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- PDB-6gqa: Cell division regulator S. pneumoniae GpsB -

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Basic information

Entry
Database: PDB / ID: 6gqa
TitleCell division regulator S. pneumoniae GpsB
ComponentsCell cycle protein GpsB
KeywordsCELL CYCLE / Bacterial cell division regulator / peptidoglycan synthesis regulator / penicillin binding protein interaction partner
Function / homologyCell cycle protein GpsB / DivIVA family / DivIVA domain / DivIVA protein / regulation of cell shape / cell cycle / cell division / cytoplasm / Cell cycle protein GpsB
Function and homology information
Biological speciesStreptococcus pneumoniae R6 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsLewis, R.J. / Rutter, Z.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/M001180/1 United Kingdom
CitationJournal: Nat Commun / Year: 2019
Title: The cell cycle regulator GpsB functions as cytosolic adaptor for multiple cell wall enzymes.
Authors: Cleverley, R.M. / Rutter, Z.J. / Rismondo, J. / Corona, F. / Tsui, H.T. / Alatawi, F.A. / Daniel, R.A. / Halbedel, S. / Massidda, O. / Winkler, M.E. / Lewis, R.J.
History
DepositionJun 7, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 23, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 30, 2019Group: Data collection / 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 / _citation_author.identifier_ORCID
Revision 1.2Jan 17, 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

Downloads & links

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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


Theoretical massNumber of molelcules
Total (without water)29,0134
Polymers29,0134
Non-polymers00
Water4,684260
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9290 Å2
ΔGint-67 kcal/mol
Surface area14300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.119, 54.454, 61.637
Angle α, β, γ (deg.)90.00, 106.13, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 7253.134 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae R6 (bacteria) / Gene: gpsB, spr0332 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8DR57
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 260 / 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: 2.3 Å3/Da / Density % sol: 46.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1M Tris.HCl pH 8.5, 0.2M magnesium chloride, 20% PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER METALJET / Wavelength: 1.34 Å
DetectorType: Bruker PHOTON II / Detector: PIXEL / Date: Aug 31, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.34 Å / Relative weight: 1
ReflectionResolution: 1.9→27.22 Å / Num. obs: 19776 / % possible obs: 100 % / Redundancy: 25.2 % / CC1/2: 0.998 / Rpim(I) all: 0.041 / Net I/σ(I): 13.9
Reflection shellResolution: 1.9→1.94 Å / Redundancy: 20.7 % / Mean I/σ(I) obs: 4 / CC1/2: 0.78 / Rpim(I) all: 0.311 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
SAINTdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4UG1

4ug1


Resolution: 1.9→26.01 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.88
RfactorNum. reflection% reflection
Rfree0.2493 921 4.67 %
Rwork0.1882 --
obs0.1911 19738 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.9→26.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1919 0 0 260 2179
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0171943
X-RAY DIFFRACTIONf_angle_d1.3992606
X-RAY DIFFRACTIONf_dihedral_angle_d13.4761176
X-RAY DIFFRACTIONf_chiral_restr0.072286
X-RAY DIFFRACTIONf_plane_restr0.008341
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-2.00020.36421240.25272668X-RAY DIFFRACTION100
2.0002-2.12540.31331210.21882686X-RAY DIFFRACTION100
2.1254-2.28940.25421210.20032693X-RAY DIFFRACTION100
2.2894-2.51970.27121390.20142654X-RAY DIFFRACTION100
2.5197-2.88390.25891260.19952690X-RAY DIFFRACTION100
2.8839-3.63180.231600.17112677X-RAY DIFFRACTION100
3.6318-26.01220.20831300.16482749X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.63510.63162.351.590.90798.0532-0.22570.07450.0517-0.31670.1157-0.257-0.70910.46640.06710.2048-0.03140.03530.0927-0.02080.1982-7.8341-5.3455-32.6688
22.1016-0.80170.89342.3994-2.14646.2425-0.1481-0.35560.01150.21550.0521-0.1147-0.8388-0.24480.02270.11890.02660.00180.1191-0.02650.1875-13.3184-8.8458-13.3016
32.8247-0.14561.07432.34421.01147.3032-0.0666-0.1176-0.1984-0.25190.1412-0.0684-0.1324-0.63730.00980.16570.0056-0.01080.1116-0.02130.2248-17.5309-9.9688-33.7983
41.8041-0.0629-0.47210.7178-1.1645.6553-0.1912-0.3159-0.3096-0.1321-0.0252-0.02020.58280.40780.14050.15350.03980.02240.07870.02760.2161-12.1265-17.5841-16.1787
51.50610.1644-0.50280.492-0.21686.0335-0.09450.1-0.10760.0741-0.1006-0.09990.79330.28360.17170.20890.01590.02610.0976-0.00370.1625-28.0518-22.07843.7862
60.86850.23810.27743.4681-3.25323.2622-0.10680.2905-0.0727-0.47750.0814-0.16220.6827-0.22230.02060.1585-0.04220.00670.2568-0.05430.2236-34.5983-18.0308-12.954
73.25670.73371.264.05251.55946.8765-0.1860.10650.4377-0.3333-0.0220.249-0.5332-0.44190.19480.14650.0559-0.04180.22840.01360.2432-38.4601-10.6535-2.0933
85.2606-2.33612.04152.7677-4.36687.9907-0.09680.16490.09960.1743-0.1049-0.14760.0747-0.2410.18920.2382-0.0134-0.00140.0686-0.0260.1582-34.1638-19.658113.9728
91.736-0.43881.91842.0812-3.19079.36530.00580.36980.07370.10380.11420.1486-0.7760.4862-0.08240.1537-0.03630.00030.17320.0020.2015-30.2545-9.6746-10.487
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 24 )
2X-RAY DIFFRACTION2chain 'A' and (resid 25 through 61 )
3X-RAY DIFFRACTION3chain 'B' and (resid -1 through 24 )
4X-RAY DIFFRACTION4chain 'B' and (resid 25 through 61 )
5X-RAY DIFFRACTION5chain 'C' and (resid -1 through 24 )
6X-RAY DIFFRACTION6chain 'C' and (resid 25 through 59 )
7X-RAY DIFFRACTION7chain 'D' and (resid -1 through 13 )
8X-RAY DIFFRACTION8chain 'D' and (resid 14 through 24 )
9X-RAY DIFFRACTION9chain 'D' and (resid 25 through 59 )

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