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- PDB-4q0c: 3.1 A resolution crystal structure of the B. pertussis BvgS perip... -

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Basic information

Entry
Database: PDB / ID: 4q0c
Title3.1 A resolution crystal structure of the B. pertussis BvgS periplasmic domain
ComponentsVirulence sensor protein BvgS
KeywordsTRANSFERASE / Bacterial extracellular solute-binding proteins / family 3 / venus fly trap / periplasmic binding protein / sensor domain / virulence regulation / environmental signals / signal perception
Function / homology
Function and homology information


histidine kinase / phosphorelay sensor kinase activity / regulation of DNA-templated transcription / ATP binding / plasma membrane
Similarity search - Function
Histidine Phosphotransfer domain / Hpt domain / Histidine-containing phosphotransfer (HPt) domain profile. / Signal transduction histidine kinase, phosphotransfer (Hpt) domain / HPT domain superfamily / Bacterial periplasmic substrate-binding proteins / PAS-associated, C-terminal / PAC domain profile. / His Kinase A (phospho-acceptor) domain / His Kinase A (phosphoacceptor) domain ...Histidine Phosphotransfer domain / Hpt domain / Histidine-containing phosphotransfer (HPt) domain profile. / Signal transduction histidine kinase, phosphotransfer (Hpt) domain / HPT domain superfamily / Bacterial periplasmic substrate-binding proteins / PAS-associated, C-terminal / PAC domain profile. / His Kinase A (phospho-acceptor) domain / His Kinase A (phosphoacceptor) domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / Signal transduction histidine kinase-related protein, C-terminal / Histidine kinase domain / Histidine kinase domain profile. / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / Bacterial extracellular solute-binding proteins, family 3 / Solute-binding protein family 3/N-terminal domain of MltF / PAS fold / PAS fold / PAS domain / PAS repeat profile. / PAS domain / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / PAS domain superfamily / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Periplasmic binding protein-like II / Histidine kinase/HSP90-like ATPase superfamily / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Virulence sensor protein BvgS
Similarity search - Component
Biological speciesBordetella pertussis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsDupre, E. / Herrou, J. / Lensink, M.F. / Wintjens, R. / Lebedev, A. / Crosson, S. / Villeret, V. / Locht, C. / Antoine, R. / Jacob-Dubuisson, F.
CitationJournal: Plos Pathog. / Year: 2015
Title: Virulence Regulation with Venus Flytrap Domains: Structure and Function of the Periplasmic Moiety of the Sensor-Kinase BvgS.
Authors: Dupre, E. / Herrou, J. / Lensink, M.F. / Wintjens, R. / Vagin, A. / Lebedev, A. / Crosson, S. / Villeret, V. / Locht, C. / Antoine, R. / Jacob-Dubuisson, F.
History
DepositionApr 1, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 11, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2015Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Virulence sensor protein BvgS
B: Virulence sensor protein BvgS
C: Virulence sensor protein BvgS
D: Virulence sensor protein BvgS


Theoretical massNumber of molelcules
Total (without water)256,4204
Polymers256,4204
Non-polymers00
Water0
1
A: Virulence sensor protein BvgS
B: Virulence sensor protein BvgS


Theoretical massNumber of molelcules
Total (without water)128,2102
Polymers128,2102
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7920 Å2
ΔGint-27 kcal/mol
Surface area38860 Å2
MethodPISA
2
C: Virulence sensor protein BvgS
D: Virulence sensor protein BvgS


Theoretical massNumber of molelcules
Total (without water)128,2102
Polymers128,2102
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8030 Å2
ΔGint-27 kcal/mol
Surface area38810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.450, 285.820, 128.150
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
Virulence sensor protein BvgS


Mass: 64105.113 Da / Num. of mol.: 4 / Fragment: periplasmic domain
Source method: isolated from a genetically manipulated source
Details: N-terminal GB1-tag and C-terminal His-tag / Source: (gene. exp.) Bordetella pertussis (bacteria) / Strain: TohamaI / Gene: BP1877, bvgS, bvgS (BP1877) / Plasmid: pGEV2 / Production host: Escherichia coli (E. coli) / Strain (production host): HMS174(DE3) / References: UniProt: P16575, histidine kinase

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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: 2.59 Å3/Da / Density % sol: 52.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 100 mM Sodium Acetate (pH 4.6), 1.6 M NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jan 16, 2007
RadiationMonochromator: Bruker AXS Microstar optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.1→20 Å / Num. all: 316034 / Num. obs: 48847 / % possible obs: 99.1 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 6.5 % / Rmerge(I) obs: 0.186 / Net I/σ(I): 11.89
Reflection shellResolution: 3.1→3.19 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.719 / Mean I/σ(I) obs: 2.68 / % possible all: 94.5

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
MOLREPphasing
PHENIX(phenix.refine: 1.8_1069)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3MPK

3mpk


Resolution: 3.1→19.989 Å / SU ML: 0.39 / σ(F): 1.99 / Phase error: 21.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2446 2000 4.1 %
Rwork0.1807 --
obs0.1833 48795 99.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.1→19.989 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15649 0 0 0 15649
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01115981
X-RAY DIFFRACTIONf_angle_d1.45221820
X-RAY DIFFRACTIONf_dihedral_angle_d13.8145728
X-RAY DIFFRACTIONf_chiral_restr0.062517
X-RAY DIFFRACTIONf_plane_restr0.0082854
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1003-3.17760.32891330.26993092X-RAY DIFFRACTION93
3.1776-3.26310.29781400.23933299X-RAY DIFFRACTION100
3.2631-3.35870.31041410.22133292X-RAY DIFFRACTION100
3.3587-3.46660.29671420.21213339X-RAY DIFFRACTION100
3.4666-3.58980.29341420.20653320X-RAY DIFFRACTION100
3.5898-3.73260.26441420.1983303X-RAY DIFFRACTION100
3.7326-3.90130.28681410.19073312X-RAY DIFFRACTION100
3.9013-4.10530.2371440.17223364X-RAY DIFFRACTION100
4.1053-4.36010.21931430.15753339X-RAY DIFFRACTION100
4.3601-4.69270.19711420.14573351X-RAY DIFFRACTION100
4.6927-5.15760.20981460.14893395X-RAY DIFFRACTION100
5.1576-5.88710.22891450.16993398X-RAY DIFFRACTION100
5.8871-7.35520.22791470.17893440X-RAY DIFFRACTION100
7.3552-19.98920.18791520.14753551X-RAY DIFFRACTION100

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