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- PDB-4iff: Structural organization of FtsB, a transmembrane protein of the b... -

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Basic information

Entry
Database: PDB / ID: 4iff
TitleStructural organization of FtsB, a transmembrane protein of the bacterial divisome
ComponentsFusion of phage phi29 Gp7 protein and Cell division protein FtsB
KeywordsCELL CYCLE / bacterial division / FtsL
Function / homology
Function and homology information


FtsBL complex / FtsQBL complex / viral scaffold / divisome complex / cell septum / FtsZ-dependent cytokinesis / division septum assembly / virion assembly / cell division site / cell division ...FtsBL complex / FtsQBL complex / viral scaffold / divisome complex / cell septum / FtsZ-dependent cytokinesis / division septum assembly / virion assembly / cell division site / cell division / DNA binding / identical protein binding / plasma membrane
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #400 / Septum formation initiator FtsL/DivIC / Cell division protein FtsB / Septum formation initiator / Bacteriophage phi-29 scaffolding protein Gp7 / Capsid assembly scaffolding protein Gp7 / Phi29 scaffolding protein / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Cell division protein FtsB / Capsid assembly scaffolding protein
Similarity search - Component
Biological speciesBacillus phage phi29 (virus)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsLaPointe, L.M. / Taylor, K.C. / Subramaniam, S. / Khadria, A. / Rayment, I. / Senes, A.
CitationJournal: Biochemistry / Year: 2013
Title: Structural Organization of FtsB, a Transmembrane Protein of the Bacterial Divisome.
Authors: Lapointe, L.M. / Taylor, K.C. / Subramaniam, S. / Khadria, A. / Rayment, I. / Senes, A.
History
DepositionDec 14, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 10, 2013Provider: repository / Type: Initial release
Revision 1.1May 22, 2013Group: Database references
Revision 1.2Aug 2, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: Fusion of phage phi29 Gp7 protein and Cell division protein FtsB
B: Fusion of phage phi29 Gp7 protein and Cell division protein FtsB
C: Fusion of phage phi29 Gp7 protein and Cell division protein FtsB
D: Fusion of phage phi29 Gp7 protein and Cell division protein FtsB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,7427
Polymers38,4664
Non-polymers2763
Water2,936163
1
A: Fusion of phage phi29 Gp7 protein and Cell division protein FtsB
B: Fusion of phage phi29 Gp7 protein and Cell division protein FtsB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,3253
Polymers19,2332
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4450 Å2
ΔGint-32 kcal/mol
Surface area10450 Å2
MethodPISA
2
C: Fusion of phage phi29 Gp7 protein and Cell division protein FtsB
D: Fusion of phage phi29 Gp7 protein and Cell division protein FtsB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4174
Polymers19,2332
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4030 Å2
ΔGint-29 kcal/mol
Surface area10870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.577, 87.577, 185.110
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein
Fusion of phage phi29 Gp7 protein and Cell division protein FtsB


Mass: 9616.423 Da / Num. of mol.: 4
Fragment: UNP P13848 residues 2-48, UNP P0A6S5 residues 28-63
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus phage phi29 (virus), (gene. exp.) Escherichia coli (E. coli)
Gene: 7 / Production host: Escherichia coli (E. coli) / References: UniProt: P13848, UniProt: P0A6S5
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


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


Mass: 18.015 Da / Num. of mol.: 163 / 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: 5.33 Å3/Da / Density % sol: 76.91 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 2.1 M ammonium sulfate, 0.6 M malonate, 5% glycerol, 100 mM Bis-Tris, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 290 K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9701 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 12, 2011
RadiationMonochromator: Rosenbaum-Rock high-resolution double-crystal monochromator. LN2 cooled first crystal, sagittal focusing 2nd crystal
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9701 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. obs: 35452 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 11.1 %
Reflection shellResolution: 2.3→2.39 Å / Redundancy: 11.4 % / Rmerge(I) obs: 0.656 / Mean I/σ(I) obs: 4.1 / Num. unique all: 408261 / Rsym value: 0.098 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-3000data collection
PHASERphasing
REFMAC5.6.0117refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→30 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.91 / SU B: 4.561 / SU ML: 0.114 / Cross valid method: THROUGHOUT / ESU R: 0.182 / ESU R Free: 0.173 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25583 1770 5 %RANDOM
Rwork0.21942 ---
obs0.22122 33598 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.479 Å2
Baniso -1Baniso -2Baniso -3
1-0.82 Å20.41 Å2-0 Å2
2--0.82 Å2-0 Å2
3----1.23 Å2
Refinement stepCycle: LAST / Resolution: 2.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2608 0 18 163 2789
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0222660
X-RAY DIFFRACTIONr_angle_refined_deg1.0291.9793597
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.9665322
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.44926.433157
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.74515473
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.5141516
X-RAY DIFFRACTIONr_chiral_restr0.0650.2402
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212060
X-RAY DIFFRACTIONr_mcbond_it3.11741630
X-RAY DIFFRACTIONr_mcangle_it5.614402615
X-RAY DIFFRACTIONr_scbond_it6.02261030
X-RAY DIFFRACTIONr_scangle_it10.14660982
LS refinement shellResolution: 2.304→2.364 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.284 138 -
Rwork0.258 2467 -
obs--99.92 %

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