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- PDB-7o39: Crystal structure of S. aureus DivIVA N terminal domain -

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Basic information

Entry
Database: PDB / ID: 7o39
TitleCrystal structure of S. aureus DivIVA N terminal domain
ComponentsDivIVA
KeywordsPROTEIN BINDING / Cell division / Divisome / molecular ruler
Function / homologyDivIVA family / DivIVA domain / DivIVA protein / cytoplasm / DivIVA domain-containing protein
Function and homology information
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsRao, V.A. / Booth, S. / Lewis, R.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MR/N002679/1 United Kingdom
CitationJournal: To Be Published
Title: Crystal structure of S. aureus DivIVA N terminal domain
Authors: Rao, V.A. / Booth, S. / Lewis, R.J.
History
DepositionApr 1, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 14, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DivIVA
B: DivIVA


Theoretical massNumber of molelcules
Total (without water)13,8202
Polymers13,8202
Non-polymers00
Water3,099172
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering, Dimer in solution, determined using SEC-MALs, SAXS, Dimer in solution, determined using SEC-SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3170 Å2
ΔGint-33 kcal/mol
Surface area6800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)28.108, 39.175, 111.249
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein DivIVA


Mass: 6909.777 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (strain NCTC 8325 / PS 47) (bacteria)
Strain: NCTC 8325 / PS 47 / Gene: SAOUHSC_01158 / Plasmid: pOPINRSF / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q2FZ83
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 172 / 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: 2.22 Å3/Da / Density % sol: 44.62 % / Description: Cubic
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M Carboxylic acids, 0.1 M Buffer system 1 pH 6.5, 37.5 % v/v MPD_P1K_P3350; Morpheus G4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97623 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 5, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97623 Å / Relative weight: 1
ReflectionResolution: 1.3→37.08 Å / Num. obs: 31216 / % possible obs: 100 % / Redundancy: 6.9 % / Biso Wilson estimate: 15.87 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.087 / Rpim(I) all: 0.051 / Rrim(I) all: 0.101 / Χ2: 0.8 / Net I/σ(I): 10.9
Reflection shellResolution: 1.3→1.32 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.556 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 1504 / CC1/2: 0.904 / Rpim(I) all: 0.339 / Rrim(I) all: 0.653 / Χ2: 0.33 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
xia2data reduction
Aimless0.6.2data scaling
PHASER2.7.17phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2WUJ

2wuj


Resolution: 1.3→36.95 Å / SU ML: 0.1175 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 15.2283
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1848 1506 4.84 %
Rwork0.1601 29617 -
obs0.1612 31123 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.98 Å2
Refinement stepCycle: LAST / Resolution: 1.3→36.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms822 0 0 172 994
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0056835
X-RAY DIFFRACTIONf_angle_d0.7471121
X-RAY DIFFRACTIONf_chiral_restr0.0602131
X-RAY DIFFRACTIONf_plane_restr0.0074147
X-RAY DIFFRACTIONf_dihedral_angle_d3.464105
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3-1.340.20121300.17932667X-RAY DIFFRACTION99.61
1.34-1.390.19851310.15762636X-RAY DIFFRACTION100
1.39-1.450.17341470.15412615X-RAY DIFFRACTION100
1.45-1.510.17381610.13832617X-RAY DIFFRACTION99.21
1.51-1.590.19381420.13782643X-RAY DIFFRACTION99.82
1.59-1.690.16121430.13092653X-RAY DIFFRACTION100
1.69-1.820.16721190.14262700X-RAY DIFFRACTION100
1.82-20.17991390.14352710X-RAY DIFFRACTION100
2-2.290.18341350.13822715X-RAY DIFFRACTION100
2.29-2.890.20051280.16152748X-RAY DIFFRACTION100
2.89-36.950.1861310.18382913X-RAY DIFFRACTION99.93

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