PDB-9sga: PENICILLIN-BINDING PROTEIN 1B (PBP-1B) IN COMPLEX WITH A MONOBACT...

ID or keywords:

Entry

Database: PDB / ID: 9sga

Title

PENICILLIN-BINDING PROTEIN 1B (PBP-1B) IN COMPLEX WITH A MONOBACTAM (21)

Components

Penicillin-binding protein 1B

Keywords

TRANSFERASE / CELL WALL / PEPTIDOGLYCAN SYNTHESIS ENZYME / DRUG-BINDING PROTEIN / MONOBACTAM

Function / homology

Function and homology information

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

Biological species

Streptococcus pneumoniae (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.5 Å

Authors

Contreras-Martel, C. / Kavas, V.

Funding support

Slovenia,

France, 5items

Organization	Grant number	Country
Slovenian Research Agency	P1-0208	Slovenia
Slovenian Research Agency	J1-50039	Slovenia
Slovenian Research Agency	J3-50123	Slovenia
French Infrastructure for Integrated Structural Biology (FRISBI)	ANR-10-INBS-05-02	France
Grenoble Alliance for Integrated Structural Cell Biology (GRAL)	ANR-17-EURE-0003	France

Citation

Journal: J.Med.Chem. / Year: 2026
Title: Structure-Activity Relationship and Crystallographic Study of New Monobactams.
Authors: Kavas, V. / Contreras-Martel, C. / Pajk, S. / Knez, D. / Martins, A. / Gould, T.A. / Roper, D.I. / Zdovc, I. / Dessen, A. / Hrast Rambaher, M. / Gobec, S.

History

Deposition	Aug 22, 2025	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Feb 18, 2026	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9sga.cif.gz	249.6 KB	Display	PDBx/mmCIF format
PDB format	pdb9sga.ent.gz		Display	PDB format
PDBx/mmJSON format	9sga.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/sg/9sga ftp://data.pdbj.org/pub/pdb/validation_reports/sg/9sga	HTTPS FTP

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Related structure data

Related structure data	9sg5C 9sg6C 9sg7C 9sg8C 9sg9C 9sgbC 9sgcC 9sgdC 9sgeC C: citing same article (ref.)
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

A: Penicillin-binding protein 1B

hetero molecules

55.4 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)	97.163, 149.084, 98.457
Angle α, β, γ (deg.)	90, 90, 90
Int Tables number	20
Space group name H-M	C222₁

Components on special symmetry positions

ID	Model	Components
1	1	A-816- CL
2	1	A-1259- HOH

#1: Protein	Penicillin-binding protein 1B Mass: 54085.879 Da / Num. of mol.: 1 / Mutation: N656G, R686Q, R687Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Strain: ATCC / Gene: pbp1b / Plasmid: PGEX-Amp / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O70038
#2: Chemical	ChemComp-A1JNU / [(2~{S},3~{S})-4-oxidanylidene-3-(2-phenylethanoylamino)butan-2-yl]sulfamic acid Mass: 300.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₂H₁₆N₂O₅S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	... ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 26 / Source method: obtained synthetically / Formula: Cl
#4: Chemical	ChemComp-TAU / 2-AMINOETHANESULFONIC ACID Mass: 125.147 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₇NO₃S / Feature type: SUBJECT OF INVESTIGATION
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 406 / 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: 3.31 Å³/Da / Density % sol: 62.85 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting 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 PILATUS3 6M / Detector: PIXEL / Date: Apr 19, 2024
Radiation	Monochromator: C(110) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.965459 Å / Relative weight: 1
Reflection	Resolution: 1.5→48.59 Å / Num. obs: 110122 / % possible obs: 96.6 % / Redundancy: 3.8 % / B_iso Wilson estimate: 35.46 Å² / CC_1/2: 0.998 / R_sym value: 0.052 / Net I/σ(I): 10.26
Reflection shell	Resolution: 1.5→1.59 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 0.75 / Num. unique obs: 17890 / CC_1/2: 0.272 / R_sym value: 0.156 / % possible all: 98.5

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0425	refinement
XDS	20230630	data reduction
XSCALE	20230630	data scaling
PHASER	2.8.3	phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.5→48.582 Å / Cor.coef. F_o:F_c: 0.978 / Cor.coef. F_o:F_c free: 0.968 / SU B: 3.032 / SU ML: 0.051 / Cross valid method: FREE R-VALUE / ESU R: 0.054 / ESU R Free: 0.058
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.1955	2092	1.9 %
R_work	0.1669	108029	-
all	0.167	-	-
obs	-	110121	96.569 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 35.035 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.2 Å²	-0 Å²	0 Å²
2-	-	-0.458 Å²	-0 Å²
3-	-	-	0.659 Å²

Refinement step

Cycle: LAST / Resolution: 1.5→48.582 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3624	0	53	406	4083

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.012	3788
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	3477
X-RAY DIFFRACTION	r_angle_refined_deg	1.299	1.81	5149
X-RAY DIFFRACTION	r_angle_other_deg	0.468	1.75	7997
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.408	5	482
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	6.595	5	18
X-RAY DIFFRACTION	r_dihedral_angle_other_2_deg	5.267	5	2
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	11.399	10	619
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	15.171	10	173
X-RAY DIFFRACTION	r_chiral_restr	0.076	0.2	567
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	4535
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	885
X-RAY DIFFRACTION	r_nbd_refined	0.217	0.2	737
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.189	0.2	3088
X-RAY DIFFRACTION	r_nbtor_refined	0.183	0.2	1858
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.076	0.2	1897
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.189	0.2	305
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.165	0.2	11
X-RAY DIFFRACTION	r_nbd_other	0.167	0.2	44
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.275	0.2	29
X-RAY DIFFRACTION	r_mcbond_it	1.776	1.935	1892
X-RAY DIFFRACTION	r_mcbond_other	1.773	1.935	1892
X-RAY DIFFRACTION	r_mcangle_it	2.485	3.473	2365
X-RAY DIFFRACTION	r_mcangle_other	2.485	3.474	2366
X-RAY DIFFRACTION	r_scbond_it	3.801	2.309	1896
X-RAY DIFFRACTION	r_scbond_other	3.802	2.309	1897
X-RAY DIFFRACTION	r_scangle_it	5.787	4.056	2777
X-RAY DIFFRACTION	r_scangle_other	5.786	4.056	2778
X-RAY DIFFRACTION	r_lrange_it	7.374	21.004	4401
X-RAY DIFFRACTION	r_lrange_other	7.244	19.721	4308

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
1.5-1.539	0.642	140	0.607	8138	0.608	8397	0.625	0.646	98.5828	0.61
1.539-1.581	0.505	140	0.488	7859	0.489	8116	0.879	0.892	98.5584	0.485
1.581-1.627	0.406	171	0.413	7567	0.413	7925	0.927	0.931	97.6404	0.399
1.627-1.677	0.38	142	0.333	7468	0.334	7713	0.946	0.954	98.6646	0.307
1.677-1.732	0.304	154	0.264	7154	0.265	7445	0.957	0.966	98.1598	0.227
1.732-1.792	0.261	144	0.222	6935	0.222	7240	0.964	0.974	97.7762	0.185
1.792-1.86	0.191	112	0.181	6716	0.181	6993	0.978	0.981	97.6405	0.146
1.86-1.936	0.19	127	0.159	6342	0.16	6706	0.979	0.985	96.4659	0.131
1.936-2.022	0.171	119	0.149	6201	0.149	6468	0.982	0.987	97.7118	0.129
2.022-2.12	0.184	118	0.151	5862	0.151	6169	0.983	0.988	96.9363	0.136
2.12-2.235	0.18	93	0.149	5559	0.149	5876	0.98	0.989	96.1879	0.141
2.235-2.37	0.174	98	0.143	5256	0.144	5587	0.985	0.989	95.8296	0.139
2.37-2.533	0.155	96	0.144	4859	0.144	5232	0.985	0.988	94.7057	0.145
2.533-2.736	0.183	107	0.152	4602	0.153	4903	0.978	0.987	96.0432	0.158
2.736-2.996	0.191	87	0.166	4219	0.167	4530	0.98	0.984	95.0552	0.181
2.996-3.348	0.171	72	0.157	3752	0.158	4099	0.985	0.986	93.291	0.179
3.348-3.863	0.155	57	0.128	3290	0.129	3639	0.987	0.99	91.9758	0.155
3.863-4.723	0.156	52	0.123	2845	0.124	3111	0.985	0.992	93.1212	0.155
4.723-6.648	0.221	45	0.184	2171	0.185	2438	0.981	0.986	90.8942	0.23
6.648-48.582	0.235	18	0.186	1235	0.187	1443	0.981	0.978	86.833	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	6.5522	0.4735	1.2627	7.5645	2.7054	9.8789	-0.1536	-0.5141	0.5577	0.1855	-0.0466	0.2633	-0.4646	-0.3047	0.2002	0.1431	-0.0063	-0.0866	0.0854	-0.0111	0.1331	22.2719	46.7803	-2.8957
2	9.1107	0.5095	3.8016	0.8167	0.4575	2.7736	-0.0704	0.0244	-0.2399	-0.0065	0.0346	-0.0219	0.0627	0.0177	0.0358	0.1671	-0.0385	0.0054	0.1347	-0.0461	0.063	28.9062	36.1541	6.0986
3	3.467	0.5794	0.4165	5.7467	-3.4993	7.612	-0.0597	-0.1275	-0.2062	0.1206	-0.1465	-0.1847	0.2489	0.0324	0.2062	0.1668	-0.0399	0.0014	0.1932	-0.0693	0.1323	31.3074	35.9476	13.728
4	2.5	0.5112	-0.0106	1.2909	-0.1183	0.9088	-0.0456	-0.1105	0.1034	0.113	-0.0277	0.0587	-0.1017	-0.0599	0.0733	0.1532	0.0014	-0.0274	0.1126	-0.0127	0.0159	11.1484	32.7886	-6.8068
5	0.5926	0.0183	0.1399	1.1301	-0.0196	0.5607	0.0203	-0.0269	-0.1204	0.021	-0.0416	0.0032	0.1124	0.0259	0.0213	0.1169	0.0026	-0.0024	0.0857	0.018	0.0311	18.7276	8.1117	-11.6112
6	4.0526	6.2758	4.8301	18.3864	9.7734	6.4185	-0.1782	0.346	-0.1727	-0.286	0.5624	-0.819	-0.1513	0.5089	-0.3841	0.1398	0.0108	-0.0247	0.2539	-0.0326	0.1083	36.0952	38.9673	-3.1909
7	0.9851	-0.2506	0.1173	0.9842	-0.0155	0.8073	-0.0013	0.0274	-0.0425	-0.0341	-0.0354	0.0117	0.0126	-0.0134	0.0367	0.1447	-0.0121	-0.0086	0.1194	0.0076	0.0053	12.5156	22.05	-18.701
8	4.227	1.3393	0.197	7.083	0.2881	2.6015	-0.1693	0.4296	-0.6605	-0.5978	0.1195	-0.125	0.559	0.0011	0.0498	0.29	0.0646	0.0435	0.1825	-0.1003	0.1267	23.331	-5.763	-31.7711
9	3.8416	0.4274	-2.3912	3.71	0.1874	6.4919	-0.1091	0.3413	-0.8088	-0.3916	-0.0137	0.1794	0.8455	-0.3603	0.1228	0.2931	-0.0071	-0.0513	0.0389	-0.0597	0.2292	14.5778	-12.142	-24.7157

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	ALL	Ap	105 - 336
2	X-RAY DIFFRACTION	2	ALL	Ap	337 - 362
3	X-RAY DIFFRACTION	3	ALL	Ap	363 - 389
4	X-RAY DIFFRACTION	4	ALL	Ap	390 - 455
5	X-RAY DIFFRACTION	5	ALL	Ap	456 - 587
6	X-RAY DIFFRACTION	6	ALL	Ap	588 - 603
7	X-RAY DIFFRACTION	7	ALL	Ap	604 - 724
8	X-RAY DIFFRACTION	8	ALL	Ap	725 - 767
9	X-RAY DIFFRACTION	9	ALL	Ap	768 - 790

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