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- PDB-6gqn: Cell division regulator, S. pneumoniae GpsB, in complex with pept... -

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Basic information

Entry
Database: PDB / ID: 6gqn
TitleCell division regulator, S. pneumoniae GpsB, in complex with peptide fragment of Penicillin Binding Protein PBP2a
Components
  • Cell cycle protein GpsB
  • SpPBP2a
KeywordsCELL CYCLE / Bacterial cell division regulator / peptidoglycan synthesis regulator / penicillin binding protein interaction partner / protein-peptide complex
Function / homology
Function and homology information


regulation of cell shape / cell cycle / cell division / cytoplasm
Similarity search - Function
Cell cycle protein GpsB / DivIVA family / DivIVA domain / DivIVA protein
Similarity search - Domain/homology
NICKEL (II) ION / Cell cycle protein GpsB
Similarity search - Component
Biological speciesStreptococcus pneumoniae R6 (bacteria)
Streptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_symmetry

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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: SpPBP2a
G: SpPBP2a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,55311
Polymers17,9184
Non-polymers6357
Water1,56787
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7060 Å2
ΔGint-116 kcal/mol
Surface area10120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.084, 26.373, 65.899
Angle α, β, γ (deg.)90.00, 106.43, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11C-204-

HOH

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Components

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


Mass: 7253.134 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae R6 (bacteria) / Gene: gpsB, spr0332 / Production host: Escherichia coli BL21(DE3) / References: UniProt: Q8DR57
#2: Protein/peptide SpPBP2a


Mass: 1706.048 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Streptococcus pneumoniae (bacteria)
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 87 / 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: 1.93 Å3/Da / Density % sol: 36.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1M Tris.HCl pH 8.5, 0.2M lithium sulphate, 40% PEG400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 9, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.8→39.85 Å / Num. obs: 13052 / % possible obs: 99.8 % / Redundancy: 3.6 % / CC1/2: 0.976 / Rpim(I) all: 0.051 / Net I/σ(I): 9
Reflection shellResolution: 1.8→1.84 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 2.2 / Num. unique obs: 763 / CC1/2: 0.883 / Rpim(I) all: 0.269 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6GQA

6gqa


Resolution: 1.8→39.846 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.01
RfactorNum. reflection% reflection
Rfree0.2254 657 5.05 %
Rwork0.1783 --
obs0.1808 13007 99.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.8→39.846 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1219 0 31 87 1337
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0151253
X-RAY DIFFRACTIONf_angle_d1.3931675
X-RAY DIFFRACTIONf_dihedral_angle_d18.589761
X-RAY DIFFRACTIONf_chiral_restr0.074184
X-RAY DIFFRACTIONf_plane_restr0.009210
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.9390.29181270.24582410X-RAY DIFFRACTION99
1.939-2.13410.22691310.18092448X-RAY DIFFRACTION99
2.1341-2.44290.23891250.17062474X-RAY DIFFRACTION100
2.4429-3.07760.19741270.18442465X-RAY DIFFRACTION100
3.0776-39.85580.22111470.16382553X-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)
17.2346.4063.01948.83581.41615.3493-0.1607-0.43780.2188-0.0691-0.11990.1439-0.4072-0.48460.21860.15540.05640.01010.1114-0.01430.1346-11.6037-2.203921.7839
27.07120.77273.30337.6143.20883.75680.0870.41950.3523-0.2794-0.05980.5539-0.0338-0.96760.11420.1481-0.0257-0.00190.32820.04310.1776-22.3481-5.75277.5476
38.42591.48747.3740.40961.25937.05780.064-0.2946-0.050.074-0.0414-0.06190.0579-0.296-0.02530.1320.00080.01150.06520.00930.1274-0.8916-8.784627.0479
43.9995-2.08573.88364.0344-3.18885.2010.23130.3324-0.252-0.25330.00790.20750.31560.2936-0.14780.1174-0.00560.0240.1067-0.02130.1219-3.3731-12.659211.5228
55.9185-0.45733.06943.0570.03053.12790.2190.77270.0613-0.2623-0.18630.15710.4351-0.2532-0.1120.1844-0.0073-0.03650.2871-0.01220.1543-20.0169-10.17234.1198
68.4795-1.45716.53110.468-1.09236.1823-0.20750.26870.31790.0978-0.0117-0.1191-0.26720.17340.17710.1522-0.01510.01240.04320.01040.13253.6295-5.717320.3373
78.1119-5.67722.0925.01050.30434.1963-0.17360.10360.7741-0.16240.1461-0.4309-0.4410.2940.0410.16280.00030.03650.29850.00830.2024-5.0494-1.43542.2018
85.38032.6391-5.70582.3355-1.14058.70950.12130.4275-0.2164-0.384-0.0764-0.14740.3603-0.38970.08080.26840.08350.05880.3591-0.03010.1299-6.101-7.1093-3.273
92.971-3.04711.91296.7692-5.91395.51930.82430.2524-0.5341-0.193-0.28520.14080.09650.3786-0.57710.4359-0.0545-0.18360.36310.07320.6114-17.7339-13.449428.0184
105.31935.0172-3.30044.9877-2.8142.4836-0.4196-0.4479-0.9888-0.4244-0.16170.00740.46380.36590.56480.24050.06110.07320.29710.06130.3151-26.7335-11.729420.0439
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -1 through 13 )
2X-RAY DIFFRACTION2chain 'A' and (resid 14 through 24 )
3X-RAY DIFFRACTION3chain 'A' and (resid 25 through 63 )
4X-RAY DIFFRACTION4chain 'B' and (resid -1 through 13 )
5X-RAY DIFFRACTION5chain 'B' and (resid 14 through 24 )
6X-RAY DIFFRACTION6chain 'B' and (resid 25 through 63 )
7X-RAY DIFFRACTION7chain 'C' and (resid 27 through 35 )
8X-RAY DIFFRACTION8chain 'C' and (resid 36 through 40 )
9X-RAY DIFFRACTION9chain 'G' and (resid 28 through 32 )
10X-RAY DIFFRACTION10chain 'G' and (resid 33 through 40 )

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