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- PDB-4fpp: Bacterial phosphotransferase -

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Basic information

Entry
Database: PDB / ID: 4fpp
TitleBacterial phosphotransferase
Componentsphosphotransferase
KeywordsTRANSFERASE / four helix bundle / Bergerat fold / similar to type I Histidine kinase / phosphotransferase / CckA / CtrA / CpdR / bacterial cytoplasme
Function / homology
Function and homology information


identical protein binding
Similarity search - Function
Histidine phosphotransferase ChpT, C-terminal / Histidine phosphotransferase C-terminal domain / Signal transduction histidine kinase, dimerisation/phosphotransfer (DHp) domain / Histidine kinase-like ATPase, C-terminal domain / Heat Shock Protein 90 / Histidine kinase/HSP90-like ATPase superfamily / Helix Hairpins / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
NICKEL (II) ION / Histidine phosphotransferase ChpT C-terminal domain-containing protein
Similarity search - Component
Biological speciesCaulobacter crescentus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.2 Å
AuthorsFioravanti, A. / Clantin, B. / Dewitte, F. / Lens, Z. / Verger, A. / Biondi, E. / Villeret, V.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2012
Title: Structural insights into ChpT, an essential dimeric histidine phosphotransferase regulating the cell cycle in Caulobacter crescentus.
Authors: Fioravanti, A. / Clantin, B. / Dewitte, F. / Lens, Z. / Verger, A. / Biondi, E.G. / Villeret, V.
History
DepositionJun 22, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 12, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2013Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _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_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: phosphotransferase
B: phosphotransferase
C: phosphotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,81410
Polymers77,4063
Non-polymers4087
Water2,846158
1
A: phosphotransferase
hetero molecules

A: phosphotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,13810
Polymers51,6042
Non-polymers5348
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_656-x+1,y,-z+3/21
Buried area3550 Å2
ΔGint-56 kcal/mol
Surface area18760 Å2
MethodPISA
2
B: phosphotransferase
C: phosphotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,7455
Polymers51,6042
Non-polymers1413
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3540 Å2
ΔGint-57 kcal/mol
Surface area18910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.540, 210.160, 93.930
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Detailsthere are three subunits in the asymmetric unit. Two subunits (B and C) form a homodimer, while the third one (A) exploits a two-fold summetry axis of the lattice to generate a similar homodimer but with exact two-fold symmetry.

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Components

#1: Protein phosphotransferase


Mass: 25802.061 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caulobacter crescentus (bacteria) / Strain: ATCC 19089 / CB15 / Gene: CC_3470 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9A2T6
#2: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 158 / 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: 3.3 Å3/Da / Density % sol: 62.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 24% PEG 4000, 0.16M magnesium chloride, 0.08M Tris-HCl pH8.5, 20% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98011 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 26, 2012
RadiationMonochromator: channel cut cryogenically cooled monochromator crystal
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98011 Å / Relative weight: 1
ReflectionResolution: 2.2→49 Å / Num. all: 52229 / Num. obs: 52206 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 8.7 % / Rmerge(I) obs: 0.099 / Net I/σ(I): 12.5
Reflection shellResolution: 2.2→2.3 Å / Redundancy: 9.2 % / Rmerge(I) obs: 0.552 / Mean I/σ(I) obs: 2.88 / Num. unique all: 6430 / % possible all: 100

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Processing

Software
NameVersionClassification
XDSdata scaling
autoSHARPphasing
REFMAC5.5.0066refinement
XDSdata reduction
RefinementMethod to determine structure: SIRAS / Resolution: 2.2→46.97 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.936 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.2 / ESU R Free: 0.182 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26376 2670 5.1 %RANDOM
all0.227 52229 --
obs0.22971 49655 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 61.931 Å2
Baniso -1Baniso -2Baniso -3
1-1.22 Å20 Å20 Å2
2---0.55 Å20 Å2
3----0.68 Å2
Refinement stepCycle: LAST / Resolution: 2.2→46.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4549 0 22 158 4729
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0224645
X-RAY DIFFRACTIONr_angle_refined_deg2.0341.9716308
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2945618
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.5523.777188
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.43215717
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0821539
X-RAY DIFFRACTIONr_chiral_restr0.1380.2717
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0213556
X-RAY DIFFRACTIONr_mcbond_it1.0491.53091
X-RAY DIFFRACTIONr_mcangle_it1.92524879
X-RAY DIFFRACTIONr_scbond_it2.9631554
X-RAY DIFFRACTIONr_scangle_it4.9424.51429
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.355 215 -
Rwork0.324 3635 -
obs--99.9 %

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