PDB-7zuj: PENICILLIN-BINDING PROTEIN 1B (PBP-1B) in complex with lactone 6A...

ID or keywords:

Entry

Database: PDB / ID: 7zuj

Title

PENICILLIN-BINDING PROTEIN 1B (PBP-1B) in complex with lactone 6Az - 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: 1.55 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
Revision 1.3	Oct 9, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	7zuj.cif.gz	202.8 KB	Display	PDBx/mmCIF format
PDB format	pdb7zuj.ent.gz		Display	PDB format
PDBx/mmJSON format	7zuj.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	7zuj_validation.pdf.gz	691.3 KB	Display	wwPDB validaton report
Full document	7zuj_full_validation.pdf.gz	695.6 KB	Display
Data in XML	7zuj_validation.xml.gz	24.3 KB	Display
Data in CIF	7zuj_validation.cif.gz	37.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/zu/7zuj ftp://data.pdbj.org/pub/pdb/validation_reports/zu/7zuj	HTTPS FTP

-
Related structure data

Related structure data	7zuhC 7zuiC 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

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

AAA: Penicillin-binding protein 1b

hetero molecules

90.7 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)	96.306, 149.053, 98.835
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-916- CL
2	1	AAA-1437- 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 RESIDUES ASN 656 GLY ENGINEERED RESIDUES ARG 686 GLN ENGINEERED RESIDUES ARG 656 GLN Source: (gene. exp.) Streptococcus pneumoniae R6 (bacteria) / Strain: ATCC BAA-255 / R6 / Gene: pbp1b, spr1909 / Plasmid: PGEX-Amp / Production host: Escherichia coli (E. coli) References: UniProt: Q7CRA4, Transferases; Acyltransferases; Aminoacyltransferases, peptidoglycan glycosyltransferase
#2: Chemical	ChemComp-KQN / 6-azido-N-[(2S)-1-oxidanylidene-1-[[(2S,3R)-3-oxidanyl-1-oxidanylidene-butan-2-yl]amino]propan-2-yl]hexanamide / Beta-lactone antibacterial agent (open form) Mass: 313.353 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₃H₂₃N₅O₄ / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	... ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 25 / Source method: obtained synthetically / Formula: Cl
#4: Chemical	ChemComp-DMS / DIMETHYL SULFOXIDE Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₆OS / Comment: DMSO, precipitant*YM
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 549 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	Y

-
Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

Crystal	Density Matthews: 3.29 Å³/Da / Density % sol: 62.66 %
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

-
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: 1.535→44.16 Å / Num. obs: 105235 / % possible obs: 98.4 % / Redundancy: 4.8 % / B_iso Wilson estimate: 35.582 Å² / CC_1/2: 0.985 / R_sym value: 0.131 / Net I/σ(I): 5.93
Reflection shell	Resolution: 1.535→1.63 Å / Redundancy: 4.6 % / Mean I/σ(I) obs: 0.74 / Num. unique obs: 17050 / CC_1/2: 0.325 / R_sym value: 1.663 / % possible all: 93.1

-
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: 1.55→44.155 Å / Cor.coef. F_o:F_c: 0.975 / Cor.coef. F_o:F_c free: 0.956 / SU B: 3.25 / SU ML: 0.055 / Cross valid method: FREE R-VALUE / ESU R: 0.057 / ESU R Free: 0.06
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.1897	2034	1.987 %
R_work	0.1654	100307	-
all	0.166	-	-
obs	-	102341	99.432 %

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: 42.832 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.906 Å²	0 Å²	-0 Å²
2-	-	-0.331 Å²	0 Å²
3-	-	-	-0.575 Å²

Refinement step

Cycle: LAST / Resolution: 1.55→44.155 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3506	0	51	549	4106

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.013	3639
X-RAY DIFFRACTION	r_bond_other_d	0	0.015	3347
X-RAY DIFFRACTION	r_angle_refined_deg	1.223	1.643	4942
X-RAY DIFFRACTION	r_angle_other_deg	1.402	1.579	7705
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.42	5	465
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	32.412	23.476	187
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	11.366	15	597
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	12.095	15	16
X-RAY DIFFRACTION	r_chiral_restr	0.062	0.2	477
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	4240
X-RAY DIFFRACTION	r_gen_planes_other	0	0.02	852
X-RAY DIFFRACTION	r_nbd_refined	0.21	0.2	771
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.193	0.2	3140
X-RAY DIFFRACTION	r_nbtor_refined	0.17	0.2	1811
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.089	0.2	1559
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.146	0.2	384
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.326	0.2	13
X-RAY DIFFRACTION	r_nbd_other	0.221	0.2	40
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.39	0.2	26
X-RAY DIFFRACTION	r_xyhbond_nbd_other	0.49	0.2	2
X-RAY DIFFRACTION	r_mcbond_it	1.911	2.414	1830
X-RAY DIFFRACTION	r_mcbond_other	1.911	2.414	1831
X-RAY DIFFRACTION	r_mcangle_it	2.451	3.619	2287
X-RAY DIFFRACTION	r_mcangle_other	2.451	3.62	2288
X-RAY DIFFRACTION	r_scbond_it	3.499	2.761	1809
X-RAY DIFFRACTION	r_scbond_other	3.498	2.763	1810
X-RAY DIFFRACTION	r_scangle_it	5.187	3.988	2649
X-RAY DIFFRACTION	r_scangle_other	5.186	3.99	2650
X-RAY DIFFRACTION	r_lrange_it	8.436	31.719	4417
X-RAY DIFFRACTION	r_lrange_other	8.37	30.304	4303

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
1.55-1.59	0.383	133	0.424	7310	0.423	7514	0.488	0.435	99.0551	0.43
1.59-1.634	0.377	157	0.386	7128	0.386	7354	0.556	0.542	99.0617	0.394
1.634-1.681	0.369	175	0.329	6929	0.33	7169	0.719	0.773	99.0933	0.328
1.681-1.733	0.229	140	0.263	6748	0.262	6937	0.871	0.868	99.2936	0.254
1.733-1.789	0.242	138	0.228	6563	0.228	6736	0.895	0.903	99.4804	0.213
1.789-1.852	0.212	124	0.2	6355	0.2	6507	0.93	0.928	99.5697	0.183
1.852-1.922	0.203	131	0.179	6158	0.179	6313	0.94	0.95	99.6198	0.164
1.922-2	0.184	127	0.167	5909	0.168	6052	0.955	0.958	99.7356	0.156
2-2.089	0.198	131	0.154	5669	0.155	5816	0.958	0.965	99.7249	0.149
2.089-2.191	0.186	91	0.146	5482	0.146	5600	0.959	0.967	99.5179	0.147
2.191-2.309	0.162	104	0.143	5120	0.143	5284	0.968	0.968	98.8645	0.151
2.309-2.448	0.158	93	0.139	4929	0.139	5035	0.969	0.971	99.7418	0.152
2.448-2.617	0.192	72	0.151	4669	0.151	4745	0.958	0.967	99.9157	0.17
2.617-2.826	0.155	71	0.159	4362	0.159	4434	0.968	0.965	99.9774	0.186
2.826-3.094	0.191	77	0.17	4000	0.17	4079	0.958	0.957	99.951	0.208
3.094-3.457	0.184	79	0.154	3615	0.155	3702	0.96	0.964	99.7839	0.196
3.457-3.988	0.224	67	0.15	3197	0.152	3285	0.886	0.928	99.3607	0.203
3.988-4.875	0.152	49	0.142	2711	0.142	2805	0.955	0.96	98.3957	0.201
4.875-6.852	0.171	51	0.161	2157	0.161	2214	0.971	0.971	99.729	0.228
6.852-44.155	0.167	24	0.176	1266	0.176	1309	0.975	0.973	98.5485	0.225

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	7.2455	-1.0463	-2.9644	0.9737	1.1823	2.6569	-0.1451	0.056	0.2548	-0.0097	0.0594	-0.0491	-0.0781	-0.0149	0.0858	0.1792	0.0774	-0.0081	0.2111	-0.0457	0.2385	29.2754	-35.1795	-6.9636
2	4.8851	1.9094	0.4922	10.1802	-4.7428	9.8291	0.0464	-0.0299	0.174	-0.2458	-0.2252	0.0587	-0.189	-0.2678	0.1788	0.1582	0.1007	-0.0067	0.2327	-0.0857	0.2509	30.216	-35.0176	-15.5947
3	10.4608	-3.7638	-10.1205	2.221	5.5184	13.9105	-0.4932	-0.015	-0.5411	0.3148	0.1389	0.1112	0.8445	0.2509	0.3543	0.2506	0.0664	0.0849	0.1486	0.0179	0.3104	24.9896	-42.7409	5.53
4	1.0368	0.0414	-0.0528	1.1453	-0.1653	0.8025	-0.0645	0.103	-0.0938	-0.1604	-0.0001	0.028	0.1419	-0.0179	0.0645	0.1065	0.0031	0.022	0.1777	-0.0194	0.1916	10.4274	-28.5496	7.1522
5	0.5729	-0.019	-0.1613	1.092	-0.1049	0.5585	0.021	0.0247	0.115	-0.0045	-0.0444	0.0045	-0.0966	0.0332	0.0234	0.0724	-0.0037	0.0015	0.1574	0.0037	0.2122	18.8825	-7.7524	11.7672
6	3.597	-6.2669	-4.5576	15.3998	9.5111	6.3355	-0.2228	-0.4695	0.2305	0.2343	0.6382	-0.6408	0.2069	0.582	-0.4154	0.142	0.0523	0.0685	0.3622	-0.0855	0.2702	35.7646	-38.6292	2.7371
7	0.8058	0.3271	-0.2315	0.9261	-0.1934	0.7197	-0.0022	-0.1025	0.0025	0.0907	-0.022	-0.0367	-0.0154	0.0651	0.0242	0.0829	0.0059	-0.0048	0.1673	0.002	0.1777	14.4866	-19.3567	22.4894
8	3.5941	-0.4601	1.7462	2.0364	-0.4078	3.5441	-0.1006	0.0934	0.1319	-0.1554	0.0154	0.072	-0.0639	-0.1541	0.0853	0.1287	-0.0017	0.011	0.1973	-0.0004	0.2283	7.768	-20.6608	9.0025
9	0.6772	0.2015	-0.2954	0.6928	-0.0567	0.8238	-0.0204	-0.1595	0.0048	0.1938	-0.0351	-0.09	-0.0323	0.1077	0.0555	0.1	0.0183	-0.0221	0.1727	0.0004	0.1753	15.3124	-20.9778	24.1815
10	4.358	-0.9625	-0.3987	14.3095	0.6826	2.7426	-0.3074	-0.7186	0.8913	0.5396	0.4082	-0.1785	-0.8288	0.399	-0.1008	0.391	-0.0955	-0.0538	0.2575	-0.2062	0.2344	20.816	10.1695	33.402
11	2.0044	-0.4805	0.3552	2.1652	-0.5057	1.8141	0.058	-0.1479	0.5249	0.1873	-0.0715	-0.3498	-0.452	0.2275	0.0135	0.2218	-0.0974	-0.0159	0.1265	-0.0823	0.2922	22.2867	6.4184	23.4825
12	13.8539	-1.526	-8.5054	2.8891	7.3564	20.6762	0.3716	-1.0763	0.2751	-0.2858	-0.4807	-0.0028	-1.1599	-0.9994	0.1091	0.7513	0.2588	0.0079	0.4147	-0.2304	0.3444	11.5314	13.4646	29.8922

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	ALL	AAA	337 - 364
2	X-RAY DIFFRACTION	2	ALL	AAA	365 - 385
3	X-RAY DIFFRACTION	3	ALL	AAA	386 - 397
4	X-RAY DIFFRACTION	4	ALL	AAA	398 - 466
5	X-RAY DIFFRACTION	5	ALL	AAA	467 - 587
6	X-RAY DIFFRACTION	6	ALL	AAA	588 - 603
7	X-RAY DIFFRACTION	7	ALL	AAA	604 - 656
8	X-RAY DIFFRACTION	8	ALL	AAA	657 - 687
9	X-RAY DIFFRACTION	9	ALL	AAA	688 - 734
10	X-RAY DIFFRACTION	10	ALL	AAA	735 - 756
11	X-RAY DIFFRACTION	11	ALL	AAA	757 - 779
12	X-RAY DIFFRACTION	12	ALL	AAA	780 - 790

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi