PDB-9ssf: PENICILLIN-BINDING PROTEIN 1B (PBP-1B) in complex with Methicilli...

ID or keywords:

Entry

Database: PDB / ID: 9ssf

Title

PENICILLIN-BINDING PROTEIN 1B (PBP-1B) in complex with Methicillin - Streptococcus pneumoniae R6

Components

Penicillin-binding protein 1B

Keywords

TRANSFERASE / CELL WALL / PEPTIDOGLYCAN SYNTHESIS ENZYME / INFECTION / DRUG-BINDING PROTEIN / ANTIBIOTICS

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 R6 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.931 Å

Authors

Flanders, P.L. / Gillingham, J.R. / Contreras-Martel, C. / Dessen, A. / Carlson, E.E. / Ambrose, E.A.

Funding support

France,

United States, 5items

Organization	Grant number	Country
Agence Nationale de la Recherche (ANR)	ANR-10-INBS-0005-02	France
Agence Nationale de la Recherche (ANR)	ANR-17-EURE-0003	France
National Institutes of Health/National Cancer Institute (NIH/NCI)	R01 GM128439A1	United States
National Institutes of Health/National Cancer Institute (NIH/NCI)	R35 GM153306	United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	5T32GM132029-5	United States

Citation

Journal: Acs Chem.Biol. / Year: 2026
Title: Structural and Dynamics Analyses of beta-Lactam Inhibition of Streptococcus pneumoniae Penicillin-Binding Protein 1b (PBP1b) Guide Interrogation of Structure-Activity Relationships.
Authors: Flanders, P.L. / Gillingham, J.R. / Contreras-Martel, C. / Dessen, A. / Carlson, E.E. / Ambrose, E.A.

History

Deposition	Sep 25, 2025	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Feb 18, 2026	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	9ssf.cif.gz	236.1 KB	Display	PDBx/mmCIF format
PDB format	pdb9ssf.ent.gz	156.5 KB	Display	PDB format
PDBx/mmJSON format	9ssf.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ss/9ssf ftp://data.pdbj.org/pub/pdb/validation_reports/ss/9ssf	HTTPS FTP

-
Related structure data

Related structure data	7zuhC 9ssdC 9sseC 9ssgC 9sshC 9ssiC C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Penicillin-binding protein 1B

hetero molecules

55.3 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration, monomer expected, native gel electrophoresis, monomer expected

Unit cell

Length a, b, c (Å)	96.517, 147.979, 99.597
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-814- 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 R6 (bacteria) / Strain: ATCC / Gene: pbp1b / Plasmid: PGEX-Amp / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O70038
#2: Chemical	ChemComp-7EP / (2R,4S)-2-[(1R)-1-{[(2,6-dimethoxyphenyl)carbonyl]amino}-2-oxoethyl]-5,5-dimethyl-1,3-thiazolidine-4-carboxylic acid / methicillin, bound form Mass: 382.431 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₇H₂₂N₂O₆S / Feature type: SUBJECT OF INVESTIGATION / Comment: antibiotic*YM
#3: Chemical	... ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: Cl
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 204 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	Y

-
Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

Crystal	Density Matthews: 3.3 Å³/Da / Density % sol: 62.72 %
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

-
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 2M / Detector: PIXEL / Date: Feb 1, 2021
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: 1.927→49.8 Å / Num. obs: 52086 / % possible obs: 96.7 % / Redundancy: 4.57 % / B_iso Wilson estimate: 45.01 Å² / CC_1/2: 0.996 / R_sym value: 0.123 / Net I/σ(I): 7.58
Reflection shell	Resolution: 1.927→2.04 Å / Redundancy: 4.63 % / Mean I/σ(I) obs: 0.6 / Num. unique obs: 7882 / CC_1/2: 0.22 / R_sym value: 2.45 / % possible all: 96.9

-
Processing

Software

Name	Version	Classification
XDS	20200417	data reduction
XSCALE	20200417	data scaling
PHASER	2.8.3	phasing
ARP/wARP	8	model building
Coot	0.8.9.2-7428	model building
REFMAC	5.8.0425	refinement

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.931→49.799 Å / Cor.coef. F_o:F_c: 0.962 / Cor.coef. F_o:F_c free: 0.947 / SU B: 11.764 / SU ML: 0.147 / Cross valid method: FREE R-VALUE / ESU R: 0.139 / ESU R Free: 0.13
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2318	2019	4.003 %
R_work	0.2063	48422	-
all	0.207	-	-
obs	-	50441	93.788 %

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: 50.876 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.065 Å²	0 Å²	-0 Å²
2-	-	-0.617 Å²	-0 Å²
3-	-	-	0.551 Å²

Refinement step

Cycle: LAST / Resolution: 1.931→49.799 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3514	0	50	204	3768

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.012	3634
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	3329
X-RAY DIFFRACTION	r_angle_refined_deg	1.292	1.81	4937
X-RAY DIFFRACTION	r_angle_other_deg	0.457	1.75	7655
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.041	5	458
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	16.385	5	20
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.28	10	593
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	15.253	10	168
X-RAY DIFFRACTION	r_chiral_restr	0.067	0.2	536
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	4371
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	849
X-RAY DIFFRACTION	r_nbd_refined	0.211	0.2	759
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.188	0.2	3038
X-RAY DIFFRACTION	r_nbtor_refined	0.183	0.2	1836
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.078	0.2	1873
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.149	0.2	183
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.185	0.2	8
X-RAY DIFFRACTION	r_nbd_other	0.155	0.2	37
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.263	0.2	15
X-RAY DIFFRACTION	r_xyhbond_nbd_other	0.021	0.2	1
X-RAY DIFFRACTION	r_mcbond_it	3.141	2.964	1826
X-RAY DIFFRACTION	r_mcbond_other	3.142	2.966	1827
X-RAY DIFFRACTION	r_mcangle_it	4.54	5.31	2280
X-RAY DIFFRACTION	r_mcangle_other	4.533	5.31	2280
X-RAY DIFFRACTION	r_scbond_it	4.597	3.414	1808
X-RAY DIFFRACTION	r_scbond_other	4.596	3.416	1809
X-RAY DIFFRACTION	r_scangle_it	7.029	6.051	2655
X-RAY DIFFRACTION	r_scangle_other	7.028	6.053	2656
X-RAY DIFFRACTION	r_lrange_it	9.037	29.884	4206
X-RAY DIFFRACTION	r_lrange_other	9.026	29.136	4175

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
1.931-1.981	0.527	143	0.564	3028	0.562	3919	0.836	0.768	80.9135	0.641
1.981-2.035	0.465	156	0.494	3567	0.493	3837	0.841	0.83	97.0289	0.499
2.035-2.094	0.605	111	0.6	2695	0.6	3725	0.484	0.607	75.3289	0.698
2.094-2.158	0.372	113	0.339	3360	0.34	3639	0.918	0.926	95.4383	0.316
2.158-2.229	0.417	122	0.318	3213	0.322	3499	0.908	0.939	95.313	0.291
2.229-2.307	0.296	114	0.381	2814	0.377	3398	0.94	0.871	86.1683	0.356
2.307-2.394	0.28	132	0.236	3117	0.237	3291	0.948	0.966	98.7238	0.195
2.394-2.491	0.266	119	0.216	2978	0.218	3152	0.963	0.972	98.2551	0.175
2.491-2.602	0.259	131	0.221	2903	0.222	3062	0.958	0.97	99.0856	0.187
2.602-2.729	0.334	107	0.252	2680	0.256	2890	0.889	0.951	96.436	0.218
2.729-2.876	0.216	116	0.202	2617	0.203	2780	0.972	0.977	98.3093	0.18
2.876-3.049	0.205	87	0.198	2474	0.198	2628	0.977	0.979	97.4505	0.181
3.049-3.259	0.233	92	0.199	2319	0.201	2482	0.969	0.981	97.1394	0.191
3.259-3.519	0.231	90	0.196	2163	0.197	2319	0.96	0.975	97.1539	0.188
3.519-3.853	0.193	82	0.153	2004	0.154	2136	0.974	0.988	97.6592	0.152
3.853-4.304	0.161	98	0.137	1781	0.139	1937	0.986	0.987	97.0057	0.141
4.304-4.964	0.131	71	0.12	1640	0.121	1743	0.99	0.992	98.1641	0.135
4.964-6.065	0.274	61	0.193	1346	0.196	1469	0.961	0.982	95.7794	0.206
6.065-8.514	0.179	47	0.156	1093	0.157	1169	0.986	0.988	97.5192	0.173
8.514-49.799	0.134	27	0.153	630	0.152	703	0.99	0.984	93.4566	0.195

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	1.6972	-0.1234	-1.0288	0.6301	0.2944	1.5485	-0.0525	0.2898	0.0354	-0.1052	0.0325	-0.0067	0.0885	-0.0876	0.0199	0.1184	0.0165	0.0024	0.2843	-0.0022	0.0398	68.5154	39.484	-1.1962
2	0.6282	0.1882	-0.0839	0.8754	-0.0313	0.6472	0.0141	0.0423	0.0503	-0.0463	0.0063	-0.0657	-0.0884	0.07	-0.0204	0.0992	0.0029	-0.0007	0.2908	0.0203	0.0146	66.9938	60.0046	13.1941
3	2.8743	1.4929	-0.7858	3.3457	0.5178	5.8098	-0.0947	0.3413	0.5201	-0.2998	0.0836	0.4839	-0.6762	-0.7759	0.0111	0.1829	0.0263	0.0111	0.2739	0.0041	0.1534	54.685	51.601	11.2973
4	1.8067	0.0118	-0.2437	1.8281	-0.1429	1.2943	0.0685	-0.2839	0.493	0.4437	-0.0548	-0.1233	-0.4966	0.1416	-0.0137	0.2754	-0.0415	-0.0271	0.3409	-0.0638	0.1449	68.0526	73.1251	28.5894

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	ALL	Ap	337 - 448
2	X-RAY DIFFRACTION	2	ALL	Ap	449 - 655
3	X-RAY DIFFRACTION	3	ALL	Ap	656 - 702
4	X-RAY DIFFRACTION	4	ALL	Ap	703 - 791

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi