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- PDB-5lv1: 2.12 A resolution structure of PtxB from Prochlorococcus marinus ... -

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Basic information

Entry
Database: PDB / ID: 5lv1
Title2.12 A resolution structure of PtxB from Prochlorococcus marinus (MIT 9301) in complex with phosphite
ComponentsPtxB
KeywordsPERIPLASMIC BINDING PROTEIN / ABC-transporter / phosphite / Prochlorococcus
Function / homology
Function and homology information


ATP-binding cassette (ABC) transporter complex / transmembrane transport
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
oxidanylphosphinate / Probable ABC transporter phosphonate/phosphite binding protein PhnD2
Similarity search - Component
Biological speciesProchlorococcus marinus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.12 Å
AuthorsBisson, C. / Adams, N.B.P. / Polyviou, D. / Bibby, T.S. / Hunter, C.N. / Hitchcock, A.
Funding support United Kingdom, 4items
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 United Kingdom
NERC/A. G. Leventis FoundationPhD studentship United Kingdom
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
DepositionSep 12, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 6, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Source and taxonomy / Category: entity_src_gen / Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id
Revision 1.2Jan 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
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PtxB
C: PtxB
B: PtxB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,2376
Polymers90,9943
Non-polymers2433
Water2,216123
1
A: PtxB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,4122
Polymers30,3311
Non-polymers811
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: PtxB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,4122
Polymers30,3311
Non-polymers811
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: PtxB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,4122
Polymers30,3311
Non-polymers811
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)152.175, 152.175, 67.915
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein PtxB


Mass: 30331.408 Da / Num. of mol.: 3 / Fragment: UNP residues 22-292
Source method: isolated from a genetically manipulated source
Details: Truncated at the N-terminus to remove a signal peptide. C-terminal His-tag
Source: (gene. exp.) Prochlorococcus marinus (strain MIT 9301) (bacteria)
Gene: P9301_12511 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A3PDP9
#2: Chemical ChemComp-78T / oxidanylphosphinate


Mass: 80.988 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: H2O3P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 123 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.49 Å3/Da / Density % sol: 50.7 %
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 0.1 M Magnesium chloride, 0.1 M sodium citrate pH 5.0 and 15 % PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92819 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 10, 2016
RadiationMonochromator: Synchrotron / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92819 Å / Relative weight: 1
ReflectionResolution: 2.12→131.79 Å / Num. obs: 51504 / % possible obs: 100 % / Redundancy: 19.1 % / CC1/2: 0.996 / Rmerge(I) obs: 0.086 / Net I/σ(I): 7.7
Reflection shellResolution: 2.12→2.16 Å / Redundancy: 15.7 % / Rmerge(I) obs: 0.733 / Mean I/σ(I) obs: 1.4 / CC1/2: 0.648 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0151refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5JVB

5jvb


Resolution: 2.12→131.79 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.908 / SU B: 6.79 / SU ML: 0.164 / Cross valid method: THROUGHOUT / ESU R: 0.237 / ESU R Free: 0.202 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26396 2541 5 %RANDOM
Rwork0.21765 ---
obs0.21993 48734 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 30.215 Å2
Baniso -1Baniso -2Baniso -3
1-0.25 Å20.13 Å20 Å2
2--0.25 Å20 Å2
3----0.81 Å2
Refinement stepCycle: 1 / Resolution: 2.12→131.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6006 0 12 123 6141
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.026127
X-RAY DIFFRACTIONr_bond_other_d0.0010.025948
X-RAY DIFFRACTIONr_angle_refined_deg1.4651.9898292
X-RAY DIFFRACTIONr_angle_other_deg0.945313788
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8925789
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.86625.462238
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.094151078
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.1221521
X-RAY DIFFRACTIONr_chiral_restr0.0830.2964
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0216856
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021239
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_it1.5182.8743165
X-RAY DIFFRACTIONr_mcbond_other1.5162.8733164
X-RAY DIFFRACTIONr_mcangle_it2.3934.3013951
X-RAY DIFFRACTIONr_mcangle_other2.3934.3023952
X-RAY DIFFRACTIONr_scbond_it2.0293.1562961
X-RAY DIFFRACTIONr_scbond_other2.0283.1552962
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.3234.6154342
X-RAY DIFFRACTIONr_long_range_B_refined4.43333.686344
X-RAY DIFFRACTIONr_long_range_B_other4.4233.6726327
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.12→2.175 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.401 177 -
Rwork0.341 3549 -
obs--99.2 %

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