-7.5

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Data collection

Diffraction	Mean temperature: 273 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.45883 Å
Detector	Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 19, 2019
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.45883 Å / Relative weight: 1
Reflection	Resolution: 1.47→42.44 Å / Num. obs: 27246 / % possible obs: 96.1 % / Redundancy: 16 % / B_iso Wilson estimate: 38.28 Å² / CC_1/2: 1 / R_rim(I) all: 0.042 / R_sym value: 0.041 / Net I/σ(I): 25.9
Reflection shell	Resolution: 1.47→1.56 Å / Redundancy: 7.5 % / Mean I/σ(I) obs: 0.56 / Num. unique obs: 3454 / CC_1/2: 0.292 / R_rim(I) all: 0.317 / R_sym value: 0.297 / % possible all: 76.1

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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: 1.471→42.435 Å / Cor.coef. F_o:F_c: 0.966 / Cor.coef. F_o:F_c free: 0.955 / SU B: 4.582 / SU ML: 0.082 / Cross valid method: FREE R-VALUE / ESU R: 0.082 / ESU R Free: 0.083
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2445	2036	7.473 %
R_work	0.2168	25210	-
all	0.219	-	-
obs	-	27246	96.262 %

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: 39.496 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.658 Å²	0.329 Å²	-0 Å²
2-	-	0.658 Å²	0 Å²
3-	-	-	-2.133 Å²

Refinement step

Cycle: LAST / Resolution: 1.471→42.435 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1178	0	6	66	1250

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.01	0.013	1198
X-RAY DIFFRACTION	r_bond_other_d	0.006	0.017	1162
X-RAY DIFFRACTION	r_angle_refined_deg	1.332	1.643	1631
X-RAY DIFFRACTION	r_angle_other_deg	1.292	1.573	2683
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.701	5	154
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	30.244	21.5	60
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.028	15	198
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	19.598	15	10
X-RAY DIFFRACTION	r_chiral_restr	0.067	0.2	157
X-RAY DIFFRACTION	r_gen_planes_refined	0.01	0.02	1343
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	239
X-RAY DIFFRACTION	r_nbd_refined	0.214	0.2	179
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.198	0.2	1087
X-RAY DIFFRACTION	r_nbtor_refined	0.155	0.2	580
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.079	0.2	553
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.143	0.2	42
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.148	0.2	1
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.22	0.2	11
X-RAY DIFFRACTION	r_nbd_other	0.236	0.2	46
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.134	0.2	6
X-RAY DIFFRACTION	r_mcbond_it	1.351	1.724	619
X-RAY DIFFRACTION	r_mcbond_other	1.349	1.723	618
X-RAY DIFFRACTION	r_mcangle_it	1.766	2.582	772
X-RAY DIFFRACTION	r_mcangle_other	1.765	2.583	773
X-RAY DIFFRACTION	r_scbond_it	1.885	1.969	579
X-RAY DIFFRACTION	r_scbond_other	1.883	1.97	580
X-RAY DIFFRACTION	r_scangle_it	2.838	2.862	859
X-RAY DIFFRACTION	r_scangle_other	2.837	2.862	860
X-RAY DIFFRACTION	r_lrange_it	5.885	21.132	1188
X-RAY DIFFRACTION	r_lrange_other	5.87	20.916	1184

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
1.471-1.509	0.453	84	0.467	1112	0.466	2031	0.321	0.223	58.8872	0.464
1.509-1.55	0.422	144	0.383	1647	0.386	2003	0.527	0.568	89.4159	0.375
1.55-1.595	0.369	172	0.341	1778	0.343	1954	0.566	0.612	99.7953	0.325
1.595-1.644	0.317	123	0.316	1781	0.316	1905	0.771	0.764	99.9475	0.301
1.644-1.698	0.344	134	0.288	1722	0.292	1856	0.788	0.806	100	0.264
1.698-1.757	0.296	126	0.264	1641	0.266	1767	0.83	0.855	100	0.232
1.757-1.823	0.251	129	0.241	1592	0.241	1722	0.898	0.897	99.9419	0.204
1.823-1.898	0.253	124	0.22	1538	0.223	1662	0.917	0.928	100	0.187
1.898-1.982	0.262	98	0.212	1482	0.215	1580	0.919	0.931	100	0.176
1.982-2.078	0.213	111	0.201	1429	0.202	1540	0.946	0.948	100	0.171
2.078-2.19	0.218	116	0.207	1330	0.208	1446	0.942	0.941	100	0.18
2.19-2.323	0.307	115	0.217	1291	0.224	1407	0.91	0.932	99.9289	0.192
2.323-2.483	0.246	103	0.221	1211	0.223	1314	0.911	0.933	100	0.2
2.483-2.681	0.256	89	0.235	1123	0.236	1212	0.923	0.931	100	0.219
2.681-2.936	0.24	86	0.227	1055	0.228	1141	0.928	0.933	100	0.228
2.936-3.28	0.251	83	0.224	946	0.226	1029	0.927	0.937	100	0.235
3.28-3.784	0.259	58	0.212	857	0.215	915	0.91	0.946	100	0.242
3.784-4.625	0.198	58	0.177	728	0.179	786	0.962	0.962	100	0.215
4.625-6.503	0.252	60	0.198	578	0.203	638	0.939	0.957	100	0.247
6.503-42.435	0.182	23	0.213	369	0.211	396	0.973	0.96	98.9899	0.257

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	20.6384	-1.4127	13.0893	13.3443	4.1067	27.3752	0.072	0.5859	-0.6629	0.2515	0.1983	-1.4749	0.0736	1.6459	-0.2703	0.2539	0.0233	0.0437	0.2215	0.0195	0.3337	5.2212	27.335	-2.3775
2	5.5315	1.4702	-0.7354	3.8211	0.4205	4.2142	0.029	-0.0583	0.0293	-0.0919	-0.0354	0.1175	0.2319	-0.2103	0.0064	0.2288	-0.0124	-0.0334	0.1409	-0.0129	0.2252	-15.7989	22.817	1.4011
3	28.3693	-4.0309	-4.2376	5.0504	5.1464	9.0224	-0.0214	-0.2004	-0.5966	0.1849	0.1951	-0.2351	0.4281	0.5115	-0.1736	0.3042	-0.0038	0.0093	0.2147	-0.0564	0.235	-3.2158	19.1562	-3.837
4	1.3274	0.1996	-0.5175	0.8509	-0.2851	2.8291	0.1221	-0.0626	-0.1372	-0.0497	-0.1197	-0.0709	0.0596	0.3044	-0.0024	0.1528	-0.0099	-0.0076	0.1436	-0.0014	0.2012	-4.5693	26.5282	7.2618
5	7.0684	2.0885	1.6869	5.3597	0.7725	7.3564	0.2234	0.0661	0.0676	0.0541	-0.0248	0.0799	-0.2232	-0.0792	-0.1985	0.2164	0.0026	0.0581	0.1641	-0.003	0.1978	-13.7609	33.7	14.162
6	2.4633	3.0969	-4.305	3.9101	-5.4552	7.6994	0.5894	-0.2451	0.1942	0.7514	-0.2121	0.2225	-1.1791	0.2037	-0.3773	0.4606	-0.1334	0.1673	0.7472	-0.2652	0.2524	-11.0993	40.4814	24.7947
7	5.1865	-2.2525	-0.1675	8.2238	-0.2501	4.3541	0.2948	-0.0404	0.2315	0.0998	-0.2713	0.1775	-0.6734	0.5175	-0.0235	0.2494	-0.1484	0.052	0.199	-0.0335	0.182	-4.9986	40.5683	15.5848
8	1.9943	-0.8346	0.1021	4.931	0.2362	4.9673	0.2515	-0.1087	-0.2608	0.2505	-0.1255	0.1811	-0.3951	0.515	-0.126	0.213	-0.0929	0.0286	0.2198	-0.0207	0.2013	-4.8178	35.6599	12.1059
9	2.7217	-0.1721	-2.2912	1.8632	-0.6151	9.0215	0.3241	-0.0195	0.1497	0.2194	-0.0333	0.2061	-0.9193	-0.4233	-0.2908	0.2658	-0.0254	0.0576	0.1433	-0.0324	0.2587	-15.6645	38.9103	18.0427
10	16.0908	-9.3143	1.6742	11.238	0.528	6.7049	-0.0434	0.8369	-0.1746	-0.5559	-0.3482	0.124	-0.4962	-0.0023	0.3917	0.2993	-0.0156	0.0059	0.1851	-0.0363	0.244	-2.9336	29.9247	-2.4384

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	ALL	AAA	100 - 105
2	X-RAY DIFFRACTION	2	ALL	AAA	106 - 119
3	X-RAY DIFFRACTION	3	ALL	AAA	120 - 125
4	X-RAY DIFFRACTION	4	ALL	AAA	126 - 174
5	X-RAY DIFFRACTION	5	ALL	AAA	175 - 188
6	X-RAY DIFFRACTION	6	ALL	AAA	189 - 198
7	X-RAY DIFFRACTION	7	ALL	AAA	199 - 210
8	X-RAY DIFFRACTION	8	ALL	AAA	211 - 224
9	X-RAY DIFFRACTION	9	ALL	AAA	225 - 245
10	X-RAY DIFFRACTION	10	ALL	AAA	246 - 254

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