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- PDB-2ftk: berylloflouride Spo0F complex with Spo0B -

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Basic information

Entry
Database: PDB / ID: 2ftk
Titleberylloflouride Spo0F complex with Spo0B
Components
  • Sporulation initiation phosphotransferase B
  • Sporulation initiation phosphotransferase F
KeywordsTRANSFERASE / Sporulation / Spo0F / Spo0B phosphorelay
Function / homology
Function and homology information


Transferases; Transferring phosphorus-containing groups / sporulation resulting in formation of a cellular spore / phosphorelay sensor kinase activity / phosphorelay signal transduction system / kinase activity / metal ion binding / cytoplasm
Similarity search - Function
Sporulation initiation phosphotransferase B (SpoOB), C-terminal domain / Sporulation initiation phosphotransferase B, C-terminal / Sporulation initiation phosphotransferase B, C-terminal domain superfamily / Sporulation initiation phospho-transferase B, C-terminal / Sporulation initiation phospho-transferase B, C-terminal / SpoOB, alpha-helical domain / Sensor_kinase_SpoOB-type, alpha-helical domain / Signal transduction histidine kinase, sporulation regulator SpoOB / Signal transduction histidine kinase, dimerisation/phosphotransfer (DHp) domain / : ...Sporulation initiation phosphotransferase B (SpoOB), C-terminal domain / Sporulation initiation phosphotransferase B, C-terminal / Sporulation initiation phosphotransferase B, C-terminal domain superfamily / Sporulation initiation phospho-transferase B, C-terminal / Sporulation initiation phospho-transferase B, C-terminal / SpoOB, alpha-helical domain / Sensor_kinase_SpoOB-type, alpha-helical domain / Signal transduction histidine kinase, sporulation regulator SpoOB / Signal transduction histidine kinase, dimerisation/phosphotransfer (DHp) domain / : / Response regulator receiver domain / cheY-homologous receiver domain / Heat Shock Protein 90 / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / Response regulator / Helix Hairpins / Rossmann fold / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Sporulation initiation phosphotransferase B / Sporulation initiation phosphotransferase F
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.05 Å
AuthorsVarughese, K.I.
CitationJournal: J.Bacteriol. / Year: 2006
Title: The Crystal Structure of Beryllofluoride Spo0F in Complex with the Phosphotransferase Spo0B Represents a Phosphotransfer Pretransition State.
Authors: Varughese, K.I. / Tsigelny, I. / Zhao, H.
History
DepositionJan 24, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 18, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sporulation initiation phosphotransferase B
B: Sporulation initiation phosphotransferase B
C: Sporulation initiation phosphotransferase B
D: Sporulation initiation phosphotransferase B
E: Sporulation initiation phosphotransferase F
F: Sporulation initiation phosphotransferase F
G: Sporulation initiation phosphotransferase F
H: Sporulation initiation phosphotransferase F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,32612
Polymers147,2288
Non-polymers974
Water00
1
A: Sporulation initiation phosphotransferase B
B: Sporulation initiation phosphotransferase B
E: Sporulation initiation phosphotransferase F
F: Sporulation initiation phosphotransferase F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,6636
Polymers73,6144
Non-polymers492
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8780 Å2
ΔGint-79 kcal/mol
Surface area25770 Å2
MethodPISA
2
C: Sporulation initiation phosphotransferase B
D: Sporulation initiation phosphotransferase B
G: Sporulation initiation phosphotransferase F
H: Sporulation initiation phosphotransferase F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,6636
Polymers73,6144
Non-polymers492
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8310 Å2
ΔGint-75 kcal/mol
Surface area26670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.467, 118.331, 168.235
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Sporulation initiation phosphotransferase B / Stage 0 sporulation protein B


Mass: 22573.559 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: spo0B, spo0D / Production host: Escherichia coli (E. coli)
References: UniProt: P06535, Transferases; Transferring phosphorus-containing groups
#2: Protein
Sporulation initiation phosphotransferase F / Stage 0 sporulation protein F


Mass: 14233.564 Da / Num. of mol.: 4 / Mutation: Y13S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: spo0F / Production host: Escherichia coli (E. coli)
References: UniProt: P06628, Transferases; Transferring phosphorus-containing groups
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
Has protein modificationY

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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: 2.48 Å3/Da / Density % sol: 50.46 %
Crystal growTemperature: 297 K / Method: vapor diffusion / pH: 8.1
Details: 0.5 M KCl, 25% PEG2000, 100mM Tris HCl ph8.1, VAPOR DIFFUSION, temperature 297K

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 14, 2005
RadiationMonochromator: Flat mirror and bent monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 3.05→19.86 Å / Num. all: 28073 / Num. obs: 28073 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 3.05→3.24 Å / % possible all: 90.8

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Processing

Software
NameClassification
Blu-Icedata collection
XDSdata reduction
CNSrefinement
XDSdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1F51

1f51


Resolution: 3.05→19.86 Å / Cross valid method: R free / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.282 1404 -Random
Rwork0.232 ---
all-28073 --
obs-28073 98.6 %-
Refine analyze
FreeObs
Luzzati coordinate error0.48 Å0.38 Å
Luzzati d res low-5 Å
Luzzati sigma a0.55 Å0.48 Å
Refinement stepCycle: LAST / Resolution: 3.05→19.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9830 0 4 0 9834
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_d0.009
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_bond_d0.01

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