PDB-5lp5: Complex between Penicillin-Binding Protein (PBP2) and MreC from H...

ID or keywords:

Entry

Database: PDB / ID: 5lp5

Title

Complex between Penicillin-Binding Protein (PBP2) and MreC from Helicobacter pylori

Components

Penicillin-binding protein 2 (Pbp2)
Rod shape-determining protein (MreC)

Keywords

HYDROLASE/ANTIBIOTIC / TRANSFERASE / CELL WALL / HYDROLASE-ANTIBIOTIC complex / HYDROLASE-ANTIBIOTIC

Function / homology

Function and homology information

peptidoglycan L,D-transpeptidase activity / serine-type D-Ala-D-Ala carboxypeptidase activity / penicillin binding / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / plasma membrane
Similarity search - Function

Biological species

Helicobacter pylori (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.74 Å

Authors

Contreras-Martel, C. / Martins, A. / Ecobichon, C. / Maragno, D.M. / Mattei, P.J. / El Ghachi, M. / Hicham, S. / Hardouin, P. / Boneca, I.G. / Dessen, A.

Funding support

France,

Brazil, 3items

Citation

Journal: Nat Commun / Year: 2017
Title: Molecular architecture of the PBP2-MreC core bacterial cell wall synthesis complex.
Authors: Contreras-Martel, C. / Martins, A. / Ecobichon, C. / Trindade, D.M. / Mattei, P.J. / Hicham, S. / Hardouin, P. / Ghachi, M.E. / Boneca, I.G. / Dessen, A.

History

Deposition	Aug 11, 2016	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Aug 23, 2017	Provider: repository / Type: Initial release
Revision 1.1	Aug 30, 2017	Group: Database references / Structure summary / Category: citation / struct / Item: _citation.title / _struct.title
Revision 1.2	Oct 18, 2017	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 / _citation_author.name
Revision 1.3	Jan 10, 2024	Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_audit_support / pdbx_initial_refinement_model / struct_ncs_dom_lim Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization / _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
Revision 1.4	Nov 13, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5lp5.cif.gz	673.6 KB	Display	PDBx/mmCIF format
PDB format	pdb5lp5.ent.gz	559.9 KB	Display	PDB format
PDBx/mmJSON format	5lp5.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	5lp5_validation.pdf.gz	477.6 KB	Display	wwPDB validaton report
Full document	5lp5_full_validation.pdf.gz	495.2 KB	Display
Data in XML	5lp5_validation.xml.gz	56 KB	Display
Data in CIF	5lp5_validation.cif.gz	76.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/lp/5lp5 ftp://data.pdbj.org/pub/pdb/validation_reports/lp/5lp5	HTTPS FTP

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Related structure data

Related structure data	5lp4SC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	3ubx-1 5drz-d 3ubx-2 3tn0-d 1iai-d 3scm-d 6fg2-2 4mne-2 3ard-d 6bpe-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) 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

A: Penicillin-binding protein 2 (Pbp2)

B: Penicillin-binding protein 2 (Pbp2)

C: Rod shape-determining protein (MreC)

D: Rod shape-determining protein (MreC)

E: Rod shape-determining protein (MreC)

F: Rod shape-determining protein (MreC)

248 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Penicillin-binding protein 2 (Pbp2)

C: Rod shape-determining protein (MreC)

E: Rod shape-determining protein (MreC)

defined by author&software
124 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Penicillin-binding protein 2 (Pbp2)

D: Rod shape-determining protein (MreC)

F: Rod shape-determining protein (MreC)

defined by author&software
124 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	338.656, 48.340, 151.513
Angle α, β, γ (deg.)	90.00, 113.02, 90.00
Int Tables number	5
Space group name H-M	C121

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
1	2	C
2	2	D
1	3	C
2	3	E
1	4	C
2	4	F
1	5	D
2	5	E
1	6	D
2	6	F
1	7	E
2	7	F

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	MET	MET	LEU	LEU	A	A	43 - 588	43 - 588
2	1	MET	MET	LEU	LEU	B	B	43 - 588	43 - 588
1	2	LYS	LYS	VAL	VAL	C	C	92 - 246	92 - 246
2	2	LYS	LYS	VAL	VAL	D	D	92 - 246	92 - 246
1	3	LYS	LYS	VAL	VAL	C	C	92 - 246	92 - 246
2	3	LYS	LYS	VAL	VAL	E	E	92 - 246	92 - 246
1	4	LYS	LYS	VAL	VAL	C	C	92 - 246	92 - 246
2	4	LYS	LYS	VAL	VAL	F	F	92 - 246	92 - 246
1	5	LYS	LYS	LYS	LYS	D	D	92 - 247	92 - 247
2	5	LYS	LYS	LYS	LYS	E	E	92 - 247	92 - 247
1	6	LYS	LYS	LYS	LYS	D	D	92 - 247	92 - 247
2	6	LYS	LYS	LYS	LYS	F	F	92 - 247	92 - 247
1	7	LYS	LYS	LYS	LYS	E	E	92 - 247	92 - 247
2	7	LYS	LYS	LYS	LYS	F	F	92 - 247	92 - 247

NCS ensembles :

ID
1
2
3
4
5
6
7

#1: Protein	Penicillin-binding protein 2 (Pbp2) Mass: 67716.859 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Helicobacter pylori (strain ATCC 700392 / 26695) (bacteria) Strain: ATCC 700392 / 26695 / Gene: HP_1565 / Plasmid: pACYDuet / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O26085
#2: Protein	Rod shape-determining protein (MreC) Mass: 28076.320 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Helicobacter pylori (strain ATCC 700392 / 26695) (bacteria) Strain: ATCC 700392 / 26695 / Gene: HP_1372 / Plasmid: pACYDuet / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Star / References: UniProt: O25924
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 69 / 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: 2.39 Å³/Da / Density % sol: 48.48 % / Description: needles
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 5%W/V PEG6000, 50MM CITRIC ACID PH 5, 9MM ZNCL2

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Data collection

Diffraction	Mean temperature: 273 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
Detector	Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 9, 2009
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.8726 Å / Relative weight: 1
Reflection	Resolution: 2.74→43.94 Å / Num. obs: 52464 / % possible obs: 86.5 % / Observed criterion σ(I): 3 / Redundancy: 2.8 % / B_iso Wilson estimate: 45.79 Å² / R_sym value: 0.073 / Net I/σ(I): 19.84
Reflection shell	Resolution: 2.74→2.9 Å / Redundancy: 2.8 % / R_merge(I) obs: 0.41 / Mean I/σ(I) obs: 3 / % possible all: 83.1

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0158	refinement
XDS		data reduction
XSCALE		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5LP4

5lp4

Resolution: 2.74→43.94 Å / Cor.coef. F_o:F_c: 0.907 / Cor.coef. F_o:F_c free: 0.879 / SU B: 49.014 / SU ML: 0.393 / Cross valid method: THROUGHOUT / ESU R Free: 0.433 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.29216	1307	2.5 %	RANDOM
R_work	0.25685	-	-	-
obs	0.25771	51156	86.57 %	-

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: 60.029 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-2.04 Å²	-0 Å²	-2.5 Å²
2-	-	6.19 Å²	-0 Å²
3-	-	-	-1.49 Å²

Refinement step

Cycle: 1 / Resolution: 2.74→43.94 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	13312	0	0	69	13381

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.019	13588
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	12805
X-RAY DIFFRACTION	r_angle_refined_deg	1.28	1.963	18374
X-RAY DIFFRACTION	r_angle_other_deg	0.854	3	29770
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.581	5	1682
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.072	25.033	604
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.372	15	2411
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	12.908	15	43
X-RAY DIFFRACTION	r_chiral_restr	0.078	0.2	2076
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	14989
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	2674
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	3.053	3.116	6752
X-RAY DIFFRACTION	r_mcbond_other	3.053	3.116	6751
X-RAY DIFFRACTION	r_mcangle_it	5.035	4.663	8426
X-RAY DIFFRACTION	r_mcangle_other	5.035	4.663	8427
X-RAY DIFFRACTION	r_scbond_it	3.056	3.433	6836
X-RAY DIFFRACTION	r_scbond_other	3.056	3.433	6837
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	5.066	5.036	9949
X-RAY DIFFRACTION	r_long_range_B_refined	9.759	58.569	53084
X-RAY DIFFRACTION	r_long_range_B_other	9.759	58.571	53077
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	32586	0.1
1	2	B	32586	0.1
2	1	C	9016	0.07
2	2	D	9016	0.07
3	1	C	8512	0.13
3	2	E	8512	0.13
4	1	C	8476	0.12
4	2	F	8476	0.12
5	1	D	8624	0.13
5	2	E	8624	0.13
6	1	D	8566	0.12
6	2	F	8566	0.12
7	1	E	9030	0.09
7	2	F	9030	0.09

LS refinement shell

Resolution: 2.74→2.811 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.517	92	-
R_work	0.469	3536	-
obs	-	-	81.79 %

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	1.0101	0.3966	0.3134	0.9231	0.2484	0.5205	0.104	-0.03	0.028	0.2741	-0.0921	0.3687	0.081	-0.3776	-0.0119	0.2067	0.0135	0.1125	0.3423	0.032	0.1825	-92.9437	-25.3803	29.292
2	0.9201	0.3199	-0.0035	0.8081	-0.0352	1.8295	0.0066	-0.2546	-0.0051	0.1993	-0.0098	-0.1226	-0.1206	0.456	0.0033	0.262	0.012	-0.005	0.4116	0.023	0.0929	-53.9627	-14.9254	50.3362
3	1.4989	-0.3961	-0.1806	0.4623	-0.4512	2.7758	-0.0311	0.7024	-0.0965	-0.2841	-0.1325	-0.28	0.2307	0.098	0.1636	0.3085	-0.0931	0.2563	0.3706	-0.1155	0.3135	-46.8995	-10.6834	109.1125
4	0.3446	0.0267	0.7941	0.6442	-0.5022	2.9233	0.0289	-0.1757	-0.0201	-0.1782	0.1614	0.0811	0.2589	-1.1125	-0.1903	0.1938	-0.0175	0.0394	0.687	0.1328	0.0527	-75.8051	2.0294	82.2614
5	1.9975	0.1012	-0.0168	1.0679	0.2694	1.359	0.0355	-0.0552	0.0414	0.0029	0.0308	0.1312	0.154	-0.2073	-0.0663	0.2782	0.0088	0.0593	0.2341	0.0436	0.1829	-99.9578	-40.2799	4.9825
6	2.2871	0.3261	0.2402	2.3225	1.1148	1.9861	-0.0851	-0.0175	0.1323	-0.0815	0.1015	0.0566	-0.0127	0.1388	-0.0164	0.2705	-0.0011	0.0659	0.2804	0.0147	0.1713	-90.5521	-32.729	5.2177
7	13.6132	6.9476	-1.1454	7.3968	-2.3297	3.4721	-0.2187	0.1194	-0.6522	-0.0784	0.182	-0.2328	0.3339	-0.0901	0.0367	0.3224	0.0684	0.0861	0.2057	-0.0201	0.2321	-40.3141	-20.0064	139.7987
8	2.2754	-0.4209	0.1488	1.7175	-0.5249	2.5358	-0.0607	0.0326	-0.1094	-0.1073	0.0096	-0.1375	0.0525	-0.0729	0.0512	0.2283	-0.0181	0.1116	0.1667	0.004	0.2308	-48.5939	-11.5787	131.8945
9	4.005	-2.2752	-2.3156	6.7145	3.4617	4.9852	-0.1151	0.2926	-0.1371	-0.0784	0.0842	0.2341	0.1797	-0.0138	0.0308	0.1773	0.0231	-0.0128	0.2585	0.0609	0.2142	-131.2009	-37.7061	-15.6881
10	3.2997	0.6039	0.0422	2.2214	-0.1644	1.7607	-0.0291	0.0721	0.3076	0.0469	-0.038	0.2128	-0.1821	-0.0799	0.0671	0.2438	0.016	0.0368	0.2855	0.0564	0.2192	-118.5365	-31.5288	-11.5149
11	4.4739	-0.6021	0.2092	1.3802	0.1932	1.3173	0.0223	-0.1876	0.2462	-0.0028	-0.1	-0.2454	-0.0779	0.1401	0.0777	0.2018	-0.0099	0.0523	0.292	0.0604	0.2214	-18.9057	-9.6049	149.7385
12	2.8605	0.1213	0.2411	1.6175	0.055	1.4756	-0.0962	-0.4591	0.2364	0.1862	0.0942	-0.1437	-0.1386	0.1193	0.002	0.1932	0.0083	0.0967	0.291	0.0321	0.262	-28.524	-1.7144	148.8568

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	41 - 226
2	X-RAY DIFFRACTION	2	A	227 - 588
3	X-RAY DIFFRACTION	3	B	43 - 148
4	X-RAY DIFFRACTION	4	B	149 - 588
5	X-RAY DIFFRACTION	5	C	92 - 181
6	X-RAY DIFFRACTION	6	C	182 - 248
7	X-RAY DIFFRACTION	7	D	92 - 107
8	X-RAY DIFFRACTION	8	D	108 - 247
9	X-RAY DIFFRACTION	9	E	92 - 116
10	X-RAY DIFFRACTION	10	E	117 - 247
11	X-RAY DIFFRACTION	11	F	92 - 177
12	X-RAY DIFFRACTION	12	F	178 - 247

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