PDB-9sg9: PENICILLIN-BINDING PROTEIN 1B (PBP-1B) IN COMPLEX WITH A MONOBACT...

ID or keywords:

Entry

Database: PDB / ID: 9sg9

Title

PENICILLIN-BINDING PROTEIN 1B (PBP-1B) IN COMPLEX WITH A MONOBACTAM (6)

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: 1.88 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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PDBx/mmCIF format	9sg9.cif.gz	234.9 KB	Display	PDBx/mmCIF format
PDB format	pdb9sg9.ent.gz		Display	PDB format
PDBx/mmJSON format	9sg9.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/9sg9 ftp://data.pdbj.org/pub/pdb/validation_reports/sg/9sg9	HTTPS FTP

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Related structure data

Related structure data	9sg5C 9sg6C 9sg7C 9sg8C 9sgaC 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
Related items in Molecule of the Month	#133 - Jan 2011 Nitric Oxide Synthase similarity (1)

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)	96.655, 148.242, 98.83
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-817- CL

#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-A1JNW / [(2~{S},3~{S})-3-[2-(3-hydroxyphenyl)ethanoylamino]-4-oxidanylidene-butan-2-yl]sulfamic acid Mass: 316.330 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₂H₁₆N₂O₆S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-SO3 / SULFITE ION Mass: 80.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO₃
#4: Chemical	... ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 26 / Source method: obtained synthetically / Formula: Cl
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 200 / 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: 3.29 Å³/Da / Density % sol: 62.59 %
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 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: 1.88→44 Å / Num. obs: 56578 / % possible obs: 97.6 % / Redundancy: 3.9 % / B_iso Wilson estimate: 56.7 Å² / CC_1/2: 0.998 / R_sym value: 0.066 / Net I/σ(I): 8.39
Reflection shell	Resolution: 1.88→1.99 Å / Redundancy: 3.9 % / Mean I/σ(I) obs: 0.48 / Num. unique obs: 8792 / CC_1/2: 0.091 / R_sym value: 0.293 / % possible all: 98

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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: 1.88→43.998 Å / Cor.coef. F_o:F_c: 0.979 / Cor.coef. F_o:F_c free: 0.964 / SU B: 10.329 / SU ML: 0.131 / Cross valid method: FREE R-VALUE / ESU R: 0.105 / ESU R Free: 0.112
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2217	2036	3.602 %
R_work	0.1779	54483	-
all	0.179	-	-
obs	-	56519	97.539 %

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: 65.819 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-2.123 Å²	-0 Å²	0 Å²
2-	-	1.148 Å²	-0 Å²
3-	-	-	0.974 Å²

Refinement step

Cycle: LAST / Resolution: 1.88→43.998 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3488	0	51	200	3739

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.012	3593
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.016	3279
X-RAY DIFFRACTION	r_angle_refined_deg	1.294	1.809	4877
X-RAY DIFFRACTION	r_angle_other_deg	0.452	1.75	7543
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.626	5	452
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	7.013	5	15
X-RAY DIFFRACTION	r_dihedral_angle_other_2_deg	0.152	5	1
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	11.971	10	586
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	14.397	10	167
X-RAY DIFFRACTION	r_chiral_restr	0.066	0.2	531
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	4310
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	838
X-RAY DIFFRACTION	r_nbd_refined	0.209	0.2	726
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.191	0.2	2929
X-RAY DIFFRACTION	r_nbtor_refined	0.181	0.2	1811
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.077	0.2	1828
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.152	0.2	153
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.224	0.2	9
X-RAY DIFFRACTION	r_nbd_other	0.184	0.2	48
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.21	0.2	11
X-RAY DIFFRACTION	r_mcbond_it	3.377	3.8	1805
X-RAY DIFFRACTION	r_mcbond_other	3.376	3.8	1805
X-RAY DIFFRACTION	r_mcangle_it	4.56	6.829	2255
X-RAY DIFFRACTION	r_mcangle_other	4.56	6.83	2256
X-RAY DIFFRACTION	r_scbond_it	4.937	4.339	1788
X-RAY DIFFRACTION	r_scbond_other	4.845	4.332	1786
X-RAY DIFFRACTION	r_scangle_it	7.442	7.72	2621
X-RAY DIFFRACTION	r_scangle_other	7.333	7.712	2619
X-RAY DIFFRACTION	r_lrange_it	9.178	38.715	4097
X-RAY DIFFRACTION	r_lrange_other	9.183	37.98	4065

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
1.88-1.929	0.434	153	0.511	3974	0.508	4252	0.696	0.631	97.0602	0.536
1.929-1.982	0.474	153	0.484	3882	0.484	4130	0.859	0.859	97.6998	0.491
1.982-2.039	0.491	159	0.415	3810	0.418	3994	0.894	0.902	99.3741	0.414
2.039-2.102	0.42	144	0.362	3751	0.365	3915	0.917	0.923	99.4891	0.343
2.102-2.17	0.328	124	0.325	3637	0.325	3786	0.938	0.939	99.3397	0.29
2.17-2.246	0.296	140	0.315	3487	0.314	3664	0.941	0.948	98.9902	0.265
2.246-2.331	0.288	117	0.268	3384	0.269	3539	0.952	0.96	98.9263	0.215
2.331-2.426	0.277	106	0.23	3168	0.231	3391	0.949	0.968	96.5497	0.185
2.426-2.533	0.263	121	0.22	3141	0.221	3300	0.962	0.972	98.8485	0.174
2.533-2.656	0.252	107	0.2	2962	0.201	3118	0.966	0.977	98.4285	0.165
2.656-2.8	0.23	115	0.191	2799	0.193	2971	0.97	0.98	98.0815	0.167
2.8-2.969	0.23	106	0.198	2655	0.2	2851	0.967	0.976	96.8432	0.182
2.969-3.173	0.266	94	0.194	2463	0.197	2676	0.96	0.978	95.5531	0.192
3.173-3.425	0.217	77	0.162	2309	0.163	2482	0.968	0.987	96.1322	0.164
3.425-3.75	0.169	79	0.14	2129	0.141	2298	0.986	0.99	96.0835	0.149
3.75-4.189	0.162	56	0.125	1948	0.126	2105	0.987	0.991	95.2019	0.14
4.189-4.829	0.185	65	0.123	1691	0.125	1850	0.979	0.991	94.9189	0.149
4.829-5.897	0.162	59	0.146	1467	0.147	1593	0.989	0.989	95.7941	0.179
5.897-8.266	0.191	41	0.154	1153	0.155	1266	0.979	0.988	94.3128	0.188
8.266-43.998	0.228	20	0.155	673	0.157	758	0.975	0.984	91.4248	0.226

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	14.3261	0.4713	-6.4679	0.7229	-0.5464	4.1902	-0.0431	0.0334	0.236	-0.1184	0.0143	-0.0606	-0.0739	0.1414	0.0288	0.3124	-0.0417	0.0051	0.2593	0.047	0.1323	19.5092	38.1823	55.5157
2	6.2728	1.1253	0.201	8.221	4.4724	10.224	-0.2158	-0.3221	0.0499	0.2573	0.042	0.1803	0.0387	0.3866	0.1738	0.2682	-0.077	0.0135	0.3026	0.1397	0.147	17.2529	38.2854	63.2584
3	13.0439	2.277	-2.8607	2.4242	-0.8309	1.8899	-0.1049	-0.0064	-0.2484	0.0363	-0.0286	0.0523	0.1717	0.0414	0.1335	0.337	0.0147	0.0057	0.2644	0.021	0.1389	38.3715	37.6635	38.8683
4	4.3784	1.4505	0.6125	2.8113	0.5732	2.7189	-0.0367	-0.5397	-0.3224	0.3974	-0.0275	-0.2772	0.2516	0.2559	0.0642	0.3331	0.0245	0.0241	0.2986	-0.0013	0.0597	36.4944	43.4764	44.7963
5	1.2574	-0.6439	-0.3144	1.6086	0.0316	1.4841	0.2198	-0.1134	0.4021	-0.0636	-0.0473	-0.2387	-0.2841	0.1577	-0.1726	0.2957	-0.0324	0.0678	0.1322	-0.0613	0.1384	34.2106	71.3093	34.8056
6	1.5813	-0.2445	-0.6939	2.4254	0.349	1.2531	0.0527	-0.2188	0.2812	0.2262	-0.0663	0.0844	-0.2379	-0.0708	0.0137	0.2664	0.0016	0.0251	0.2075	-0.0709	0.0802	24.4474	60.6012	41.6912
7	7.5705	5.0047	-6.8486	16.6859	-9.701	8.6786	-0.3882	0.3211	-0.0667	-0.3994	0.7065	0.7265	0.5463	-0.9278	-0.3183	0.2352	-0.1101	-0.01	0.4737	0.0602	0.1468	14.0415	35.3714	46.0789
8	2.8078	-1.2972	-0.4688	1.7086	0.5634	1.1471	-0.0479	0.0176	0.0191	-0.017	-0.0357	0.1552	-0.0552	-0.0806	0.0837	0.3014	-0.0003	-0.0057	0.2559	-0.0109	0.0275	32.6889	54.0101	26.119
9	6.6494	0.6223	3.1856	3.6928	0.6214	7.0957	-0.135	-0.2366	0.2347	0.2009	0.1357	-0.4774	-0.5117	0.5373	-0.0007	0.3033	0.0054	0.0565	0.2692	-0.0265	0.1354	40.6296	54.326	40.2387
10	1.83	-0.8326	-0.1635	1.9583	-0.4229	1.3318	0.0765	0.1784	0.3057	-0.252	-0.0849	0.0327	-0.2669	-0.1335	0.0084	0.385	0.0146	-0.0217	0.2843	0.0038	0.0782	31.6656	58.1963	23.8979
11	2.5387	0.8821	1.1974	3.6738	0.6629	1.9246	-0.0819	0.4445	0.8392	-0.4115	0.1922	0.2809	-0.8137	0.1336	-0.1103	0.5678	0.0987	0.2288	0.1345	0.1577	0.4709	28.7101	82.3863	21.879

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	ALL	Ap	337 - 362
2	X-RAY DIFFRACTION	2	ALL	Ap	363 - 389
3	X-RAY DIFFRACTION	3	ALL	Ap	390 - 415
4	X-RAY DIFFRACTION	4	ALL	Ap	416 - 454
5	X-RAY DIFFRACTION	5	ALL	Ap	455 - 528
6	X-RAY DIFFRACTION	6	ALL	Ap	529 - 583
7	X-RAY DIFFRACTION	7	ALL	Ap	584 - 602
8	X-RAY DIFFRACTION	8	ALL	Ap	603 - 650
9	X-RAY DIFFRACTION	9	ALL	Ap	651 - 689
10	X-RAY DIFFRACTION	10	ALL	Ap	690 - 742
11	X-RAY DIFFRACTION	11	ALL	Ap	743 - 787

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