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

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Basic information

Entry
Database: PDB / ID: 9sse
TitlePENICILLIN-BINDING PROTEIN 1B (PBP-1B) in complex with Ampicillin - Streptococcus pneumoniae R6
ComponentsPenicillin-binding protein 1B
KeywordsTRANSFERASE / 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
Glycosyl transferase, family 51 / Penicillin binding protein transglycosylase domain / : / Transglycosylase / Penicillin-binding protein, transpeptidase / Penicillin binding protein transpeptidase domain / Beta-lactamase/transpeptidase-like / Lysozyme-like domain superfamily
Similarity search - Domain/homology
Chem-AIX / Penicillin-binding protein 1B
Similarity search - Component
Biological speciesStreptococcus pneumoniae R6 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 Å
AuthorsFlanders, P.L. / Gillingham, J.R. / Contreras-Martel, C. / Dessen, A. / Carlson, E.E. / Ambrose, E.A.
Funding support France, United States, 5items
OrganizationGrant numberCountry
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
CitationJournal: 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
DepositionSep 25, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 18, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Penicillin-binding protein 1B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,21724
Polymers54,0861
Non-polymers1,13123
Water5,945330
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis, monomer expected, gel filtration, monomer expected
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2870 Å2
ΔGint-203 kcal/mol
Surface area18990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.275, 148.859, 99.386
Angle α, β, γ (deg.)90, 90, 90
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-815-

CL

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Components

#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-AIX / (2R,4S)-2-[(1R)-1-{[(2R)-2-amino-2-phenylacetyl]amino}-2-oxoethyl]-5,5-dimethyl-1,3-thiazolidine-4-carboxylic acid / AMPICILLIN (open form)


Mass: 351.421 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H21N3O4S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical...
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 330 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.3 Å3/Da / Density % sol: 62.76 %
Crystal growTemperature: 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

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.965459 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Feb 1, 2021
RadiationMonochromator: C(110) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.965459 Å / Relative weight: 1
ReflectionResolution: 1.788→48.14 Å / Num. obs: 66996 / % possible obs: 99.4 % / Redundancy: 4.32 % / Biso Wilson estimate: 39.987 Å2 / CC1/2: 0.996 / Rsym value: 0.087 / Net I/σ(I): 8.82
Reflection shellResolution: 1.788→1.9 Å / Redundancy: 4.49 % / Mean I/σ(I) obs: 1.2 / Num. unique obs: 10910 / CC1/2: 0.479 / Rsym value: 1.221 / % possible all: 99.7

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Processing

Software
NameVersionClassification
XDS20200417data reduction
XSCALE20200417data scaling
PHASER2.8.3phasing
ARP/wARP8model building
Coot0.8.9.2-7428model building
REFMAC5.8.0425refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.79→48.138 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.969 / SU B: 4.996 / SU ML: 0.072 / Cross valid method: FREE R-VALUE / ESU R: 0.086 / ESU R Free: 0.084
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.189 2052 3.063 %
Rwork0.1679 64944 -
all0.169 --
obs-66996 99.368 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 40.046 Å2
Baniso -1Baniso -2Baniso -3
1--0.111 Å2-0 Å2-0 Å2
2--0.391 Å20 Å2
3----0.281 Å2
Refinement stepCycle: LAST / Resolution: 1.79→48.138 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3506 0 46 330 3882
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0123649
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163356
X-RAY DIFFRACTIONr_angle_refined_deg1.2021.8084963
X-RAY DIFFRACTIONr_angle_other_deg0.4221.757717
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3285467
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.872517
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.2710601
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.39810169
X-RAY DIFFRACTIONr_chiral_restr0.0660.2542
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024398
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02858
X-RAY DIFFRACTIONr_nbd_refined0.2130.2772
X-RAY DIFFRACTIONr_symmetry_nbd_other0.190.23059
X-RAY DIFFRACTIONr_nbtor_refined0.1860.21848
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0780.21843
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1270.2281
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1960.29
X-RAY DIFFRACTIONr_nbd_other0.1890.239
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1420.214
X-RAY DIFFRACTIONr_mcbond_it2.6052.8611829
X-RAY DIFFRACTIONr_mcbond_other2.6052.8611829
X-RAY DIFFRACTIONr_mcangle_it3.4465.1232288
X-RAY DIFFRACTIONr_mcangle_other3.4475.1252289
X-RAY DIFFRACTIONr_scbond_it4.6463.3571820
X-RAY DIFFRACTIONr_scbond_other4.6453.3571821
X-RAY DIFFRACTIONr_scangle_it7.1955.9052668
X-RAY DIFFRACTIONr_scangle_other7.1945.9052669
X-RAY DIFFRACTIONr_lrange_it8.17928.4994340
X-RAY DIFFRACTIONr_lrange_other8.13727.7094286
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.79-1.8360.5191470.49847760.49849330.910.91199.79730.502
1.836-1.8870.3381550.3846810.37948580.9540.93699.54710.378
1.887-1.9410.3161340.29644780.29746340.9490.95199.52520.282
1.941-2.0010.251230.24144000.24145350.9640.96699.73540.218
2.001-2.0660.2161550.21142430.21144160.9690.96699.59240.187
2.066-2.1390.1921430.17841230.17942750.9760.9899.78950.156
2.139-2.2190.1691260.15840090.15941400.9810.98599.87920.14
2.219-2.310.211250.1638020.16139510.9730.98599.39260.143
2.31-2.4120.1821090.14736620.14838180.9810.98798.7690.135
2.412-2.530.2121220.15635060.15836400.9770.98599.67030.146
2.53-2.6660.1911070.15733590.15834710.9770.98599.85590.149
2.666-2.8270.212940.17632130.17733190.9750.98199.63840.173
2.827-3.0220.255890.19429920.19630970.9590.97899.48340.196
3.022-3.2630.195910.18227560.18228810.9780.98398.81990.191
3.263-3.5730.181880.15425790.15526890.9860.98899.18190.168
3.573-3.9920.134770.13423160.13424250.9890.9998.68040.156
3.992-4.6040.098380.11820660.11721630.9950.99297.27230.147
4.604-5.6260.184490.14417710.14518410.9840.9998.85930.18
5.626-7.9020.176480.15813980.15814550.9860.98899.38140.192
7.902-48.1380.138320.1498140.1488760.990.98696.57530.217
Refinement TLS params.Method: refined / Origin x: 18.2354 Å / Origin y: -17.5693 Å / Origin z: 12.3357 Å
111213212223313233
T0.0189 Å20.0044 Å2-0.006 Å2-0.0321 Å20.0095 Å2--0.0177 Å2
L0.8018 °2-0.0595 °2-0.2521 °2-0.5781 °20.0128 °2--0.7373 °2
S0.0063 Å °-0.0287 Å °0.0799 Å °0.0351 Å °-0.007 Å °-0.0351 Å °-0.0576 Å °0.0492 Å °0.0007 Å °
Refinement TLS groupSelection: ALL

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