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- PDB-6emn: HtxB from Pseudomonas stutzeri in complex with phosphite to 1.25 ... -

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Basic information

Entry
Database: PDB / ID: 6emn
TitleHtxB from Pseudomonas stutzeri in complex with phosphite to 1.25 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 / oxidanylphosphinate / Probable phosphite transport system-binding protein HtxB
Function and homology information
Biological speciesPseudomonas stutzeri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 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
DepositionOct 3, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 17, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 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 / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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_conn.ptnr2_symmetry

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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)30,5645
Polymers30,3351
Non-polymers2294
Water4,288238
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area510 Å2
ΔGint-1 kcal/mol
Surface area11490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.280, 55.200, 126.330
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 Probable phosphite transport system-binding protein HtxB


Mass: 30334.533 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Construct has a truncated N-terminus to remove signal peptide and C-terminal an 6xHis-tag.
Source: (gene. exp.) Pseudomonas stutzeri (bacteria) / Gene: htxB / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O69061
#2: Chemical ChemComp-78T / oxidanylphosphinate


Mass: 80.988 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H2O3P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 238 / 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: 2.31 Å3/Da / Density % sol: 46.87 % / Description: Rods.
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 0.2 M magnesium chloride, 0.1 M Na acetate (pH 5) and 20% PEG 6000.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92819 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 4, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92819 Å / Relative weight: 1
ReflectionResolution: 1.25→50.62 Å / Num. obs: 78831 / % possible obs: 100 % / Redundancy: 5.9 % / CC1/2: 0.998 / Rpim(I) all: 0.046 / Net I/σ(I): 9.3
Reflection shellResolution: 1.25→1.27 Å / Redundancy: 4.6 % / Mean I/σ(I) obs: 1 / Num. unique obs: 3871 / CC1/2: 0.403 / Rpim(I) all: 0.89 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ME4

5me4


Resolution: 1.25→50.58 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.976 / SU B: 1.554 / SU ML: 0.029 / Cross valid method: THROUGHOUT / ESU R: 0.038 / ESU R Free: 0.038 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16992 3886 4.9 %RANDOM
Rwork0.14523 ---
obs0.14648 74858 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 21.977 Å2
Baniso -1Baniso -2Baniso -3
1-1.07 Å20 Å20 Å2
2--0.29 Å20 Å2
3----1.36 Å2
Refinement stepCycle: 1 / Resolution: 1.25→50.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2000 0 13 238 2251
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0192091
X-RAY DIFFRACTIONr_bond_other_d0.0020.022017
X-RAY DIFFRACTIONr_angle_refined_deg1.5351.9692830
X-RAY DIFFRACTIONr_angle_other_deg1.51434676
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0545267
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.76924.47185
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.66215367
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.936159
X-RAY DIFFRACTIONr_chiral_restr0.0970.2304
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212337
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02452
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_it2.3181.5441041
X-RAY DIFFRACTIONr_mcbond_other1.91.5341040
X-RAY DIFFRACTIONr_mcangle_it2.3392.3121302
X-RAY DIFFRACTIONr_mcangle_other2.4062.3141303
X-RAY DIFFRACTIONr_scbond_it6.2652.0681050
X-RAY DIFFRACTIONr_scbond_other6.2612.0681050
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.9872.8411524
X-RAY DIFFRACTIONr_long_range_B_refined5.37914.3432448
X-RAY DIFFRACTIONr_long_range_B_other5.37914.352449
X-RAY DIFFRACTIONr_rigid_bond_restr16.7634108
X-RAY DIFFRACTIONr_sphericity_free39.961587
X-RAY DIFFRACTIONr_sphericity_bonded28.68854209
LS refinement shellResolution: 1.25→1.282 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.317 272 -
Rwork0.284 5465 -
obs--99.88 %

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