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- PDB-5jvb: 1.95A resolution structure of PtxB from Trichodesmium erythraeum ... -

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Basic information

Entry
Database: PDB / ID: 5jvb
Title1.95A resolution structure of PtxB from Trichodesmium erythraeum IMS101 in complex with phosphite
ComponentsPhosphonate ABC transporter, periplasmic phosphonate-binding protein
KeywordsTRANSPORT PROTEIN / periplasmic binding protein (PBP) / phosphite transpoter / cyanobacteria
Function / homology
Function and homology information


ATP-binding cassette (ABC) transporter complex / transmembrane transport / metal ion binding
Similarity search - Function
Phosphate/phosphite/phosphonate ABC transporter, periplasmic binding protein / ABC transporter, phosphonate, periplasmic substrate-binding protein / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / Prokaryotic membrane lipoprotein lipid attachment site profile. / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHONATE / Phosphonate ABC transporter, periplasmic phosphonate-binding protein
Similarity search - Component
Biological speciesTrichodesmium erythraeum
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsBisson, C. / Adams, N.B.P. / Polyviou, D. / Bibby, T.S. / Hunter, C.N. / Hitchcock, A.
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 11, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Nov 29, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2017Group: 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 1.2Jan 10, 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: Phosphonate ABC transporter, periplasmic phosphonate-binding protein
B: Phosphonate ABC transporter, periplasmic phosphonate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,5074
Polymers62,3472
Non-polymers1602
Water73941
1
A: Phosphonate ABC transporter, periplasmic phosphonate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,2532
Polymers31,1731
Non-polymers801
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Phosphonate ABC transporter, periplasmic phosphonate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,2532
Polymers31,1731
Non-polymers801
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)54.340, 69.310, 66.530
Angle α, β, γ (deg.)90.00, 93.07, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Phosphonate ABC transporter, periplasmic phosphonate-binding protein


Mass: 31173.436 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trichodesmium erythraeum (strain IMS101) (bacteria)
Strain: IMS101 / Gene: Tery_0366 / Production host: Escherichia coli (E. coli) / References: UniProt: Q119I9
#2: Chemical ChemComp-2PO / PHOSPHONATE


Mass: 79.980 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: HO3P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 41 / 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: 2.01 Å3/Da / Density % sol: 38.7 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: 0.2 M NaCl, 0.1 M phosphate-citrate buffer pH 4.2 and 20 % PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96861 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 4, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96861 Å / Relative weight: 1
ReflectionResolution: 1.95→47.96 Å / Num. obs: 35004 / % possible obs: 97.2 % / Redundancy: 3.6 % / CC1/2: 0.994 / Rmerge(I) obs: 0.081 / Net I/σ(I): 7.3
Reflection shellResolution: 1.95→2 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 1.3 / % possible all: 98.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSxia2data reduction
Aimlessxia2data scaling
PHASERMr Bumpphasing
BUCCANEERmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3P7I

3p7i


Resolution: 1.95→47.96 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.927 / SU B: 6.27 / SU ML: 0.167 / Cross valid method: THROUGHOUT / ESU R: 0.207 / ESU R Free: 0.185 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26654 1802 5.2 %RANDOM
Rwork0.21499 ---
obs0.21762 33184 97.01 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 42.988 Å2
Baniso -1Baniso -2Baniso -3
1--0.53 Å20 Å2-0.1 Å2
2--0.76 Å20 Å2
3----0.22 Å2
Refinement stepCycle: 1 / Resolution: 1.95→47.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3920 0 8 41 3969
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.023996
X-RAY DIFFRACTIONr_bond_other_d0.0020.023916
X-RAY DIFFRACTIONr_angle_refined_deg1.4771.9815399
X-RAY DIFFRACTIONr_angle_other_deg0.94639060
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5665507
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.18326.491171
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.6515735
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.894158
X-RAY DIFFRACTIONr_chiral_restr0.0840.2617
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214510
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02818
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_it2.6584.0532028
X-RAY DIFFRACTIONr_mcbond_other2.6574.0522027
X-RAY DIFFRACTIONr_mcangle_it3.9926.0612532
X-RAY DIFFRACTIONr_mcangle_other3.9916.0632533
X-RAY DIFFRACTIONr_scbond_it2.9654.4671968
X-RAY DIFFRACTIONr_scbond_other2.9644.4661969
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.8186.5122867
X-RAY DIFFRACTIONr_long_range_B_refined7.01831.6014290
X-RAY DIFFRACTIONr_long_range_B_other7.00431.6044280
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.419 124 -
Rwork0.378 2498 -
obs--98.83 %

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