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- PDB-3zih: Bacillus subtilis SepF, C-terminal domain -

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Basic information

Entry
Database: PDB / ID: 3zih
TitleBacillus subtilis SepF, 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 Å
AuthorsDuman, R.E. / 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 1.2Jan 24, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain
Revision 1.3May 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

Downloads & links

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Assembly

Deposited unit
A: CELL DIVISION PROTEIN SEPF
B: CELL DIVISION PROTEIN SEPF


Theoretical massNumber of molelcules
Total (without water)21,3502
Polymers21,3502
Non-polymers00
Water1,06359
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2160 Å2
ΔGint-9.5 kcal/mol
Surface area8230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.456, 40.456, 170.331
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114A52 - 125
2114B52 - 125

NCS oper: (Code: given
Matrix: (-0.592, -0.2553, 0.7645), (-0.2205, -0.861, -0.4583), (0.7752, -0.4398, 0.4534)
Vector: -43.3, -21.05, 16.46)

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Components

#1: Protein CELL DIVISION PROTEIN SEPF / SEPF FROM BACILLUS SUBTILIS


Mass: 10674.944 Da / Num. of mol.: 2 / Fragment: C-TERMINAL DOMAIN, RESIDUES 57-151
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACILLUS SUBTILIS (bacteria) / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: O31728
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 59 / 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: 1.97 Å3/Da / Density % sol: 37.68 % / Description: NONE
Crystal growDetails: 30% PEG 8000, 0.2 M AMMONIUM SULPHATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9762
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 15, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.9→42.58 Å / Num. obs: 13575 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 9.6 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 14.5
Reflection shellResolution: 1.9→2 Å / Redundancy: 8.6 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 4.5 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→50 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.923 / SU B: 4.042 / SU ML: 0.113 / Cross valid method: THROUGHOUT / ESU R: 0.175 / ESU R Free: 0.171 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.24596 587 5 %RANDOM
Rwork0.18447 ---
obs0.18761 11067 99.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 23.937 Å2
Baniso -1Baniso -2Baniso -3
1-0.71 Å20.36 Å20 Å2
2--0.71 Å20 Å2
3----1.07 Å2
Refinement stepCycle: LAST / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1230 0 0 59 1289
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0221244
X-RAY DIFFRACTIONr_bond_other_d0.0010.02832
X-RAY DIFFRACTIONr_angle_refined_deg1.8151.9491684
X-RAY DIFFRACTIONr_angle_other_deg1.10632028
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6125157
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.0392460
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.22915217
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6061512
X-RAY DIFFRACTIONr_chiral_restr0.1320.2201
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021391
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02245
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_it1.4673.5787
X-RAY DIFFRACTIONr_mcbond_other0.4623.5322
X-RAY DIFFRACTIONr_mcangle_it2.56641278
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.0915457
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.2956.5406
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
Refine LS restraints NCS

Ens-ID: 1 / Number: 896 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Amedium positional0.550.5
2Bmedium positional0.550.5
1Amedium thermal1.362
2Bmedium thermal1.362
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.33 37 -
Rwork0.212 810 -
obs--100 %

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