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

ID or keywords:

Entry

Database: PDB / ID: 9sgd

Title

PENICILLIN-BINDING PROTEIN 1B (PBP-1B) IN COMPLEX WITH A MONOBACTAM (26)

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: 1.571 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	9sgd.cif.gz	248.5 KB	Display	PDBx/mmCIF format
PDB format	pdb9sgd.ent.gz		Display	PDB format
PDBx/mmJSON format	9sgd.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/9sgd ftp://data.pdbj.org/pub/pdb/validation_reports/sg/9sgd	HTTPS FTP

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Related structure data

Related structure data	9sg5C 9sg6C 9sg7C 9sg8C 9sg9C 9sgaC 9sgbC 9sgcC 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

55.7 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)	97.239, 148.297, 98.144
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
2	1	A-1213- HOH

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Protein , 1 types, 1 molecules A

#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

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Non-polymers , 5 types, 406 molecules

#2: Chemical	ChemComp-A1JNT / [(2~{S},3~{S})-3-[[2-(2-azanyl-1,3-thiazol-4-yl)-2-(2-methoxy-2-oxidanylidene-ethoxy)imino-ethanoyl]amino]-4-oxidanylidene-butan-2-yl]sulfamic acid Mass: 423.422 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₂H₁₇N₅O₈S₂ / 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.: 27 / Source method: obtained synthetically / Formula: Cl
#5: Chemical	ChemComp-TAU / 2-AMINOETHANESULFONIC ACID Mass: 125.147 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₇NO₃S
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 376 / Source method: isolated from a natural source / Formula: H₂O

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Details

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: 62.56 %
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: Jun 25, 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→43.57 Å / Num. obs: 94733 / % possible obs: 95.9 % / Redundancy: 3.4 % / B_iso Wilson estimate: 42.78 Å² / CC_1/2: 0.998 / R_sym value: 0.053 / Net I/σ(I): 10.29
Reflection shell	Resolution: 1.57→1.66 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 0.73 / Num. unique obs: 14612 / CC_1/2: 0.227 / R_sym value: 0.173 / % possible all: 97

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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: 1.571→43.567 Å / Cor.coef. F_o:F_c: 0.976 / Cor.coef. F_o:F_c free: 0.965 / SU B: 3.974 / SU ML: 0.064 / Cross valid method: FREE R-VALUE / ESU R: 0.066 / ESU R Free: 0.069
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2052	2067	2.183 %
R_work	0.1767	92600	-
all	0.177	-	-
obs	-	94667	95.948 %

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: 44.83 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.766 Å²	-0 Å²	0 Å²
2-	-	-0.332 Å²	-0 Å²
3-	-	-	-0.434 Å²

Refinement step

Cycle: LAST / Resolution: 1.571→43.567 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3624	0	65	376	4065

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.012	3772
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	3453
X-RAY DIFFRACTION	r_angle_refined_deg	1.294	1.809	5126
X-RAY DIFFRACTION	r_angle_other_deg	0.456	1.752	7943
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.41	5	480
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	20.305	7.174	23
X-RAY DIFFRACTION	r_dihedral_angle_other_2_deg	3.108	15	3
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	11.133	10	618
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	15.024	10	174
X-RAY DIFFRACTION	r_chiral_restr	0.072	0.2	562
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	4529
X-RAY DIFFRACTION	r_gen_planes_other	0	0.02	875
X-RAY DIFFRACTION	r_nbd_refined	0.216	0.2	737
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.194	0.2	3062
X-RAY DIFFRACTION	r_nbtor_refined	0.182	0.2	1880
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.077	0.2	1871
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.131	0.2	245
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.227	0.2	12
X-RAY DIFFRACTION	r_nbd_other	0.217	0.2	43
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.196	0.2	27
X-RAY DIFFRACTION	r_mcbond_it	2.293	2.529	1890
X-RAY DIFFRACTION	r_mcbond_other	2.29	2.528	1890
X-RAY DIFFRACTION	r_mcangle_it	3.08	4.536	2362
X-RAY DIFFRACTION	r_mcangle_other	3.079	4.538	2363
X-RAY DIFFRACTION	r_scbond_it	4.178	2.968	1882
X-RAY DIFFRACTION	r_scbond_other	4.178	2.968	1883
X-RAY DIFFRACTION	r_scangle_it	6.08	5.247	2758
X-RAY DIFFRACTION	r_scangle_other	6.078	5.247	2759
X-RAY DIFFRACTION	r_lrange_it	7.79	26.897	4356
X-RAY DIFFRACTION	r_lrange_other	7.772	26.013	4304

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
1.571-1.612	0.624	150	0.643	6893	0.642	7264	0.696	0.683	96.9576	0.652
1.612-1.656	0.551	159	0.554	6698	0.554	6985	0.907	0.904	98.1675	0.552
1.656-1.704	0.443	128	0.489	6613	0.488	6886	0.929	0.925	97.8943	0.469
1.704-1.756	0.428	143	0.389	6348	0.39	6635	0.929	0.948	97.8297	0.347
1.756-1.814	0.318	147	0.299	6107	0.3	6483	0.957	0.961	96.4677	0.252
1.814-1.877	0.245	129	0.234	5995	0.234	6238	0.969	0.971	98.1725	0.188
1.877-1.948	0.226	128	0.199	5770	0.199	6037	0.971	0.976	97.6975	0.16
1.948-2.027	0.19	106	0.177	5566	0.177	5827	0.979	0.981	97.34	0.15
2.027-2.117	0.193	125	0.171	5269	0.171	5574	0.979	0.983	96.7707	0.153
2.117-2.22	0.189	108	0.163	4984	0.164	5345	0.98	0.986	95.2666	0.151
2.22-2.34	0.166	101	0.156	4841	0.156	5106	0.984	0.987	96.7881	0.15
2.34-2.481	0.178	115	0.151	4482	0.152	4805	0.984	0.987	95.6712	0.151
2.481-2.652	0.165	83	0.148	4257	0.149	4550	0.981	0.987	95.3846	0.154
2.652-2.864	0.194	92	0.171	3877	0.172	4244	0.981	0.983	93.5203	0.187
2.864-3.136	0.222	80	0.187	3572	0.188	3903	0.968	0.98	93.5691	0.21
3.136-3.504	0.212	80	0.166	3194	0.167	3545	0.975	0.984	92.3554	0.195
3.504-4.041	0.17	63	0.141	2842	0.142	3169	0.979	0.988	91.6693	0.179
4.041-4.939	0.18	65	0.136	2365	0.137	2689	0.985	0.99	90.3682	0.178
4.939-6.94	0.224	43	0.184	1866	0.185	2118	0.976	0.984	90.1322	0.239
6.94-43.567	0.203	22	0.176	1061	0.176	1255	0.968	0.978	86.2948	0.263

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	3.6364	0.4192	-1.7866	0.7147	-0.1341	2.8092	-0.2807	-0.0676	-0.1927	-0.0919	0.0454	-0.062	0.2553	0.2114	0.2353	0.067	-0.0428	0.0419	0.1734	0.0679	0.1324	21.6497	34.5722	52.0175
2	3.8753	0.3076	-0.1768	5.8537	3.3435	8.3559	-0.0752	-0.0298	0.2068	0.0706	-0.1377	0.0869	-0.2179	0.0079	0.2129	0.124	-0.0464	0.0122	0.2369	0.0669	0.2119	17.0653	38.3325	62.4999
3	2.3427	0.254	-0.1183	1.5942	0.3277	1.1948	-0.1088	-0.1988	-0.0675	0.1933	0.0066	-0.0657	0.1559	0.086	0.1023	0.0618	0.0148	0.033	0.1959	0.0154	0.1164	37.4795	41.1709	42.1639
4	0.7567	-0.1506	-0.1604	0.79	0.119	0.7434	0.0422	-0.1091	0.1458	0.013	-0.0392	0.0486	-0.1685	-0.0137	-0.003	0.0406	-0.0004	0.0028	0.1548	-0.0506	0.1218	29.489	60.5418	35.4851
5	4.9584	0.298	3.0582	2.575	0.9012	6.1815	-0.1659	-0.141	0.3197	0.1814	0.0776	-0.2431	-0.3585	0.3436	0.0883	0.104	-0.0008	0.0178	0.1913	-0.0115	0.1703	40.8974	53.5236	40.2252
6	1.3179	-0.6217	-0.1888	1.5491	0.1477	1.5286	0.0972	0.1666	0.3089	-0.3251	-0.1479	0.0192	-0.3508	-0.1189	0.0508	0.1422	0.0282	-0.0267	0.1726	0.0026	0.1271	31.6347	61.3134	22.8373
7	4.3389	1.8991	-0.2055	4.2579	0.8456	2.7651	0.2277	0.3055	0.8349	-0.5462	-0.0413	0.147	-0.9585	-0.0436	-0.1864	0.4069	0.0678	0.0903	0.0546	0.0742	0.2486	29.3902	81.0952	21.8959

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	ALL	Ap	105 - 362
2	X-RAY DIFFRACTION	2	ALL	Ap	363 - 389
3	X-RAY DIFFRACTION	3	ALL	Ap	390 - 454
4	X-RAY DIFFRACTION	4	ALL	Ap	455 - 656
5	X-RAY DIFFRACTION	5	ALL	Ap	657 - 689
6	X-RAY DIFFRACTION	6	ALL	Ap	690 - 748
7	X-RAY DIFFRACTION	7	ALL	Ap	749 - 790

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