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- PDB-4ug3: B. subtilis GpsB N-terminal Domain -

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Basic information

Entry
Database: PDB / ID: 4ug3
TitleB. subtilis GpsB N-terminal Domain
ComponentsCELL CYCLE PROTEIN GPSB
KeywordsCELL CYCLE / BACTERIAL GROWTH REGULATION / CELL WALL SYNTHESIS / CELL DIVISION
Function / homologyCell cycle protein GpsB / DivIVA family / DivIVA domain / DivIVA protein / peptidoglycan-based cell wall biogenesis / regulation of cell shape / cell division / cytoplasm / Cell cycle protein GpsB
Function and homology information
Biological speciesBACILLUS SUBTILIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsRismondo, J. / Cleverley, R.M. / Lane, H.V. / Grohennig, S. / Steglich, A. / Moller, L. / Krishna Mannala, G. / Hain, T. / Lewis, R.J. / Halbedel, S.
CitationJournal: Mol.Microbiol. / Year: 2016
Title: Structure of the Bacterial Cell Division Determinant Gpsb and its Interaction with Penicillin Binding Proteins.
Authors: Rismondo, J. / Cleverley, R.M. / Lane, H.V. / Grosshennig, S. / Steglich, A. / Moller, L. / Mannala, G.K. / Hain, T. / Lewis, R.J. / Halbedel, S.
History
DepositionMar 21, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 25, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 9, 2016Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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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)33,6544
Polymers33,6544
Non-polymers00
Water362
1
A: CELL CYCLE PROTEIN GPSB
B: CELL CYCLE PROTEIN GPSB


Theoretical massNumber of molelcules
Total (without water)16,8272
Polymers16,8272
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4420 Å2
ΔGint-35.9 kcal/mol
Surface area9140 Å2
MethodPISA
2
C: CELL CYCLE PROTEIN GPSB
D: CELL CYCLE PROTEIN GPSB


Theoretical massNumber of molelcules
Total (without water)16,8272
Polymers16,8272
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3850 Å2
ΔGint-32.5 kcal/mol
Surface area7260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.672, 39.893, 77.277
Angle α, β, γ (deg.)90.00, 103.28, 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 / GPSB


Mass: 8413.601 Da / Num. of mol.: 4 / Fragment: N-TERMINAL DOMAIN, UNP RESIDUES 1-68
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACILLUS SUBTILIS (bacteria) / Strain: 168 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0CI74
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 2.31 Å3/Da / Density % sol: 46.72 % / Description: NONE
Crystal growpH: 6.5
Details: 0.05M BIS TRIS PH 6.5, 0.05M AMMONIUM SULPHATE, 30% PENTAERYTHRITOL ETHOXYLATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97949
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 14, 2015
RadiationMonochromator: SI (111) DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.8→50.3 Å / Num. obs: 7791 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 10.6
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 3.7 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0107refinement
XDSdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4UG1

4ug1


Resolution: 2.8→50.3 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.848 / SU B: 17.384 / SU ML: 0.338 / Cross valid method: THROUGHOUT / ESU R Free: 0.462 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.30114 801 10.3 %RANDOM
Rwork0.21626 ---
obs0.2245 6984 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 53.503 Å2
Baniso -1Baniso -2Baniso -3
1-0.24 Å2-0 Å2-0.13 Å2
2--0.09 Å20 Å2
3----0.24 Å2
Refinement stepCycle: LAST / Resolution: 2.8→50.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1944 0 0 2 1946
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0191965
X-RAY DIFFRACTIONr_bond_other_d0.0010.021951
X-RAY DIFFRACTIONr_angle_refined_deg1.4381.9862611
X-RAY DIFFRACTIONr_angle_other_deg0.88134539
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5785226
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.54326.944108
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.02715443
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.529154
X-RAY DIFFRACTIONr_chiral_restr0.0750.2283
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022140
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02398
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.1725.09916
X-RAY DIFFRACTIONr_mcbond_other3.1735.087915
X-RAY DIFFRACTIONr_mcangle_it4.9057.6141138
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.6295.4771049
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.433 58 -
Rwork0.259 524 -
obs--99.66 %

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