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- PDB-3ub9: Periplasmic portion of the Helicobacter pylori chemoreceptor TlpB... -

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Basic information

Entry
Database: PDB / ID: 3ub9
TitlePeriplasmic portion of the Helicobacter pylori chemoreceptor TlpB with hydroxyurea bound
Componentschemoreceptor TlpB
KeywordsMEMBRANE PROTEIN / homodimer / four-helix bundle / PAS domain
Function / homology
Function and homology information


signal transduction / plasma membrane
Similarity search - Function
Single Cache domain 2 / Single Cache domain 2 / Cache_2 / Methyl-accepting chemotaxis protein (MCP) signalling domain / Methyl-accepting chemotaxis protein (MCP) signalling domain / Bacterial chemotaxis sensory transducers domain profile. / Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer). / HAMP domain / HAMP (Histidine kinases, Adenylyl cyclases, Methyl binding proteins, Phosphatases) domain / HAMP domain profile. ...Single Cache domain 2 / Single Cache domain 2 / Cache_2 / Methyl-accepting chemotaxis protein (MCP) signalling domain / Methyl-accepting chemotaxis protein (MCP) signalling domain / Bacterial chemotaxis sensory transducers domain profile. / Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer). / HAMP domain / HAMP (Histidine kinases, Adenylyl cyclases, Methyl binding proteins, Phosphatases) domain / HAMP domain profile. / HAMP domain / PAS domain / Beta-Lactamase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
N-HYDROXYUREA / Methyl-accepting chemotaxis transmembrane sensory protein (MCP-like protein)
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.42 Å
AuthorsHenderson, J.N. / Sweeney, E.G. / Goers, J. / Wreden, C. / Hicks, K.G. / Parthasarathy, R. / Guillemin, K.J. / Remington, S.J.
CitationJournal: Structure / Year: 2012
Title: Structure and proposed mechanism for the pH-sensing Helicobacter pylori chemoreceptor TlpB.
Authors: Goers Sweeney, E. / Henderson, J.N. / Goers, J. / Wreden, C. / Hicks, K.G. / Foster, J.K. / Parthasarathy, R. / Remington, S.J. / Guillemin, K.
History
DepositionOct 23, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 27, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 9, 2013Group: Database references
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _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: chemoreceptor TlpB
B: chemoreceptor TlpB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,27612
Polymers41,3752
Non-polymers90110
Water8,521473
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5560 Å2
ΔGint-81 kcal/mol
Surface area14360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.611, 81.539, 94.554
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Detailsbiological unit is the same as asym.

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Components

#1: Protein chemoreceptor TlpB


Mass: 20687.516 Da / Num. of mol.: 2 / Fragment: Periplasmic portion
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Strain: SS1 / Plasmid: pBH4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B6JPK4*PLUS
#2: Chemical ChemComp-NHY / N-HYDROXYUREA / 1-HYDROXYUREA


Mass: 76.055 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH4N2O2 / Comment: medication*YM
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 473 / 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: 3.71 Å3/Da / Density % sol: 66.83 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M Bis-Tris pH 7.0, 2.0 M ammonium sulfate, vapor diffusion, hanging drop, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.97 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 15, 2008 / Details: Rh/Pt coated Si
RadiationMonochromator: DOUBLE-CRYSTAL, SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.42→50 Å / Num. all: 116572 / Num. obs: 113775 / % possible obs: 97.6 % / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Rmerge(I) obs: 0.062 / Χ2: 0.916 / Net I/σ(I): 13.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.42-1.452.60.39470660.648191.5
1.45-1.492.80.30974390.659197.4
1.49-1.533.10.25275960.684198.5
1.53-1.573.50.22375630.742198.6
1.57-1.633.50.18576430.754198.8
1.63-1.683.60.15275780.784198.7
1.68-1.753.60.12676150.867198.7
1.75-1.833.60.10476060.983198.6
1.83-1.933.70.08376320.988198.3
1.93-2.053.70.0776061.02198.1
2.05-2.213.70.06176490.968198.3
2.21-2.433.70.05876361.028198.2
2.43-2.783.70.05576751.057198.1
2.78-3.53.70.05176951.099197.4
3.5-503.60.04877761.158194.8

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.42→40.65 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.965 / WRfactor Rfree: 0.1539 / WRfactor Rwork: 0.1289 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.9376 / SU B: 1.039 / SU ML: 0.019 / SU R Cruickshank DPI: 0.0388 / SU Rfree: 0.0393 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.039 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1567 5716 5 %RANDOM
Rwork0.1326 ---
all0.1338 113696 --
obs0.1338 113696 97.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 61.11 Å2 / Biso mean: 17.1805 Å2 / Biso min: 5.98 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å2-0 Å20 Å2
2---0.07 Å20 Å2
3---0.09 Å2
Refinement stepCycle: LAST / Resolution: 1.42→40.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2562 0 55 473 3090
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0222794
X-RAY DIFFRACTIONr_bond_other_d00.021868
X-RAY DIFFRACTIONr_angle_refined_deg1.5931.9783791
X-RAY DIFFRACTIONr_angle_other_deg0.96934577
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5975365
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.31324.885131
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.24715479
X-RAY DIFFRACTIONr_dihedral_angle_4_deg6.839159
X-RAY DIFFRACTIONr_chiral_restr0.1120.2397
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023153
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02576
X-RAY DIFFRACTIONr_mcbond_it2.6691.51683
X-RAY DIFFRACTIONr_mcbond_other1.3721.5692
X-RAY DIFFRACTIONr_mcangle_it3.62722703
X-RAY DIFFRACTIONr_scbond_it5.75631111
X-RAY DIFFRACTIONr_scangle_it7.5424.51068
X-RAY DIFFRACTIONr_rigid_bond_restr2.88634662
X-RAY DIFFRACTIONr_sphericity_free17.1373473
X-RAY DIFFRACTIONr_sphericity_bonded7.6734597
LS refinement shellResolution: 1.421→1.458 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.264 428 -
Rwork0.216 7679 -
all-8107 -
obs--95.51 %

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