PDB-7zuh: PENICILLIN-BINDING PROTEIN 1B (PBP-1B) Streptococcus pneumoniae R6

ID or keywords:

Entry

Database: PDB / ID: 7zuh

Title

PENICILLIN-BINDING PROTEIN 1B (PBP-1B) Streptococcus pneumoniae R6

Components

Penicillin-binding protein 1b

Keywords

TRANSFERASE / CELL WALL / PEPTIDOGLYCAN SYNTHESIS ENZYME / INFECTION / DRUG-BINDING PROTEIN / LACTAM ANTIBIOTICS

Function / homology

Function and homology information

peptidoglycan glycosyltransferase / peptidoglycan glycosyltransferase activity / serine-type D-Ala-D-Ala carboxypeptidase activity / Transferases; Acyltransferases; Aminoacyltransferases / acyltransferase activity / penicillin binding / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / outer membrane-bounded periplasmic space ...
Similarity search - Function

Biological species

Streptococcus pneumoniae R6 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.467 Å

Authors

Flanders, P.L. / Contreras-Martel, C. / Martins, A. / Brown, N.W. / Shirley, J.D. / Nauta, K.M. / Dessen, A. / Carlson, E.E. / Ambrose, E.A.

Funding support

France,

United States, 6items

Organization	Grant number	Country
Agence Nationale de la Recherche (ANR)	ANR-10-INBS-0005-02	France
Agence Nationale de la Recherche (ANR)	ANR-17-EURE-0003	France
National Institutes of Health/National Center for Research Resources (NIH/NCRR)	R01 GM128439	United States
National Institutes of Health/National Center for Research Resources (NIH/NCRR)	K12 GM119955	United States
National Institutes of Health/National Center for Research Resources (NIH/NCRR)	TL1R002493	United States
National Institutes of Health/National Center for Research Resources (NIH/NCRR)	UL1TR002494	United States

Citation

Journal: Acs Chem.Biol. / Year: 2022
Title: Combined Structural Analysis and Molecular Dynamics Reveal Penicillin-Binding Protein Inhibition Mode with beta-Lactones.
Authors: Flanders, P.L. / Contreras-Martel, C. / Brown, N.W. / Shirley, J.D. / Martins, A. / Nauta, K.N. / Dessen, A. / Carlson, E.E. / Ambrose, E.A.

History

Deposition	May 12, 2022	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Nov 2, 2022	Provider: repository / Type: Initial release
Revision 1.1	Nov 30, 2022	Group: Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2	Jan 31, 2024	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	7zuh.cif.gz	209.5 KB	Display	PDBx/mmCIF format
PDB format	pdb7zuh.ent.gz		Display	PDB format
PDBx/mmJSON format	7zuh.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

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

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Related structure data

Related structure data	7zuiC 7zujC 7zukC 7zulC 2bg1S C: citing same article (ref.) S: Starting model for refinement
Similar structure data	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: Penicillin-binding protein 1b

hetero molecules

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

1

Idetical with deposited unit
defined by author
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	95.681, 147.016, 98.709
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	20
Space group name H-M	C222₁

Components on special symmetry positions

ID	Model	Components
1	1	AAA-917- CL
2	1	AAA-1555- HOH
3	1	AAA-1663- HOH

#1: Protein	Penicillin-binding protein 1b Mass: 89461.227 Da / Num. of mol.: 1 / Mutation: N656G R686Q R687Q Source method: isolated from a genetically manipulated source Details: ENGINEERED RESIDUE ASN 656 TO GLY ENGINEERED RESIDUE ARG 686 TO GLN ENGINEERED RESIDUE ARG 687 TO GLN Source: (gene. exp.) Streptococcus pneumoniae R6 (bacteria) / Strain: ATCC BAA-255 / R6 / Gene: pbp1b, spr1909 / Plasmid: PGEX-Amp / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: Q7CRA4, Transferases; Acyltransferases; Aminoacyltransferases, peptidoglycan glycosyltransferase
#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.: 25 / Source method: obtained synthetically / Formula: Cl
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 677 / 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: 3.32 Å³/Da / Density % sol: 61.84 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.2 Details: 50MM HEPES PH 7.2, 3M NACL, 0.6-0.9M AMMONIUM SULFATE

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.965459 Å
Detector	Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 10, 2021
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.965459 Å / Relative weight: 1
Reflection	Resolution: 1.467→43.06 Å / Num. obs: 117495 / % possible obs: 99.5 % / Redundancy: 5.2 % / B_iso Wilson estimate: 30.38 Å² / CC_1/2: 0.998 / R_sym value: 0.078 / Net I/σ(I): 11.77
Reflection shell	Resolution: 1.467→1.55 Å / Redundancy: 4.9 % / Mean I/σ(I) obs: 0.87 / Num. unique obs: 17059 / CC_1/2: 0.298 / R_sym value: 1.973 / % possible all: 99.3

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0267	refinement
XDS	20210323	data reduction
XSCALE	20210323	data scaling
PHASER	2.8.3	phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 2BG1 WITHOUT RESIDUES 654 TO 660

2bg1

Resolution: 1.467→43.051 Å / Cor.coef. F_o:F_c: 0.97 / Cor.coef. F_o:F_c free: 0.97 / SU B: 2.587 / SU ML: 0.046 / Cross valid method: FREE R-VALUE / ESU R: 0.059 / ESU R Free: 0.057
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.1995	2358	2.007 %
R_work	0.1894	115137	-
all	0.19	-	-
obs	-	117495	99.107 %

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: 46.129 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.483 Å²	0 Å²	-0 Å²
2-	-	-0.109 Å²	0 Å²
3-	-	-	-0.373 Å²

Refinement step

Cycle: LAST / Resolution: 1.467→43.051 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3615	0	26	677	4318

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.013	3721
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.015	3421
X-RAY DIFFRACTION	r_angle_refined_deg	1.234	1.641	5061
X-RAY DIFFRACTION	r_angle_other_deg	0.988	1.577	7882
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.757	5	478
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	33.903	24.076	184
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.052	15	615
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	20.246	15	14
X-RAY DIFFRACTION	r_chiral_restr	0.062	0.2	496
X-RAY DIFFRACTION	r_gen_planes_refined	0.034	0.02	4331
X-RAY DIFFRACTION	r_gen_planes_other	0.029	0.02	857
X-RAY DIFFRACTION	r_nbd_refined	0.217	0.2	826
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.191	0.2	3427
X-RAY DIFFRACTION	r_nbtor_refined	0.178	0.2	1872
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.089	0.2	1731
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.168	0.2	477
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.124	0.2	7
X-RAY DIFFRACTION	r_nbd_other	0.137	0.2	28
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.186	0.2	35
X-RAY DIFFRACTION	r_mcbond_it	2.473	2.571	1886
X-RAY DIFFRACTION	r_mcbond_other	2.461	2.569	1885
X-RAY DIFFRACTION	r_mcangle_it	3.102	3.852	2357
X-RAY DIFFRACTION	r_mcangle_other	3.101	3.854	2358
X-RAY DIFFRACTION	r_scbond_it	3.757	2.876	1835
X-RAY DIFFRACTION	r_scbond_other	3.756	2.877	1836
X-RAY DIFFRACTION	r_scangle_it	5.462	4.171	2698
X-RAY DIFFRACTION	r_scangle_other	5.461	4.172	2699
X-RAY DIFFRACTION	r_lrange_it	9.103	34.869	4656
X-RAY DIFFRACTION	r_lrange_other	8.913	32.366	4457

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
1.467-1.505	0.343	177	0.376	8011	0.375	8687	0.547	0.521	94.2558	0.381
1.505-1.547	0.33	196	0.349	8229	0.348	8487	0.534	0.527	99.2695	0.355
1.547-1.591	0.334	175	0.324	8060	0.324	8256	0.735	0.72	99.7456	0.326
1.591-1.64	0.312	157	0.311	7799	0.311	7976	0.866	0.856	99.7493	0.311
1.64-1.694	0.296	148	0.285	7581	0.285	7761	0.9	0.903	99.5877	0.281
1.694-1.753	0.245	145	0.262	7331	0.262	7511	0.924	0.919	99.534	0.253
1.753-1.819	0.255	150	0.223	7050	0.224	7240	0.926	0.94	99.4475	0.212
1.819-1.894	0.207	131	0.195	6834	0.195	7000	0.946	0.957	99.5	0.18
1.894-1.978	0.209	151	0.175	6523	0.176	6709	0.949	0.956	99.4783	0.159
1.978-2.074	0.169	116	0.151	6284	0.152	6428	0.958	0.967	99.5644	0.137
2.074-2.186	0.145	114	0.137	5994	0.137	6121	0.972	0.974	99.7876	0.126
2.186-2.318	0.211	118	0.157	5662	0.158	5796	0.961	0.973	99.7239	0.15
2.318-2.477	0.207	89	0.178	5345	0.178	5445	0.974	0.976	99.798	0.176
2.477-2.675	0.241	103	0.21	4981	0.211	5107	0.971	0.973	99.5496	0.212
2.675-2.929	0.218	88	0.216	4582	0.216	4709	0.956	0.964	99.1718	0.228
2.929-3.273	0.193	66	0.188	4150	0.188	4259	0.948	0.962	98.9904	0.209
3.273-3.776	0.132	74	0.153	3672	0.152	3787	0.98	0.976	98.9174	0.178
3.776-4.616	0.139	65	0.135	3139	0.135	3234	0.982	0.98	99.0724	0.162
4.616-6.491	0.196	60	0.151	2467	0.152	2536	0.962	0.97	99.6451	0.18
6.491-43.051	0.229	35	0.274	1442	0.273	1497	0.973	0.97	98.664	0.284

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	11.9366	1.2084	-0.155	3.6898	3.598	4.0143	-0.8703	-1.5054	0.9254	-1.5422	-0.1152	0.6636	-1.3118	-0.3621	0.9855	0.8256	0.0186	-0.2494	0.4637	-0.3926	0.4754	23.0063	46.6183	-3.3984
2	8.7826	1.0613	3.2161	0.7099	0.7877	2.4769	-0.0931	-0.092	-0.2036	-0.0118	0.0442	-0.0949	-0.0174	0.0162	0.0489	0.2392	-0.0527	0.0057	0.1994	-0.0483	0.207	28.2856	35.6416	5.9082
3	2.7138	1.1918	-0.3755	6.125	-3.6946	7.9164	-0.0719	-0.0176	-0.1924	0.1799	-0.1263	-0.2132	0.206	-0.0485	0.1982	0.198	-0.0525	-0.002	0.2202	-0.0786	0.2471	30.8206	35.3768	13.6931
4	1.1284	0.0326	0.0628	0.9762	-0.1337	0.8972	-0.0607	-0.0588	0.1415	0.1152	-0.0156	-0.0127	-0.1492	-0.0218	0.0763	0.2001	-0.003	-0.0316	0.1547	-0.0172	0.1792	11.8534	29.6641	-7.4844
5	0.591	-0.0023	0.1667	1.1203	-0.1425	0.6972	0.0198	-0.0273	-0.0971	0.0002	-0.046	-0.0107	0.1262	0.0083	0.0262	0.1709	-0.0006	0.0003	0.1369	0.0094	0.1878	18.6801	6.9582	-11.9407
6	5.1625	7.0793	4.8389	12.9703	7.2928	4.6744	-0.2541	0.2714	0.0214	-0.3432	0.3489	-0.4136	-0.2341	0.29	-0.0948	0.1702	-0.0671	-0.0274	0.3049	-0.0612	0.2497	33.8549	39.2188	-2.499
7	1.8521	-0.7008	0.0609	1.2924	-0.2986	0.812	-0.0227	-0.0096	-0.0249	-0.0531	-0.0228	-0.03	0.0477	0.0088	0.0454	0.2063	-0.013	0.0003	0.1819	-0.0046	0.1784	15.2534	19.2372	-21.9531
8	3.4996	0.5106	-2.5259	1.772	-1.0219	4.8478	-0.1099	-0.0212	-0.1142	0.071	0.0298	0.111	0.1153	-0.2092	0.0802	0.2101	0.0031	-0.0199	0.1808	-0.0117	0.2085	8.3423	20.7252	-9.3555
9	0.749	-0.1431	0.1323	0.8299	-0.0476	0.928	-0.0414	0.1148	0.0636	-0.1606	-0.0416	-0.078	-0.0322	0.0666	0.0831	0.1712	-0.0195	-0.0013	0.1467	0.0167	0.1511	14.9068	24.7798	-23.1655
10	5.6519	0.4931	-1.6498	9.8868	-0.1008	3.965	-0.1742	0.1426	-0.7661	-0.3197	0.0795	0.1187	0.7353	0.0536	0.0947	0.4002	0.076	0.0304	0.2026	-0.1383	0.2296	20.2126	-11.3147	-31.3286
11	2.6113	1.3935	-0.4218	3.6929	-0.6153	2.1453	-0.0319	0.337	-0.4976	-0.4874	0.0286	-0.1338	0.5483	0.0022	0.0032	0.3505	0.0646	0.0093	0.1206	-0.1023	0.2385	19.1797	-8.0042	-27.9022

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	ALL	AAA	105 - 119
2	X-RAY DIFFRACTION	2	ALL	AAA	337 - 362
3	X-RAY DIFFRACTION	3	ALL	AAA	363 - 389
4	X-RAY DIFFRACTION	4	ALL	AAA	390 - 466
5	X-RAY DIFFRACTION	5	ALL	AAA	467 - 584
6	X-RAY DIFFRACTION	6	ALL	AAA	585 - 601
7	X-RAY DIFFRACTION	7	ALL	AAA	602 - 657
8	X-RAY DIFFRACTION	8	ALL	AAA	658 - 687
9	X-RAY DIFFRACTION	9	ALL	AAA	688 - 727
10	X-RAY DIFFRACTION	10	ALL	AAA	728 - 744
11	X-RAY DIFFRACTION	11	ALL	AAA	745 - 790

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