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- PDB-6ght: HtxB D206A protein variant from Pseudomonas stutzeri in complex w... -

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Basic information

Entry
Database: PDB / ID: 6ght
TitleHtxB D206A protein variant from Pseudomonas stutzeri in complex with hypophosphite to 1.12 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 / ACETIC ACID / FORMIC ACID / phosphinate / Probable phosphite transport system-binding protein HtxB
Function and homology information
Biological speciesPseudomonas stutzeri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.12 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 9, 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)30,5245
Polymers30,2911
Non-polymers2334
Water4,378243
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area330 Å2
ΔGint1 kcal/mol
Surface area11480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.082, 55.241, 125.903
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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: 30290.525 Da / Num. of mol.: 1 / Mutation: D206A
Source method: isolated from a genetically manipulated source
Details: C-terminal 6xHis tag D206A mutation / 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, 247 molecules

#2: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#3: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#4: Chemical ChemComp-HP4 / phosphinate / Hypophosphite


Mass: 64.988 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H2O2P
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 243 / 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: 2.3 Å3/Da / Density % sol: 46.54 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Bis-Tris pH 5.5 and 25 % (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97951 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 4, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97951 Å / Relative weight: 1
ReflectionResolution: 1.12→50.64 Å / Num. obs: 108281 / % possible obs: 99.9 % / Redundancy: 8.2 % / CC1/2: 0.999 / Rpim(I) all: 0.027 / Net I/σ(I): 10.7
Reflection shellResolution: 1.12→1.139 Å / Redundancy: 4.5 % / Mean I/σ(I) obs: 0.4 / Num. unique obs: 5252 / CC1/2: 0.322 / Rpim(I) all: 1.59 / % possible all: 98.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0222refinement
TRUNCATEdata reduction
Aimlessdata scaling
REFMACDirectly by refinement.phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ME4

5me4


Resolution: 1.12→50.64 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.974 / SU B: 1.466 / SU ML: 0.028 / Cross valid method: THROUGHOUT / ESU R: 0.031 / ESU R Free: 0.032 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1867 5337 4.9 %RANDOM
Rwork0.15984 ---
obs0.16116 102535 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 21.567 Å2
Baniso -1Baniso -2Baniso -3
1-1.14 Å20 Å20 Å2
2---0.04 Å20 Å2
3----1.1 Å2
Refinement stepCycle: 1 / Resolution: 1.12→50.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2033 0 14 243 2290
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0152145
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171976
X-RAY DIFFRACTIONr_angle_refined_deg1.5821.7582909
X-RAY DIFFRACTIONr_angle_other_deg1.5081.7364640
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3375278
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.821.7580
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.85215334
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.334159
X-RAY DIFFRACTIONr_chiral_restr0.0840.2277
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0212412
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02400
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_it2.8611.6371071
X-RAY DIFFRACTIONr_mcbond_other2.8611.6381071
X-RAY DIFFRACTIONr_mcangle_it2.8452.461341
X-RAY DIFFRACTIONr_mcangle_other2.7842.461341
X-RAY DIFFRACTIONr_scbond_it7.5192.1331074
X-RAY DIFFRACTIONr_scbond_other7.5282.1321074
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.0962.9591562
X-RAY DIFFRACTIONr_long_range_B_refined4.74321.612517
X-RAY DIFFRACTIONr_long_range_B_other4.74221.6232518
X-RAY DIFFRACTIONr_rigid_bond_restr18.61834121
X-RAY DIFFRACTIONr_sphericity_free24.5365148
X-RAY DIFFRACTIONr_sphericity_bonded20.9554162
LS refinement shellResolution: 1.12→1.149 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.444 376 -
Rwork0.425 7124 -
obs--95.06 %

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