PDB-9sg6: PENICILLIN-BINDING PROTEIN 1B (PBP-1B) IN COMPLEX WITH A MONOBACT...

ID or keywords:

Entry

Database: PDB / ID: 9sg6

Title

PENICILLIN-BINDING PROTEIN 1B (PBP-1B) IN COMPLEX WITH A MONOBACTAM (10)

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: 1.74 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	9sg6.cif.gz	243.1 KB	Display	PDBx/mmCIF format
PDB format	pdb9sg6.ent.gz		Display	PDB format
PDBx/mmJSON format	9sg6.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/9sg6 ftp://data.pdbj.org/pub/pdb/validation_reports/sg/9sg6	HTTPS FTP

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Related structure data

Related structure data	9sg5C 9sg7C 9sg8C 9sg9C 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

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)	96.483, 149.563, 99.467
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-817- CL
3	1	A-1222- 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-A1JNV / [(2~{S},3~{S})-3-[2-(4-nitrophenyl)ethanoylamino]-4-oxidanylidene-butan-2-yl]sulfamic acid Mass: 345.328 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₂H₁₅N₃O₇S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	... ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 28 / Source method: obtained synthetically / Formula: Cl
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 329 / 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: 63.09 %
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: 1.74→44.3 Å / Num. obs: 71443 / % possible obs: 96.7 % / Redundancy: 4.2 % / B_iso Wilson estimate: 48.21 Å² / CC_1/2: 0.999 / R_sym value: 0.058 / Net I/σ(I): 9.88
Reflection shell	Resolution: 1.74→1.84 Å / Redundancy: 4.1 % / Mean I/σ(I) obs: 0.53 / Num. unique obs: 11001 / CC_1/2: 0.206 / R_sym value: 1.8 / % possible all: 97.7

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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: 1.74→44.291 Å / Cor.coef. F_o:F_c: 0.977 / Cor.coef. F_o:F_c free: 0.969 / SU B: 6.206 / SU ML: 0.089 / Cross valid method: FREE R-VALUE / ESU R: 0.085 / ESU R Free: 0.086
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2015	2185	3.061 %
R_work	0.1754	69207	-
all	0.176	-	-
obs	-	71392	96.669 %

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: 51.83 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.305 Å²	0 Å²	-0 Å²
2-	-	0.42 Å²	0 Å²
3-	-	-	-0.725 Å²

Refinement step

Cycle: LAST / Resolution: 1.74→44.291 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3515	0	51	329	3895

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.012	3685
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	3372
X-RAY DIFFRACTION	r_angle_refined_deg	1.298	1.811	5012
X-RAY DIFFRACTION	r_angle_other_deg	0.461	1.751	7754
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.696	5	470
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	11.459	7.727	22
X-RAY DIFFRACTION	r_dihedral_angle_other_2_deg	6.791	5	2
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	11.844	10	603
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	15.225	10	171
X-RAY DIFFRACTION	r_chiral_restr	0.071	0.2	545
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	4444
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	868
X-RAY DIFFRACTION	r_nbd_refined	0.208	0.2	724
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.183	0.2	2951
X-RAY DIFFRACTION	r_nbtor_refined	0.18	0.2	1812
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.076	0.2	1812
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.133	0.2	232
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.176	0.2	15
X-RAY DIFFRACTION	r_nbd_other	0.164	0.2	55
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.187	0.2	20
X-RAY DIFFRACTION	r_mcbond_it	2.691	2.995	1835
X-RAY DIFFRACTION	r_mcbond_other	2.687	2.996	1835
X-RAY DIFFRACTION	r_mcangle_it	3.494	5.372	2296
X-RAY DIFFRACTION	r_mcangle_other	3.496	5.374	2297
X-RAY DIFFRACTION	r_scbond_it	4.49	3.524	1850
X-RAY DIFFRACTION	r_scbond_other	4.489	3.525	1851
X-RAY DIFFRACTION	r_scangle_it	6.86	6.237	2708
X-RAY DIFFRACTION	r_scangle_other	6.859	6.238	2709
X-RAY DIFFRACTION	r_lrange_it	9.167	31.431	4245
X-RAY DIFFRACTION	r_lrange_other	9.115	30.298	4191

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
1.74-1.785	0.574	145	0.657	5003	0.655	5406	0.766	0.8	95.2275	0.685
1.785-1.834	0.532	148	0.559	5047	0.558	5238	0.813	0.802	99.1791	0.56
1.834-1.887	0.441	161	0.456	4944	0.455	5140	0.92	0.907	99.3191	0.452
1.887-1.945	0.406	124	0.378	4776	0.378	4971	0.916	0.931	98.5717	0.36
1.945-2.009	0.31	134	0.3	4663	0.3	4844	0.954	0.954	99.0297	0.259
2.009-2.079	0.235	136	0.247	4475	0.247	4661	0.969	0.962	98.9273	0.201
2.079-2.157	0.25	141	0.213	4336	0.215	4521	0.961	0.971	99.0268	0.17
2.157-2.245	0.2	164	0.177	4098	0.178	4345	0.975	0.982	98.0898	0.142
2.245-2.345	0.198	138	0.171	3952	0.172	4193	0.978	0.983	97.5435	0.14
2.345-2.459	0.178	110	0.157	3778	0.157	3978	0.983	0.986	97.7376	0.131
2.459-2.591	0.175	129	0.151	3582	0.152	3804	0.98	0.987	97.5552	0.134
2.591-2.748	0.21	106	0.161	3407	0.163	3625	0.977	0.986	96.9103	0.151
2.748-2.937	0.241	82	0.182	3185	0.184	3402	0.966	0.981	96.0317	0.177
2.937-3.171	0.219	95	0.194	2926	0.195	3177	0.974	0.98	95.0897	0.198
3.171-3.472	0.205	101	0.165	2644	0.167	2941	0.98	0.987	93.3356	0.176
3.472-3.879	0.184	68	0.145	2395	0.146	2663	0.984	0.989	92.4897	0.162
3.879-4.473	0.168	74	0.122	2073	0.124	2363	0.983	0.991	90.8591	0.146
4.473-5.465	0.159	58	0.135	1765	0.136	2015	0.988	0.991	90.4715	0.165
5.465-7.67	0.168	41	0.167	1369	0.167	1600	0.984	0.988	88.125	0.2
7.67-44.291	0.153	30	0.156	789	0.156	959	0.99	0.983	85.4015	0.212

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	20.7091	-4.557	-8.2792	3.6078	1.1217	9.1073	-0.221	0.3324	-0.2609	-0.068	0.0198	0.3731	0.5553	-0.324	0.2012	0.1935	0.0379	-0.0112	0.2364	-0.05	0.1886	19.259	-37.7896	-2.4898
2	8.3407	0.494	-2.336	2.6011	-1.1483	5.8436	-0.1403	0.1168	0.4681	0.0528	-0.0493	-0.2841	-0.7168	0.2688	0.1896	0.1442	0.0096	-0.0311	0.1922	-0.0448	0.2266	37.5381	-33.8282	-10.7807
3	4.8436	-0.7734	0.8511	8.7704	-5.8861	12.0055	-0.0378	0.0744	-0.0292	-0.2696	-0.0208	0.1144	0.1217	-0.2986	0.0587	0.0982	0.0578	0.0215	0.2257	-0.085	0.2242	30.2876	-36.8131	-13.7857
4	1.3485	0.0441	-0.0847	1.6746	-0.1728	0.9799	-0.0649	0.1865	-0.1441	-0.1895	0.0038	0.0488	0.1606	-0.0546	0.0611	0.0475	0.0061	0.0244	0.2162	-0.0104	0.1691	11.6639	-30.0132	7.3117
5	0.8834	-0.0309	-0.3385	1.3007	-0.1302	0.9537	0.0984	0.0943	0.2213	-0.049	-0.0556	0.0393	-0.2413	0.0169	-0.0427	0.0667	0.0009	0.0179	0.1412	0.0317	0.2039	18.8417	-7.7117	11.8107
6	0.7701	-3.5065	-2.282	18.4779	11.2792	7.2037	-0.0906	-0.102	0.0787	0.2187	0.5415	-1.0256	0.2276	0.5353	-0.4508	0.0326	0.0535	0.0377	0.3498	-0.0095	0.2442	34.749	-32.1264	7.0245
7	1.209	0.5066	-0.6121	0.6939	-0.3202	0.7752	0.0297	-0.1242	0.0521	0.0879	-0.0523	0.0138	-0.0583	0.0264	0.0226	0.015	0.0012	-0.0019	0.1597	0.0018	0.1598	11.4962	-19.8712	23.5359
8	6.1334	-0.6934	3.0549	2.6233	-0.7702	5.913	-0.0839	0.125	0.2637	-0.2055	0.0367	0.1822	-0.1825	-0.2867	0.0472	0.123	-0.0119	0.0259	0.175	-0.0029	0.2194	7.5113	-20.7243	9.1025
9	1.721	0.8545	0.076	2.148	0.2001	1.5844	0.0678	-0.2247	0.3166	0.3344	-0.1251	-0.0396	-0.322	0.1592	0.0573	0.1373	-0.0363	-0.0251	0.1924	-0.019	0.1534	16.9755	-12.8724	26.3883
10	3.0224	-0.7462	0.7521	3.7064	-0.5638	2.5164	-0.0106	-0.3592	0.6506	0.4623	0.0709	-0.0307	-0.7122	-0.0475	-0.0603	0.2925	-0.0642	0.0528	0.1323	-0.1101	0.2961	19.2043	6.9852	27.231

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	ALL	Ap	336 - 349
2	X-RAY DIFFRACTION	2	ALL	Ap	350 - 364
3	X-RAY DIFFRACTION	3	ALL	Ap	365 - 389
4	X-RAY DIFFRACTION	4	ALL	Ap	390 - 466
5	X-RAY DIFFRACTION	5	ALL	Ap	467 - 587
6	X-RAY DIFFRACTION	6	ALL	Ap	588 - 610
7	X-RAY DIFFRACTION	7	ALL	Ap	611 - 656
8	X-RAY DIFFRACTION	8	ALL	Ap	657 - 689
9	X-RAY DIFFRACTION	9	ALL	Ap	690 - 748
10	X-RAY DIFFRACTION	10	ALL	Ap	749 - 790

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