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- PDB-3zii: Bacillus subtilis SepF G109K, C-terminal domain -

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Basic information

Entry
Database: PDB / ID: 3zii
TitleBacillus subtilis SepF G109K, C-terminal domain
ComponentsCELL DIVISION PROTEIN SEPF
KeywordsCELL CYCLE
Function / homology
Function and homology information


cell septum assembly / division septum assembly / FtsZ-dependent cytokinesis / identical protein binding / cytoplasm
Similarity search - Function
Cell division protein SepF / SepF-like protein / Cell division protein SepF/SepF-related / SepF-like superfamily / Cell division protein SepF / Translation Initiation Factor IF3 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Cell division protein SepF
Similarity search - Component
Biological speciesBACILLUS SUBTILIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsDuman, R. / Ishikawa, S. / Celik, I. / Ogasawara, N. / Lowe, J. / Hamoen, L.W.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Structural and Genetic Analyses Reveal the Protein Sepf as a New Membrane Anchor for the Z Ring.
Authors: Duman, R. / Ishikawa, S. / Celik, I. / Strahl, H. / Ogasawara, N. / Troc, P. / Lowe, J. / Hamoen, L.W.
History
DepositionJan 9, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 27, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2013Group: Database references
Revision 1.2May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
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

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Assembly

Deposited unit
A: CELL DIVISION PROTEIN SEPF


Theoretical massNumber of molelcules
Total (without water)10,7471
Polymers10,7471
Non-polymers00
Water54030
1
A: CELL DIVISION PROTEIN SEPF

A: CELL DIVISION PROTEIN SEPF


Theoretical massNumber of molelcules
Total (without water)21,4942
Polymers21,4942
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area2510 Å2
ΔGint-9.6 kcal/mol
Surface area8720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.010, 80.140, 51.820
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein CELL DIVISION PROTEIN SEPF


Mass: 10747.072 Da / Num. of mol.: 1 / Fragment: C-TERMINAL DOMAIN, RESIDUES 57-151 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACILLUS SUBTILIS (bacteria) / Plasmid: PHIS17 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): C41 / References: UniProt: O31728
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / 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: 2.14 Å3/Da / Density % sol: 42.51 % / Description: NONE
Crystal growDetails: 15% (V/V) ETHANOL, 0.1M TRIS PH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9
DetectorDate: Sep 4, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.2→51.82 Å / Num. obs: 4701 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 6.8 % / Biso Wilson estimate: 19.58 Å2 / Rmerge(I) obs: 0.15 / Net I/σ(I): 8.8
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 7 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 4.5 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→25.91 Å / SU ML: 0.24 / σ(F): 1.4 / Phase error: 21.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.245 216 4.6 %
Rwork0.1945 --
obs0.1968 4683 99.96 %
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 27.961 Å2 / ksol: 0.351 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.9123 Å20 Å20 Å2
2--4.2714 Å20 Å2
3----6.1837 Å2
Refinement stepCycle: LAST / Resolution: 2.2→25.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms640 0 0 30 670
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007647
X-RAY DIFFRACTIONf_angle_d0.947875
X-RAY DIFFRACTIONf_dihedral_angle_d14.541243
X-RAY DIFFRACTIONf_chiral_restr0.067105
X-RAY DIFFRACTIONf_plane_restr0.003114
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2002-2.77160.25691160.18042178X-RAY DIFFRACTION100
2.7716-25.91180.23831000.2012289X-RAY DIFFRACTION100

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