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- PDB-6ghq: HtxB D206N protein variant from Pseudomonas stutzeri in a partial... -

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Basic information

Entry
Database: PDB / ID: 6ghq
TitleHtxB D206N protein variant from Pseudomonas stutzeri in a partially open conformation to 1.53 A resolution
ComponentsProbable phosphite transport system-binding protein HtxB
KeywordsTRANSPORT PROTEIN / Periplasmic binding protein / phosphite / hypophosphite / ABC-transporter
Function / homologyPhosphate/phosphite/phosphonate ABC transporter, periplasmic binding protein / ABC transporter, phosphonate, periplasmic substrate-binding protein / ATP-binding cassette (ABC) transporter complex / transmembrane transport / FORMIC ACID / Probable phosphite transport system-binding protein HtxB
Function and homology information
Biological speciesPseudomonas stutzeri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.53 Å
AuthorsBisson, C. / Robertson, A.J. / Hitchcock, A. / Adams, N.B.
CitationJournal: Sci Rep / Year: 2019
Title: Phosphite binding by the HtxB periplasmic binding protein depends on the protonation state of the ligand.
Authors: Adams, N.B.P. / Robertson, A.J. / Hunter, C.N. / Hitchcock, A. / Bisson, C.
History
DepositionMay 8, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 22, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.pdbx_details
Revision 1.2Jul 24, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Jan 17, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Probable phosphite transport system-binding protein HtxB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,8096
Polymers30,3341
Non-polymers4755
Water4,053225
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area890 Å2
ΔGint-3 kcal/mol
Surface area12690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.810, 118.450, 35.430
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Probable phosphite transport system-binding protein HtxB


Mass: 30333.545 Da / Num. of mol.: 1 / Mutation: D206N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas stutzeri (bacteria) / Gene: htxB / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O69061

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Non-polymers , 5 types, 230 molecules

#2: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER


Mass: 209.240 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 225 / 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: 2.45 Å3/Da / Density % sol: 49.73 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.2 M ammonium sulphate, 0.1 M Bis-Tris pH 5.5 and 25 % (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9718 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 23, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9718 Å / Relative weight: 1
ReflectionResolution: 1.53→43.47 Å / Num. obs: 45946 / % possible obs: 99.9 % / Redundancy: 6.7 % / CC1/2: 0.999 / Rpim(I) all: 0.017 / Net I/σ(I): 19.1
Reflection shellResolution: 1.53→1.56 Å / Redundancy: 6.1 % / Mean I/σ(I) obs: 1.4 / Num. unique obs: 3342 / CC1/2: 0.602 / Rpim(I) all: 0.517 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ME4

5me4


Resolution: 1.53→45.43 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.965 / SU B: 1.794 / SU ML: 0.063 / Cross valid method: THROUGHOUT / ESU R: 0.076 / ESU R Free: 0.077 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21309 2288 5 %RANDOM
Rwork0.18787 ---
obs0.1892 43578 99.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.344 Å2
Baniso -1Baniso -2Baniso -3
1-1.73 Å20 Å20 Å2
2---1.25 Å20 Å2
3----0.47 Å2
Refinement stepCycle: 1 / Resolution: 1.53→45.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2070 0 30 225 2325
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0142160
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172000
X-RAY DIFFRACTIONr_angle_refined_deg1.4631.662919
X-RAY DIFFRACTIONr_angle_other_deg0.9861.6554690
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7615270
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.37723.29997
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.48715373
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.68159
X-RAY DIFFRACTIONr_chiral_restr0.1010.2277
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022388
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02392
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.332.8151074
X-RAY DIFFRACTIONr_mcbond_other4.3292.8161075
X-RAY DIFFRACTIONr_mcangle_it4.7384.2181343
X-RAY DIFFRACTIONr_mcangle_other4.7394.221344
X-RAY DIFFRACTIONr_scbond_it20.543.4511086
X-RAY DIFFRACTIONr_scbond_other20.5773.4541082
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other19.1754.8561570
X-RAY DIFFRACTIONr_long_range_B_refined14.47835.2142494
X-RAY DIFFRACTIONr_long_range_B_other14.4835.2222495
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.53→1.57 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.327 205 -
Rwork0.32 3130 -
obs--99.73 %

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