PDB-7zul: PENICILLIN-BINDING PROTEIN 1B (PBP-1B) in complex with 8Az lacton...

ID or keywords:

Entry

Database: PDB / ID: 7zul

Title

PENICILLIN-BINDING PROTEIN 1B (PBP-1B) in complex with 8Az lactone - 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: 1.744 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 23, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7zul.cif.gz	199.4 KB	Display	PDBx/mmCIF format
PDB format	pdb7zul.ent.gz		Display	PDB format
PDBx/mmJSON format	7zul.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	7zul_validation.pdf.gz	786.5 KB	Display	wwPDB validaton report
Full document	7zul_full_validation.pdf.gz	794 KB	Display
Data in XML	7zul_validation.xml.gz	22.4 KB	Display
Data in CIF	7zul_validation.cif.gz	33.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/zu/7zul ftp://data.pdbj.org/pub/pdb/validation_reports/zu/7zul	HTTPS FTP

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Related structure data

Related structure data	7zuhC 7zuiC 7zujC 7zukC 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

90.8 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)	96.934, 149.773, 98.872
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-928- CL

#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 TO GLY ENGINEERED RESIDUE ARG TO GLN ENGINEERED RESIDUE ARG 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-JWL / 6-azido-N-[(2R)-1-oxidanylidene-1-[[(2S,3R)-3-oxidanyl-1-oxidanylidene-butan-2-yl]amino]-3-phenyl-propan-2-yl]hexanamide / Beta-lactone antibacterial agent (open form) Mass: 389.449 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₉H₂₇N₅O₄ / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	... ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 27 / Source method: obtained synthetically / Formula: Cl
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 383 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
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: 3.33 Å³/Da / Density % sol: 63.05 %
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: Feb 1, 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: 1.744→42.251 Å / Num. obs: 71666 / % possible obs: 97.1 % / Redundancy: 4.7 % / B_iso Wilson estimate: 38.906 Å² / CC_1/2: 0.996 / R_sym value: 0.1025 / Net I/σ(I): 8.01
Reflection shell	Resolution: 1.744→1.85 Å / Redundancy: 4.4 % / Mean I/σ(I) obs: 0.65 / Num. unique obs: 11252 / CC_1/2: 0.248 / R_sym value: 1.972 / % possible all: 91.6

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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: 1.744→42.251 Å / Cor.coef. F_o:F_c: 0.971 / Cor.coef. F_o:F_c free: 0.96 / SU B: 5.879 / SU ML: 0.089 / Cross valid method: FREE R-VALUE / ESU R: 0.087 / ESU R Free: 0.088
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2063	2192	3.059 %
R_work	0.1802	69473	-
all	0.181	-	-
obs	-	71665	97.736 %

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: 52.285 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.993 Å²	-0 Å²	-0 Å²
2-	-	1.993 Å²	-0 Å²
3-	-	-	0 Å²

Refinement step

Cycle: LAST / Resolution: 1.744→42.251 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3506	0	55	383	3944

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.013	3649
X-RAY DIFFRACTION	r_bond_other_d	0	0.015	3355
X-RAY DIFFRACTION	r_angle_refined_deg	1.242	1.642	4958
X-RAY DIFFRACTION	r_angle_other_deg	1.329	1.578	7727
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.272	5	467
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	33.292	23.656	186
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	11.929	15	600
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.911	15	15
X-RAY DIFFRACTION	r_chiral_restr	0.06	0.2	479
X-RAY DIFFRACTION	r_chiral_restr_other	0.001	0.2	1
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.02	4255
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	855
X-RAY DIFFRACTION	r_nbd_refined	0.203	0.2	724
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.188	0.2	3047
X-RAY DIFFRACTION	r_nbtor_refined	0.166	0.2	1795
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.087	0.2	1529
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.135	0.2	270
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.133	0.2	12
X-RAY DIFFRACTION	r_nbd_other	0.194	0.2	32
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.22	0.2	17
X-RAY DIFFRACTION	r_xyhbond_nbd_other	0.109	0.2	1
X-RAY DIFFRACTION	r_mcbond_it	2.529	3.166	1832
X-RAY DIFFRACTION	r_mcbond_other	2.524	3.166	1831
X-RAY DIFFRACTION	r_mcangle_it	3.116	4.741	2290
X-RAY DIFFRACTION	r_mcangle_other	3.117	4.742	2291
X-RAY DIFFRACTION	r_scbond_it	4.202	3.581	1817
X-RAY DIFFRACTION	r_scbond_other	4.12	3.578	1816
X-RAY DIFFRACTION	r_scangle_it	5.899	5.197	2661
X-RAY DIFFRACTION	r_scangle_other	5.898	5.2	2662
X-RAY DIFFRACTION	r_lrange_it	8.473	39.02	4252
X-RAY DIFFRACTION	r_lrange_other	8.434	38.247	4194

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
1.744-1.79	0.538	142	0.511	4863	0.512	5351	0.633	0.63	93.5339	0.52
1.79-1.838	0.432	143	0.44	4941	0.44	5235	0.553	0.586	97.1156	0.445
1.838-1.892	0.394	142	0.352	4769	0.353	5077	0.721	0.73	96.7304	0.348
1.892-1.95	0.335	135	0.295	4708	0.296	4949	0.837	0.845	97.8582	0.278
1.95-2.014	0.259	142	0.259	4554	0.259	4795	0.89	0.893	97.9353	0.227
2.014-2.084	0.286	134	0.253	4412	0.254	4638	0.892	0.906	98.0164	0.218
2.084-2.163	0.232	130	0.217	4291	0.218	4489	0.926	0.932	98.4852	0.181
2.163-2.251	0.227	142	0.199	4105	0.2	4322	0.93	0.94	98.2647	0.164
2.251-2.35	0.204	125	0.175	3970	0.176	4141	0.944	0.956	98.8892	0.143
2.35-2.465	0.207	124	0.172	3804	0.173	3973	0.948	0.955	98.8674	0.141
2.465-2.598	0.221	117	0.175	3604	0.177	3770	0.944	0.954	98.7003	0.149
2.598-2.754	0.189	115	0.166	3390	0.167	3593	0.96	0.962	97.5508	0.15
2.754-2.944	0.211	115	0.179	3250	0.18	3385	0.949	0.955	99.4092	0.168
2.944-3.178	0.214	100	0.172	3021	0.174	3146	0.944	0.958	99.2053	0.173
3.178-3.48	0.192	93	0.149	2786	0.151	2913	0.95	0.965	98.8328	0.159
3.48-3.887	0.154	86	0.128	2520	0.129	2657	0.973	0.977	98.0805	0.143
3.887-4.482	0.154	61	0.137	2241	0.137	2336	0.965	0.974	98.5445	0.159
4.482-5.474	0.153	63	0.146	1862	0.147	2009	0.977	0.977	95.8188	0.173
5.474-7.677	0.202	46	0.169	1519	0.17	1583	0.96	0.96	98.8629	0.193
7.677-42.251	0.209	37	0.201	864	0.202	956	0.82	0.895	94.2469	0.243

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	12.5636	-1.5148	-5.5624	1.4967	1.6024	3.2623	-0.2254	-0.0073	0.0688	-0.0034	0.0881	-0.0008	0.0457	-0.0019	0.1373	0.376	0.0635	0.0002	0.1422	-0.0385	0.2248	28.8467	-36.0521	-6.2914
2	3.6276	-1.1693	0.6382	10.7207	-5.7179	9.6206	-0.005	0.0698	0.1631	-0.1007	-0.1243	-0.1574	-0.135	-0.224	0.1293	0.3233	0.1005	-0.0094	0.1023	-0.0946	0.2574	31.1745	-35.5852	-14.631
3	15.7804	-3.4523	-11.1367	1.7959	5.1911	15.1931	-0.5032	-0.2535	-0.964	0.2941	0.0487	0.0876	0.8603	0.1759	0.4545	0.402	0.0882	0.0327	0.0402	0.0444	0.3174	23.4611	-41.7684	8.4997
4	1.1376	0.1445	-0.0271	1.0241	-0.1987	0.5669	-0.0701	0.1076	-0.0883	-0.1649	0.0251	0.0389	0.1439	-0.0172	0.0449	0.3606	-0.0017	0.0203	0.0172	-0.0123	0.1524	10.4502	-28.7334	6.9602
5	0.7817	0.0965	-0.2626	1.2877	-0.1855	0.7684	0.0456	0.0313	0.1847	-0.0419	-0.0213	0.0249	-0.1357	0.0333	-0.0243	0.3163	-0.0063	0.0107	0.0043	0.0081	0.1913	18.9073	-7.8876	11.7863
6	4.0491	-6.9128	-5.7097	20.147	9.6966	8.0695	-0.1815	-0.5756	0.3344	0.2917	0.7092	-0.9026	0.1935	0.8	-0.5277	0.308	0.103	0.0348	0.2394	-0.0412	0.3181	36.0338	-38.7529	2.8841
7	1.0645	0.3049	-0.2549	1.0826	-0.1045	0.86	-0.0068	-0.0826	0.0237	0.0476	-0.0171	-0.0244	0.003	0.0473	0.0239	0.3484	0.0129	0.0102	0.0109	-0.0007	0.1614	12.7618	-21.7622	18.967
8	8.3037	-4.0249	1.4583	13.0315	-1.4936	3.054	-0.0132	-0.2601	1.2594	0.9229	0.0808	-0.0243	-0.7061	0.263	-0.0677	0.5534	-0.1133	0.0385	0.1581	-0.1932	0.4129	20.7774	11.3938	32.3607
9	4.4597	-1.5118	0.9775	3.5511	-1.1058	2.8162	0.0605	-0.4565	0.6927	0.4417	0.0537	-0.1129	-0.6622	0.0807	-0.1142	0.5403	-0.1005	0.0354	0.0783	-0.1286	0.2965	19.1267	6.9564	27.438

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	ALL	AAA	337 - 362
2	X-RAY DIFFRACTION	2	ALL	AAA	363 - 388
3	X-RAY DIFFRACTION	3	ALL	AAA	389 - 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 - 726
8	X-RAY DIFFRACTION	8	ALL	AAA	727 - 747
9	X-RAY DIFFRACTION	9	ALL	AAA	748 - 790

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