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- PDB-7rcz: Crystal structure of C. difficile SpoVD in complex with ampicillin -

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Basic information

Entry
Database: PDB / ID: 7rcz
TitleCrystal structure of C. difficile SpoVD in complex with ampicillin
ComponentsStage V sporulation protein D (Sporulation specific penicillin-binding protein)
KeywordsPEPTIDE BINDING PROTEIN / Peptidoglycan / PBP / PBP2 / cell wall / transpeptidase / b-lactam / gram-positive / spore / sporulation
Function / homologyDI(HYDROXYETHYL)ETHER / N-PROPANOL / Chem-ZZ7 / :
Function and homology information
Biological speciesClostridioides difficile (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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 1.3Nov 13, 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: Stage V sporulation protein D (Sporulation specific penicillin-binding protein)
B: Stage V sporulation protein D (Sporulation specific penicillin-binding protein)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,67320
Polymers121,2042
Non-polymers2,46918
Water5,729318
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4840 Å2
ΔGint-104 kcal/mol
Surface area43180 Å2
Unit cell
Length a, b, c (Å)76.640, 95.620, 176.770
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Stage V sporulation protein D (Sporulation specific penicillin-binding protein)


Mass: 60601.922 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridioides difficile (strain R20291) (bacteria)
Strain: R20291 / Gene: spoVD, CDR20291_2544
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: C9YPN0

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Non-polymers , 7 types, 336 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#4: Chemical ChemComp-POL / N-PROPANOL / 1-PROPONOL


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#7: Chemical ChemComp-ZZ7 / (2R,4S)-2-[(R)-{[(2R)-2-amino-2-phenylacetyl]amino}(carboxy)methyl]-5,5-dimethyl-1,3-thiazolidine-4-carboxylic acid / AMPICILLIN (open form)


Mass: 367.420 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H21N3O5S / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 318 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.69 Å3/Da / Density % sol: 54.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 15 % PEG 3350, 0.2 M AmSO4, 10 % PropOH, 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: 19-ID / Wavelength: 0.97911 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 21, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97911 Å / Relative weight: 1
ReflectionResolution: 2.2→49.58 Å / Num. obs: 62415 / % possible obs: 94.6 % / Redundancy: 3.5 % / CC1/2: 0.985 / Rmerge(I) obs: 0.105 / Rpim(I) all: 0.063 / Rrim(I) all: 0.123 / Net I/σ(I): 7.3
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
2.2-2.253.40.51511944720.8590.2990.5862.596.8
10.08-49.533.70.08222886230.9590.0490.09714.281.5

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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: 6UN1

6un1


Resolution: 2.2→49.58 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.933 / SU B: 6.018 / SU ML: 0.148 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.247 / ESU R Free: 0.195 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2252 3192 5.1 %RANDOM
Rwork0.1871 ---
obs0.1891 59183 93.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 142.75 Å2 / Biso mean: 41.966 Å2 / Biso min: 14.08 Å2
Baniso -1Baniso -2Baniso -3
1--3.23 Å20 Å2-0 Å2
2--1.2 Å20 Å2
3---2.03 Å2
Refinement stepCycle: final / Resolution: 2.2→49.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7855 0 141 319 8315
Biso mean--75.28 37.8 -
Num. residues----1014
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0138278
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177783
X-RAY DIFFRACTIONr_angle_refined_deg1.5181.66211201
X-RAY DIFFRACTIONr_angle_other_deg1.2161.59618174
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.12351021
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.91823.883358
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.096151470
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.131530
X-RAY DIFFRACTIONr_chiral_restr0.0670.21086
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.028992
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021546
LS refinement shellResolution: 2.2→2.257 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.259 266 -
Rwork0.246 4421 -
all-4687 -
obs--96.22 %

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