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- PDB-5an5: B. subtilis GpsB C-terminal Domain -

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Basic information

Entry
Database: PDB / ID: 5an5
TitleB. subtilis GpsB C-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 / regulation of cell shape / cell cycle / cell division / cytoplasm / Cell cycle protein GpsB
Function and homology information
Biological speciesBACILLUS SUBTILIS SUBSP. SUBTILIS STR. 168 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.2 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
DepositionSep 4, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 25, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 9, 2016Group: Database references
Revision 2.0Oct 23, 2019Group: Atomic model / Data collection / Other / Category: atom_site / pdbx_database_status
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_database_status.status_code_sf
Revision 2.1May 8, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: CELL CYCLE PROTEIN GPSB
C: CELL CYCLE PROTEIN GPSB
D: CELL CYCLE PROTEIN GPSB
E: CELL CYCLE PROTEIN GPSB
F: CELL CYCLE PROTEIN GPSB
G: CELL CYCLE PROTEIN GPSB
H: CELL CYCLE PROTEIN GPSB
I: CELL CYCLE PROTEIN GPSB
J: CELL CYCLE PROTEIN GPSB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,99011
Polymers27,8069
Non-polymers1842
Water4,234235
1
B: CELL CYCLE PROTEIN GPSB
H: CELL CYCLE PROTEIN GPSB
I: CELL CYCLE PROTEIN GPSB


Theoretical massNumber of molelcules
Total (without water)9,2693
Polymers9,2693
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2330 Å2
ΔGint-18.6 kcal/mol
Surface area4820 Å2
MethodPISA
2
C: CELL CYCLE PROTEIN GPSB
D: CELL CYCLE PROTEIN GPSB
J: CELL CYCLE PROTEIN GPSB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,3614
Polymers9,2693
Non-polymers921
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2630 Å2
ΔGint-17.6 kcal/mol
Surface area5370 Å2
MethodPISA
3
E: CELL CYCLE PROTEIN GPSB
F: CELL CYCLE PROTEIN GPSB
G: CELL CYCLE PROTEIN GPSB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,3614
Polymers9,2693
Non-polymers921
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2220 Å2
ΔGint-18.8 kcal/mol
Surface area4200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)32.594, 36.203, 43.179
Angle α, β, γ (deg.)85.59, 89.32, 65.53
Int Tables number1
Space group name H-MP1

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Components

#1: Protein/peptide
CELL CYCLE PROTEIN GPSB / / GUIDING PBP1-SHUTTLING PROTEIN / GPSB


Mass: 3089.546 Da / Num. of mol.: 9 / Fragment: C-TERMINAL DOMAIN, UNP RESIDUES 76-98
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACILLUS SUBTILIS SUBSP. SUBTILIS STR. 168 (bacteria)
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0CI74
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 235 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsRESIDUES NUMBERED -4 TO 0 (GMSA SEQUENCE) ARE DERIVED FROM THE EXPRESSION VECTOR

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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: 1.67 Å3/Da / Density % sol: 26.19 % / Description: NONE
Crystal growpH: 7.5 / Details: 0.2M SODIUM FLUORIDE, 20% PEG 3350, pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.61992
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 4, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.61992 Å / Relative weight: 1
ReflectionResolution: 1.2→43.04 Å / Num. obs: 54744 / % possible obs: 97.8 % / Observed criterion σ(I): 0 / Redundancy: 5.3 % / Biso Wilson estimate: 10.33 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 57.4
Reflection shellResolution: 1.2→1.22 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.13 / Mean I/σ(I) obs: 14.2 / % possible all: 96.6

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XDSdata scaling
Arcimboldophasing
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 1.2→29.659 Å / SU ML: 0.08 / σ(F): 1.98 / Phase error: 16.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1634 1186 2.2 %
Rwork0.1454 --
obs0.1458 54723 97.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 58.6 Å2 / ksol: 0.43 e/Å3
Displacement parametersBiso mean: 16 Å2
Refinement stepCycle: LAST / Resolution: 1.2→29.659 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1576 0 12 235 1823
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081670
X-RAY DIFFRACTIONf_angle_d1.0582243
X-RAY DIFFRACTIONf_dihedral_angle_d12.237616
X-RAY DIFFRACTIONf_chiral_restr0.063254
X-RAY DIFFRACTIONf_plane_restr0.005284
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2-1.25460.17971460.12956601X-RAY DIFFRACTION97
1.2546-1.32080.17171460.12066584X-RAY DIFFRACTION97
1.3208-1.40350.14971490.12056680X-RAY DIFFRACTION97
1.4035-1.51190.16711500.12466673X-RAY DIFFRACTION98
1.5119-1.6640.16421480.12516699X-RAY DIFFRACTION98
1.664-1.90480.181440.14336764X-RAY DIFFRACTION98
1.9048-2.39970.14631500.14966770X-RAY DIFFRACTION99
2.3997-29.66760.16571530.1616766X-RAY DIFFRACTION99

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