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- PDB-1f51: A TRANSIENT INTERACTION BETWEEN TWO PHOSPHORELAY PROTEINS TRAPPED... -

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Basic information

Entry
Database: PDB / ID: 1f51
TitleA TRANSIENT INTERACTION BETWEEN TWO PHOSPHORELAY PROTEINS TRAPPED IN A CRYSTAL LATTICE REVEALS THE MECHANISM OF MOLECULAR RECOGNITION AND PHOSPHOTRANSFER IN SINGAL TRANSDUCTION
Components
  • SPORULATION INITIATION PHOSPHOTRANSFERASE B
  • SPORULATION INITIATION PHOSPHOTRANSFERASE F
KeywordsTRANSFERASE / TWO COMPONENT SYSTEM / SINGAL TRANDUCTION / RESPONSE REGULATOR / PHOSPHOTRANSFERASE / SPORULATION / 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 Å
AuthorsZapf, J. / Sen, U. / Madhusudan, M. / Hoch, J.A. / Varughese, K.I.
CitationJournal: Structure Fold.Des. / Year: 2000
Title: A transient interaction between two phosphorelay proteins trapped in a crystal lattice reveals the mechanism of molecular recognition and phosphotransfer in signal transduction.
Authors: Zapf, J. / Sen, U. / Madhusudan, M. / Hoch, J.A. / Varughese, K.I.
History
DepositionJun 11, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 23, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / 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.pdbx_dist_value / _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_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_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
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)139,90511
Polymers139,8328
Non-polymers733
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)69,9656
Polymers69,9164
Non-polymers492
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8730 Å2
ΔGint-78 kcal/mol
Surface area26380 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)69,9405
Polymers69,9164
Non-polymers241
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.974, 117.774, 170.736
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


Mass: 21382.242 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Plasmid: PET20B
References: UniProt: P06535, Transferases; Transferring phosphorus-containing groups
#2: Protein
SPORULATION INITIATION PHOSPHOTRANSFERASE F


Mass: 13575.812 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Plasmid: PET20B
References: UniProt: P06628, Transferases; Transferring phosphorus-containing groups
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg

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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: 2.62 Å3/Da / Density % sol: 53.11 %
Crystal growpH: 8.1 / Details: 0.5M KCL, 24% PEG2K AND ALF3 AT pH8.1
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
19 mg/mlSpo0F1drop
210.3 mg/mlSpo0B1drop
32 mM1dropMgCl2
410 mM1dropAlCl3
530 mM1dropNaF
60.5 M1reservoirKCl
724 %PEG20001reservoir
8100 mMTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 1, 1998 / Details: PT COATED SI FLAT MIRROR BENT FOR VERTICAL FOCUS
RadiationMonochromator: SI BENT CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 3→45 Å / Num. obs: 29914 / % possible obs: 99 % / Redundancy: 4.1 % / Rsym value: 7.6 / Net I/σ(I): 18
Reflection shellResolution: 3→3.14 Å / Mean I/σ(I) obs: 3.1 / % possible all: 98.7
Reflection
*PLUS
Num. measured all: 122403 / Rmerge(I) obs: 0.076
Reflection shell
*PLUS
% possible obs: 98.7 %

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Processing

Software
NameVersionClassification
AMoREphasing
CNS0.4refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1SRR AND 1IXM

1srr

1ixm


Resolution: 3→45 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 503956.52 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.268 1368 5.1 %RANDOM
Rwork0.228 ---
obs0.229 26820 88.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 11.18 Å2 / ksol: 0.273 e/Å3
Displacement parametersBiso mean: 54.3 Å2
Baniso -1Baniso -2Baniso -3
1--2.08 Å20 Å20 Å2
2--7.09 Å20 Å2
3----5.01 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.35 Å
Luzzati d res low-5 Å
Luzzati sigma a0.53 Å0.45 Å
Refinement stepCycle: LAST / Resolution: 3→45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9748 0 3 0 9751
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.93
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 3→3.19 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.332 174 4.9 %
Rwork0.309 3367 -
obs--71.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAM&_1_TOPOLOGY_INFILE_2
X-RAY DIFFRACTION3CIS_PEPTIDE.PARAM&_1_TOPOLOGY_INFILE_3
X-RAY DIFFRACTION4WATER_REP.PARAM
X-RAY DIFFRACTION5&_1_PARAMETER_INFILE_5
Software
*PLUS
Name: CNS / Version: 0.4 / Classification: refinement
Refinement
*PLUS
σ(F): 2 / % reflection Rfree: 5.1 % / Rfactor obs: 0.228
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.014
X-RAY DIFFRACTIONc_angle_deg1.9
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.93
LS refinement shell
*PLUS
Rfactor Rfree: 0.332 / % reflection Rfree: 4.9 % / Rfactor Rwork: 0.309

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