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- PDB-5o2k: Native apo-structure of Pseudomonas stutzeri PtxB to 2.1 A resolution -

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Basic information

Entry
Database: PDB / ID: 5o2k
TitleNative apo-structure of Pseudomonas stutzeri PtxB to 2.1 A resolution
ComponentsProbable phosphite transport system-binding protein PtxB
KeywordsTRANSPORT PROTEIN / phosphite / ABC transporters / marine bacteria / PBP / SBP
Function / homologyPhosphate/phosphite/phosphonate ABC transporter, periplasmic binding protein / ABC transporter, phosphonate, periplasmic substrate-binding protein / ATP-binding cassette (ABC) transporter complex / Periplasmic binding protein-like II / transmembrane transport / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta / Probable phosphite transport system-binding protein PtxB
Function and homology information
Biological speciesPseudomonas stutzeri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsBisson, C. / Hitchcock, A.
Funding support United Kingdom, 5items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/M000265/1 United Kingdom
Biotechnology and Biological Sciences Research CouncilBB/M011305/1 United Kingdom
European Research Council338895
European Union283570
Diamond Light SourceBAG applications MX-8987 and MX-12788
CitationJournal: Nat Commun / Year: 2017
Title: The molecular basis of phosphite and hypophosphite recognition by ABC-transporters.
Authors: Bisson, C. / Adams, N.B.P. / Stevenson, B. / Brindley, A.A. / Polyviou, D. / Bibby, T.S. / Baker, P.J. / Hunter, C.N. / Hitchcock, A.
History
DepositionMay 21, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 6, 2017Provider: repository / Type: Initial release
Revision 1.1May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: Probable phosphite transport system-binding protein PtxB
A: Probable phosphite transport system-binding protein PtxB
B: Probable phosphite transport system-binding protein PtxB
C: Probable phosphite transport system-binding protein PtxB
E: Probable phosphite transport system-binding protein PtxB
F: Probable phosphite transport system-binding protein PtxB


Theoretical massNumber of molelcules
Total (without water)181,0396
Polymers181,0396
Non-polymers00
Water5,405300
1
D: Probable phosphite transport system-binding protein PtxB


Theoretical massNumber of molelcules
Total (without water)30,1731
Polymers30,1731
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Probable phosphite transport system-binding protein PtxB


Theoretical massNumber of molelcules
Total (without water)30,1731
Polymers30,1731
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: Probable phosphite transport system-binding protein PtxB


Theoretical massNumber of molelcules
Total (without water)30,1731
Polymers30,1731
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
C: Probable phosphite transport system-binding protein PtxB


Theoretical massNumber of molelcules
Total (without water)30,1731
Polymers30,1731
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Probable phosphite transport system-binding protein PtxB


Theoretical massNumber of molelcules
Total (without water)30,1731
Polymers30,1731
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Probable phosphite transport system-binding protein PtxB


Theoretical massNumber of molelcules
Total (without water)30,1731
Polymers30,1731
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)87.947, 136.640, 90.843
Angle α, β, γ (deg.)90.00, 115.02, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 30173.084 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Details: C-terminal 6x His-tag / Source: (gene. exp.) Pseudomonas stutzeri (bacteria) / Gene: ptxB / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O69052
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 300 / 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: 2.73 Å3/Da / Density % sol: 54.98 % / Description: rods
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1 M tri-sodium citrate pH 5.5 and 20 % (w/v) PEG 3000

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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: Feb 2, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97951 Å / Relative weight: 1
ReflectionResolution: 2.1→79.75 Å / Num. obs: 113030 / % possible obs: 99.9 % / Redundancy: 6.7 % / CC1/2: 0.992 / Rpim(I) all: 0.078 / Net I/σ(I): 6.3
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 6.7 % / Mean I/σ(I) obs: 1.2 / Num. unique obs: 5565 / CC1/2: 0.535 / Rpim(I) all: 0.625 / % possible all: 98.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→79.69 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.897 / SU B: 8.462 / SU ML: 0.205 / Cross valid method: THROUGHOUT / ESU R: 0.234 / ESU R Free: 0.205 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28218 5605 5 %RANDOM
Rwork0.23624 ---
obs0.2386 107119 99.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.041 Å2
Baniso -1Baniso -2Baniso -3
1--1.56 Å20 Å20.21 Å2
2---1.77 Å20 Å2
3---2.19 Å2
Refinement stepCycle: 1 / Resolution: 2.1→79.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12055 0 0 300 12355
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01912294
X-RAY DIFFRACTIONr_bond_other_d0.0020.0211486
X-RAY DIFFRACTIONr_angle_refined_deg1.5211.97416673
X-RAY DIFFRACTIONr_angle_other_deg0.967326658
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.76751554
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.96824.674552
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.215152071
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8381566
X-RAY DIFFRACTIONr_chiral_restr0.0840.21874
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02113774
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022396
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_it2.2073.4976234
X-RAY DIFFRACTIONr_mcbond_other2.2043.4976233
X-RAY DIFFRACTIONr_mcangle_it3.4115.2347782
X-RAY DIFFRACTIONr_mcangle_other3.4125.2347783
X-RAY DIFFRACTIONr_scbond_it2.3663.7996060
X-RAY DIFFRACTIONr_scbond_other2.3663.86061
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.7745.5688892
X-RAY DIFFRACTIONr_long_range_B_refined5.34840.56213228
X-RAY DIFFRACTIONr_long_range_B_other5.34440.58113196
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.411 406 -
Rwork0.377 7777 -
obs--98.55 %

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