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- PDB-6gp7: Cell division regulator, B. subtilis GpsB, in complex with peptid... -

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Basic information

Entry
Database: PDB / ID: 6gp7
TitleCell division regulator, B. subtilis GpsB, in complex with peptide fragment of Penicillin Binding Protein PBP1A
Components
  • Cell cycle protein GpsB
  • PBP1A
KeywordsCELL CYCLE / Bacterial cell division regulator / peptidoglycan synthesis regulator / penicillin binding protein interaction partner / protein-peptide complex
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 speciesBacillus subtilis subsp. subtilis str. 168 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95001799213 Å
AuthorsCleverley, R.M. / Lewis, R.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 5, 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.ptnr1_symmetry / _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.ptnr3_symmetry / _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.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Cell cycle protein GpsB
A: Cell cycle protein GpsB
D: PBP1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,2764
Polymers17,2523
Non-polymers241
Water1,33374
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: surface plasmon resonance, protein-peptide interaction confirmed by fluorescence polarisation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5140 Å2
ΔGint-41 kcal/mol
Surface area7940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)31.472, 53.753, 85.912
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 Cell cycle protein GpsB / Guiding PBP1-shuttling protein


Mass: 7610.684 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. subtilis str. 168
Gene: gpsB, ypsB, BSU22180 / Production host: Escherichia coli BL21(DE3) / References: UniProt: P0CI74
#2: Protein/peptide PBP1A


Mass: 2030.251 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 74 / 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: 2.34 Å3/Da / Density % sol: 47.42 %
Crystal growTemperature: 295 K / Method: vapor diffusion / pH: 7.5
Details: 0.1 M HEPES/MOPS pH 7.5, 12.5% MPD, 12.5 % PEG 1000 12.5% PEG 3350, 0.03M MgCl2, 0.03M CaCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 13, 1996
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 1.95→45.6 Å / Num. obs: 11206 / % possible obs: 100 % / Redundancy: 7 % / Biso Wilson estimate: 24.8484214955 Å2 / CC1/2: 0.994 / Rpim(I) all: 0.059 / Net I/σ(I): 8.8
Reflection shellResolution: 1.95→2 Å / Redundancy: 7.1 % / Mean I/σ(I) obs: 2.1 / Num. unique obs: 768 / CC1/2: 0.72 / Rpim(I) all: 0.473 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4UG3

4ug3


Resolution: 1.95001799213→45.5686210377 Å / SU ML: 0.161620864616 / Cross valid method: FREE R-VALUE / σ(F): 1.37278577122 / Phase error: 22.7922494119
RfactorNum. reflection% reflection
Rfree0.21352917101 528 4.7303350654 %
Rwork0.186944583663 --
obs0.188286986987 11162 99.9552252172 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 34.5778482729 Å2
Refinement stepCycle: LAST / Resolution: 1.95001799213→45.5686210377 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1045 0 1 74 1120
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005938191611881055
X-RAY DIFFRACTIONf_angle_d0.6725055390121407
X-RAY DIFFRACTIONf_chiral_restr0.0385771520787154
X-RAY DIFFRACTIONf_plane_restr0.00344422931547184
X-RAY DIFFRACTIONf_dihedral_angle_d12.7387863015656
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-2.14630.2431678682821190.2067409774172595X-RAY DIFFRACTION99.8528329654
2.1463-2.45680.2137839397991350.1813595406472614X-RAY DIFFRACTION99.9636363636
2.4568-3.09520.2442859198621330.1967420702652639X-RAY DIFFRACTION100
3.0952-45.5810.1950445642931410.1799579835242786X-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)
15.9393609505-5.08786951729-1.34272609038.839801483321.502118722365.274381489210.105590524088-0.5155185218930.5742875461260.415198017771-0.0559780778772-0.376225368478-0.4116612790980.402141765974-0.06307379953730.301023531578-0.1006006798330.03338920673250.2256971789790.01912033878580.2564270591966.565360548415.90155621618-6.33638573084
24.39933305576-4.119048893321.677725160255.86833476297-1.109400802544.15933389764-0.1097053210710.008275223534350.163911712109-0.010888955262-0.0775775694138-0.227681167812-0.1862931464110.1646070283280.004221165841780.100080954349-0.0349077563111-0.003180078347320.1687580944440.0346393089210.16296081328312.0838097665-10.9248020175-3.44785889758
33.49308909142-5.566077529140.09783718676956.78627056951-0.701846341080.9478840634810.3335138740850.1165513359670.327097235035-0.494169314041-0.179791305947-0.336814687195-0.396214182209-0.102103354434-0.02457091901410.3467188101090.03860509886830.04207787571460.2248960048430.05618062224830.253260834408-2.9784296369.84583709854-13.8302300326
44.3448199299-2.287057396731.148811061622.2011681916-0.323790798470.8142011975940.133333998204-0.00428138408965-0.106963424692-0.178250783623-0.02891635525940.2451827316650.0580284284936-0.0584070732512-0.03926831599990.158041810633-0.00934885205323-0.0026611364750.1889071656130.01479867032230.156624608531.3344761605-9.78933388376-7.97818753824
55.47798265812-6.193387981563.471860635095.06653857052-3.32484521221.74834495702-0.297939408719-0.411374867490.2131151909030.3410548207950.344167220202-0.0247444703092-0.448483543272-0.460927801043-0.120578188660.2763855186670.08318329606020.006741404433550.2693324875250.03190835633260.306954048978-7.309460262657.65331707446-5.80198911886
62.873845712741.98995937854-2.72831488794.2230807165-2.442015540583.49537273781-0.252233691293-0.140923865397-0.508235111602-0.1347234796370.198463570675-0.1604531482460.2318228100890.7274876493670.1639566893890.259631320836-0.02855229273950.05407412437320.3448508535-0.008944211689990.23299507220814.45447327-4.18129642759-16.4730321842
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 5 through 15 )
2X-RAY DIFFRACTION2chain 'B' and (resid 16 through 26 )
3X-RAY DIFFRACTION3chain 'B' and (resid 27 through 63 )
4X-RAY DIFFRACTION4chain 'A' and (resid 5 through 26 )
5X-RAY DIFFRACTION5chain 'A' and (resid 27 through 62 )
6X-RAY DIFFRACTION6chain 'D' and (resid 5 through 15 )

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