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- PDB-8e2c: N-terminal domain of S. aureus GpsB in complex with PBP4 fragment -

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Basic information

Entry
Database: PDB / ID: 8e2c
TitleN-terminal domain of S. aureus GpsB in complex with PBP4 fragment
Components
  • Cell cycle protein GpsB
  • PBP4
KeywordsPEPTIDE BINDING PROTEIN / Peptidoglycan / PBP / PBP4 / MRSA / GpsB / PBP2a cell wall / transpeptidase / b-lactam / gram-positive / sporulation / cell division / bacterial cell division / diviva / divisome
Function / homologyCell cycle protein GpsB / DivIVA family / DivIVA domain / DivIVA protein / regulation of cell shape / cell division / cytoplasm / Cell cycle protein GpsB
Function and homology information
Biological speciesStaphylococcus aureus subsp. aureus COL (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsSacco, M. / Chen, Y.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI161762 United States
CitationJournal: Elife / Year: 2024
Title: Staphylococcus aureus FtsZ and PBP4 bind to the conformationally dynamic N-terminal domain of GpsB.
Authors: Sacco, M.D. / Hammond, L.R. / Noor, R.E. / Bhattacharya, D. / McKnight, L.J. / Madsen, J.J. / Zhang, X. / Butler, S.G. / Kemp, M.T. / Jaskolka-Brown, A.C. / Khan, S.J. / Gelis, I. / Eswara, P. / Chen, Y.
History
DepositionAug 14, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 9, 2023Provider: repository / Type: Initial release
Revision 1.1May 8, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cell cycle protein GpsB
B: Cell cycle protein GpsB
C: PBP4


Theoretical massNumber of molelcules
Total (without water)17,6503
Polymers17,6503
Non-polymers00
Water724
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)29.350, 73.760, 42.370
Angle α, β, γ (deg.)90.000, 103.560, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Cell cycle protein GpsB / Guiding PBP1-shuttling protein


Mass: 8328.440 Da / Num. of mol.: 2 / Fragment: N-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus COL (bacteria)
Strain: COL / Gene: gpsB, SACOL1484
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q5HFX8
#2: Protein/peptide PBP4


Mass: 993.211 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus COL (bacteria)
Gene: pbp4
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O

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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: 2.53 Å3/Da / Density % sol: 51.31 % / Description: Plate-like
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 25 % PEG 4000, 0.1 M Tris pH 8.0, and 0.2 M Na Acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97934 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 17, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.4→41.19 Å / Num. obs: 6596 / % possible obs: 95.7 % / Redundancy: 5.2 % / CC1/2: 0.991 / Rmerge(I) obs: 0.101 / Rpim(I) all: 0.048 / Rrim(I) all: 0.113 / Net I/σ(I): 10.8 / Num. measured all: 34441 / Scaling rejects: 198
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
2.4-2.495.20.43436707110.8850.2060.4834.996.6
8.98-41.1950.0876541310.990.0480.117.592.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0266refinement
PDB_EXTRACT3.27data extraction
iMOSFLMdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4UG3

4ug3


Resolution: 2.4→36.91 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.918 / SU B: 10.727 / SU ML: 0.244 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.523 / ESU R Free: 0.287 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2575 634 9.6 %RANDOM
Rwork0.2197 ---
obs0.2235 5949 95.08 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 107.33 Å2 / Biso mean: 38.619 Å2 / Biso min: 19.71 Å2
Baniso -1Baniso -2Baniso -3
1-0.63 Å2-0 Å2-2.9 Å2
2--4.41 Å2-0 Å2
3----3.26 Å2
Refinement stepCycle: final / Resolution: 2.4→36.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1157 0 0 4 1161
Biso mean---33.33 -
Num. residues----139
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0131167
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171146
X-RAY DIFFRACTIONr_angle_refined_deg1.3151.651551
X-RAY DIFFRACTIONr_angle_other_deg1.2131.6112653
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3985136
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.86923.83673
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.37915253
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.626158
X-RAY DIFFRACTIONr_chiral_restr0.0510.2145
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021289
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02247
LS refinement shellResolution: 2.4→2.463 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.343 63 -
Rwork0.268 434 -
all-497 -
obs--95.58 %

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