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

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Basic information

Entry
Database: PDB / ID: 7rcx
TitleCrystal structure of C. difficile penicillin-binding protein 2 in apo form
ComponentsPenicillin-binding protein
KeywordsPEPTIDE BINDING PROTEIN / Peptidoglycan / PBP / PBP2 / cell wall / transpeptidase / b-lactam / gram-positive / spore / sporulation
Function / homology:
Function and homology information
Biological speciesClostridioides difficile (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 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

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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)104,4266
Polymers103,9801
Non-polymers4465
Water21612
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)65.300, 122.460, 70.730
Angle α, β, γ (deg.)90.000, 103.400, 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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.65 Å3/Da / Density % sol: 53.51 %
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: 200 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.98557 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 8, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98557 Å / Relative weight: 1
ReflectionResolution: 2.85→48.86 Å / Num. obs: 23251 / % possible obs: 92.2 % / Redundancy: 3.1 % / CC1/2: 0.994 / Rmerge(I) obs: 0.081 / Rpim(I) all: 0.054 / Rrim(I) all: 0.098 / Net I/σ(I): 10.6
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
2.85-32.90.483925931420.7530.3250.5842.186
9.01-48.813.20.03225187930.9910.0220.03928.896.2

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
REFMAC5.8.0258refinement
PDB_EXTRACT3.27data extraction
MOSFLMdata reduction
MoRDaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6G9F

6g9f


Resolution: 2.85→48.86 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.882 / SU B: 18.733 / SU ML: 0.358 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.437 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2723 1135 4.9 %RANDOM
Rwork0.2082 ---
obs0.2114 22087 91.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 194.09 Å2 / Biso mean: 68.704 Å2 / Biso min: 27.26 Å2
Baniso -1Baniso -2Baniso -3
1--0.21 Å2-0 Å22.22 Å2
2--0.87 Å20 Å2
3----1.54 Å2
Refinement stepCycle: final / Resolution: 2.85→48.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6343 0 22 12 6377
Biso mean--93.23 40.05 -
Num. residues----811
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0136471
X-RAY DIFFRACTIONr_bond_other_d0.0020.0176061
X-RAY DIFFRACTIONr_angle_refined_deg1.3771.6448717
X-RAY DIFFRACTIONr_angle_other_deg1.2081.58714157
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4255807
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.50124.344320
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.158151204
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1191527
X-RAY DIFFRACTIONr_chiral_restr0.0570.2840
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.027176
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021229
LS refinement shellResolution: 2.85→2.924 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.416 54 -
Rwork0.299 1412 -
all-1466 -
obs--78.99 %

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