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- PDB-7rcy: Crystal structure of C. difficile penicillin-binding protein 2 in... -

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Basic information

Entry
Database: PDB / ID: 7rcy
TitleCrystal structure of C. difficile penicillin-binding protein 2 in complex with ceftobiprole
ComponentsPenicillin-binding protein
KeywordsPEPTIDE BINDING PROTEIN / Peptidoglycan / PBP / PBP2 / cell wall / transpeptidase / b-lactam / gram-positive / spore / sporulation
Function / homologyChem-RB6 / :
Function and homology information
Biological speciesClostridioides difficile (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsSacco, M. / Chen, Y.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI161762
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM133617 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM128624 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM008804 United States
CitationJournal: Nat Commun / Year: 2022
Title: A unique class of Zn 2+ -binding serine-based PBPs underlies cephalosporin resistance and sporogenesis in Clostridioides difficile.
Authors: Sacco, M.D. / Wang, S. / Adapa, S.R. / Zhang, X. / Lewandowski, E.M. / Gongora, M.V. / Keramisanou, D. / Atlas, Z.D. / Townsend, J.A. / Gatdula, J.R. / Morgan, R.T. / Hammond, L.R. / Marty, ...Authors: Sacco, M.D. / Wang, S. / Adapa, S.R. / Zhang, X. / Lewandowski, E.M. / Gongora, M.V. / Keramisanou, D. / Atlas, Z.D. / Townsend, J.A. / Gatdula, J.R. / Morgan, R.T. / Hammond, L.R. / Marty, M.T. / Wang, J. / Eswara, P.J. / Gelis, I. / Jiang, R.H.Y. / Sun, X. / Chen, Y.
History
DepositionJul 8, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 23, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 10, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Penicillin-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,5823
Polymers103,9801
Non-polymers6022
Water19811
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)64.700, 196.390, 70.970
Angle α, β, γ (deg.)90.000, 105.660, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Penicillin-binding protein


Mass: 103980.461 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridioides difficile (strain R20291) (bacteria)
Strain: R20291 / Gene: CDR20291_0985
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: C9YK84
#2: Chemical ChemComp-RB6 / (2R)-2-[(1R)-1-{[(2Z)-2-(5-amino-1,2,4-thiadiazol-3-yl)-2-(hydroxyimino)acetyl]amino}-2-oxoethyl]-5-({2-oxo-1-[(3R)-pyr rolidin-3-yl]-2,5-dihydro-1H-pyrrol-3-yl}methyl)-3,6-dihydro-2H-1,3-thiazine-4-carboxylic acid / BAL 9141, bound form / ceftobiprole, bound form


Mass: 536.585 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H24N8O6S2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / 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: 4.18 Å3/Da / Density % sol: 70.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 15% PEG 4000, 0.2 M AmSO4, 0.1 M Na Citrate pH 5.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 20, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→53.84 Å / Num. obs: 28449 / % possible obs: 83.9 % / Redundancy: 2.6 % / CC1/2: 0.981 / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.06 / Rrim(I) all: 0.103 / Net I/σ(I): 9.3 / Num. measured all: 73171 / Scaling rejects: 38
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
3-3.162.60.5391024640180.6750.4050.677281.6
9.49-53.842.70.03726729910.9550.0270.04624.389.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
Aimless0.7.4data scaling
PDB_EXTRACT3.27data extraction
MOSFLMdata reduction
MoRDaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6g9f

6g9f


Resolution: 3→50.01 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.899 / SU B: 18.09 / SU ML: 0.322 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.849 / ESU R Free: 0.425 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY LINK C05 LIG A1001 OG SER A 492 1555 1555
RfactorNum. reflection% reflectionSelection details
Rfree0.2664 1483 5.2 %RANDOM
Rwork0.2073 ---
obs0.2104 26959 83.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 193.2 Å2 / Biso mean: 78.726 Å2 / Biso min: 30 Å2
Baniso -1Baniso -2Baniso -3
1--2.12 Å2-0 Å23.08 Å2
2---1.39 Å2-0 Å2
3---1.54 Å2
Refinement stepCycle: final / Resolution: 3→50.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6479 0 37 11 6527
Biso mean--83.85 42.62 -
Num. residues----828
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0136622
X-RAY DIFFRACTIONr_bond_other_d0.0020.0176220
X-RAY DIFFRACTIONr_angle_refined_deg1.4661.6548924
X-RAY DIFFRACTIONr_angle_other_deg1.2391.59214536
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2575825
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.11524.41322
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.918151238
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0911527
X-RAY DIFFRACTIONr_chiral_restr0.0590.2862
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.027347
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021242
LS refinement shellResolution: 3→3.078 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.374 108 -
Rwork0.343 1918 -
all-2026 -
obs--79.73 %

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