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- PDB-8e2b: N-terminal domain of S. aureus GpsB -

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Basic information

Entry
Database: PDB / ID: 8e2b
TitleN-terminal domain of S. aureus GpsB
ComponentsCell cycle protein GpsB
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: 1.95 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: Cell cycle protein GpsB
D: Cell cycle protein GpsB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,9585
Polymers33,8664
Non-polymers921
Water7,620423
1
A: Cell cycle protein GpsB
B: Cell cycle protein GpsB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,0253
Polymers16,9332
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5010 Å2
ΔGint-37 kcal/mol
Surface area9320 Å2
MethodPISA
2
C: Cell cycle protein GpsB
D: Cell cycle protein GpsB


Theoretical massNumber of molelcules
Total (without water)16,9332
Polymers16,9332
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4920 Å2
ΔGint-40 kcal/mol
Surface area9120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.520, 37.470, 79.250
Angle α, β, γ (deg.)90.000, 100.620, 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: 8466.587 Da / Num. of mol.: 4 / 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: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 423 / 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: 2.31 Å3/Da / Density % sol: 46.67 % / Description: Plate-like
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 30 % PEG 3350, 0.4 M NaCl, and 0.1 M Tris pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 2, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.95→47.92 Å / Num. obs: 20772 / % possible obs: 90.7 % / Redundancy: 3.3 % / CC1/2: 0.985 / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.05 / Rrim(I) all: 0.093 / Net I/σ(I): 9.7
Reflection shell

Diffraction-ID: 1 / Redundancy: 3.2 %

Resolution (Å)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.95-20.212484615020.9570.1370.2544.194.8
8.94-47.880.0488272560.980.0330.05914.796.5

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Processing

Software
NameVersionClassification
Aimless0.7.7data scaling
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
iMOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4UG1

4ug1


Resolution: 1.95→47.92 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.916 / SU B: 3.833 / SU ML: 0.112 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.211 / ESU R Free: 0.18 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.234 1075 5.2 %RANDOM
Rwork0.1814 ---
obs0.1841 19696 90.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 80.64 Å2 / Biso mean: 22.286 Å2 / Biso min: 2.21 Å2
Baniso -1Baniso -2Baniso -3
1--1.9 Å20 Å2-0.66 Å2
2--0.17 Å2-0 Å2
3---1.85 Å2
Refinement stepCycle: final / Resolution: 1.95→47.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2282 0 6 427 2715
Biso mean--35.19 36.74 -
Num. residues----275
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0132367
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162298
X-RAY DIFFRACTIONr_angle_refined_deg1.3211.6513158
X-RAY DIFFRACTIONr_angle_other_deg1.2481.6095333
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6455283
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.64523.862145
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.83715515
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0761516
X-RAY DIFFRACTIONr_chiral_restr0.060.2293
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022663
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02497
LS refinement shellResolution: 1.95→2.001 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.264 77 -
Rwork0.192 1504 -
all-1581 -
obs--94.73 %

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