PDB-9sg5: PENICILLIN-BINDING PROTEIN 1B (PBP-1B) IN COMPLEX WITH A MONOBACT...

ID or keywords:

Entry

Database: PDB / ID: 9sg5

Title

PENICILLIN-BINDING PROTEIN 1B (PBP-1B) IN COMPLEX WITH A MONOBACTAM (9)

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: 1.57 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	9sg5.cif.gz	252.1 KB	Display	PDBx/mmCIF format
PDB format	pdb9sg5.ent.gz		Display	PDB format
PDBx/mmJSON format	9sg5.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/9sg5 ftp://data.pdbj.org/pub/pdb/validation_reports/sg/9sg5	HTTPS FTP

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Related structure data

Related structure data	9sg6C 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

55.5 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)	96.943, 148.82, 98.636
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

#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: Plasmid / Details (production host): PGEX-Amp / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O70038
#2: Chemical	ChemComp-A1JNO / [(2~{S},3~{S})-3-[2-(1~{H}-indol-3-yl)ethanoylamino]-4-oxidanylidene-butan-2-yl]sulfamic acid Mass: 339.367 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₄H₁₇N₃O₅S / 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: Chemical	ChemComp-TAU / 2-AMINOETHANESULFONIC ACID Mass: 125.147 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₇NO₃S
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 465 / 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: 3.3 Å³/Da / Density % sol: 62.77 %
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: 1.57→41.11 Å / Num. obs: 95014 / % possible obs: 95.6 % / Redundancy: 3.1 % / B_iso Wilson estimate: 39.01 Å² / CC_1/2: 0.999 / R_sym value: 0.04 / Net I/σ(I): 11.51
Reflection shell	Resolution: 1.57→1.66 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 0.81 / Num. unique obs: 14754 / CC_1/2: 0.245 / R_sym value: 1.4 / % possible all: 97.5

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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: 1.57→41.109 Å / Cor.coef. F_o:F_c: 0.98 / Cor.coef. F_o:F_c free: 0.978 / SU B: 3.541 / SU ML: 0.056 / Cross valid method: FREE R-VALUE / ESU R: 0.061 / ESU R Free: 0.06
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.1742	2072	2.181 %
R_work	0.1624	92941	-
all	0.163	-	-
obs	-	95013	95.635 %

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: 39.316 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.709 Å²	-0 Å²	-0 Å²
2-	-	0.719 Å²	-0 Å²
3-	-	-	-0.011 Å²

Refinement step

Cycle: LAST / Resolution: 1.57→41.109 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3615	0	57	465	4137

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.012	3801
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	3490
X-RAY DIFFRACTION	r_angle_refined_deg	1.292	1.808	5175
X-RAY DIFFRACTION	r_angle_other_deg	0.446	1.751	8028
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.718	5	485
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	6.908	5	18
X-RAY DIFFRACTION	r_dihedral_angle_other_2_deg	7.509	5	2
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	11.926	10	621
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	15.546	10	172
X-RAY DIFFRACTION	r_chiral_restr	0.07	0.2	570
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	4561
X-RAY DIFFRACTION	r_gen_planes_other	0	0.02	887
X-RAY DIFFRACTION	r_nbd_refined	0.215	0.2	771
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.198	0.2	3133
X-RAY DIFFRACTION	r_nbtor_refined	0.184	0.2	1882
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.078	0.2	1894
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.158	0.2	311
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.163	0.2	13
X-RAY DIFFRACTION	r_nbd_other	0.191	0.2	61
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.231	0.2	27
X-RAY DIFFRACTION	r_mcbond_it	2.133	2.257	1894
X-RAY DIFFRACTION	r_mcbond_other	2.129	2.257	1894
X-RAY DIFFRACTION	r_mcangle_it	2.818	4.044	2369
X-RAY DIFFRACTION	r_mcangle_other	2.818	4.046	2370
X-RAY DIFFRACTION	r_scbond_it	4.438	2.72	1907
X-RAY DIFFRACTION	r_scbond_other	4.439	2.72	1908
X-RAY DIFFRACTION	r_scangle_it	6.573	4.783	2796
X-RAY DIFFRACTION	r_scangle_other	6.572	4.783	2797
X-RAY DIFFRACTION	r_lrange_it	8.284	24.886	4484
X-RAY DIFFRACTION	r_lrange_other	8.194	23.054	4385

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
1.57-1.611	0.537	164	0.582	6942	0.581	7259	0.709	0.694	97.8923	0.586
1.611-1.655	0.536	144	0.51	6727	0.511	7072	0.909	0.904	97.1578	0.5
1.655-1.703	0.401	140	0.427	6549	0.427	6945	0.942	0.928	96.3139	0.406
1.703-1.755	0.421	144	0.34	6421	0.341	6685	0.928	0.946	98.2049	0.303
1.755-1.812	0.263	156	0.271	6222	0.271	6511	0.966	0.963	97.9573	0.229
1.812-1.876	0.263	121	0.214	5959	0.215	6272	0.96	0.974	96.9388	0.174
1.876-1.947	0.197	131	0.185	5729	0.185	6091	0.977	0.979	96.2075	0.149
1.947-2.026	0.186	121	0.162	5408	0.163	5848	0.98	0.984	94.5451	0.133
2.026-2.116	0.159	131	0.151	5308	0.151	5638	0.985	0.987	96.4704	0.132
2.116-2.219	0.177	110	0.145	5097	0.145	5385	0.985	0.989	96.6945	0.131
2.219-2.338	0.177	87	0.139	4823	0.139	5115	0.984	0.989	95.9922	0.128
2.338-2.48	0.146	102	0.137	4478	0.138	4856	0.986	0.989	94.3163	0.132
2.48-2.65	0.154	87	0.145	4131	0.145	4568	0.985	0.988	92.338	0.145
2.65-2.862	0.178	105	0.159	3959	0.159	4284	0.98	0.985	94.8646	0.167
2.862-3.133	0.188	94	0.173	3623	0.173	3938	0.978	0.983	94.388	0.188
3.133-3.5	0.182	55	0.151	3292	0.151	3579	0.981	0.988	93.5177	0.172
3.5-4.037	0.13	64	0.121	2808	0.121	3180	0.99	0.992	90.3145	0.146
4.037-4.933	0.116	55	0.11	2465	0.11	2716	0.993	0.994	92.7835	0.14
4.933-6.926	0.159	34	0.172	1905	0.172	2132	0.99	0.988	90.9475	0.21
6.926-41.109	0.13	27	0.171	1095	0.17	1267	0.99	0.984	88.5556	0.237

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	2.975	-0.6563	-1.6481	0.5898	0.6115	1.9959	-0.2229	0.0499	-0.2896	0.0825	-0.0184	0.0414	0.119	-0.1535	0.2414	0.1524	0.0506	0.0209	0.1058	-0.0724	0.086	26.899	-39.6246	-3.0367
2	3.7727	-0.6351	-0.127	6.2711	-3.4279	8.3403	-0.1002	0.0758	0.2124	-0.1737	-0.0851	-0.1443	-0.1846	-0.1233	0.1853	0.1826	0.0523	-0.004	0.1809	-0.088	0.1789	31.1927	-35.8122	-13.8318
3	2.4676	-0.4296	-0.0541	1.3672	-0.1256	0.7611	-0.0325	0.1195	-0.1947	-0.1352	-0.0585	0.0721	0.1365	-0.0643	0.091	0.1594	0.0032	0.0299	0.0926	-0.0167	0.0579	10.7315	-33.2874	7.4186
4	0.7603	-0.0638	-0.2213	1.2135	0.0216	0.6459	0.0132	0.0727	0.1369	-0.0569	-0.0358	0.0243	-0.1288	0.0083	0.0225	0.1329	-0.0016	-0.0006	0.0481	0.0352	0.0554	18.692	-8.7844	11.1737
5	4.0294	-6.566	-5.4122	19.9423	11.4624	8.1237	-0.2381	-0.3587	0.1463	0.4359	0.6897	-0.8925	0.2341	0.6155	-0.4516	0.1655	-0.0116	0.0404	0.256	-0.0587	0.1483	35.9959	-38.8762	3.0137
6	1.072	0.2562	-0.1315	0.996	0.0357	0.8815	-0.0141	-0.0199	0.0348	0.0261	-0.0512	0.0019	-0.0212	-0.0105	0.0653	0.1471	0.0142	0.005	0.0778	0.0135	0.0484	12.5039	-22.0034	18.7723
7	3.5852	-1.1054	0.4107	4.9559	0.1923	3.2316	-0.1085	-0.4025	0.6588	0.5091	0.0369	-0.1852	-0.6338	0.0681	0.0715	0.3146	-0.074	-0.0404	0.0961	-0.0973	0.1707	22.8686	6.295	30.2818
8	3.2389	-0.4048	0.2006	4.0584	2.0202	21.2324	-0.1513	-0.4942	0.9299	0.408	-0.0404	0.1786	-0.9834	-0.534	0.1917	0.3187	0.0259	0.01	0.0908	-0.1446	0.3118	12.671	13.2919	25.9422

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	ALL	Ap	302 - 362
2	X-RAY DIFFRACTION	2	ALL	Ap	363 - 389
3	X-RAY DIFFRACTION	3	ALL	Ap	390 - 451
4	X-RAY DIFFRACTION	4	ALL	Ap	452 - 587
5	X-RAY DIFFRACTION	5	ALL	Ap	588 - 603
6	X-RAY DIFFRACTION	6	ALL	Ap	604 - 724
7	X-RAY DIFFRACTION	7	ALL	Ap	725 - 773
8	X-RAY DIFFRACTION	8	ALL	Ap	774 - 790

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