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- PDB-4f1u: Subatomic resolution structure of a high affinity periplasmic pho... -

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Basic information

Entry
Database: PDB / ID: 4f1u
TitleSubatomic resolution structure of a high affinity periplasmic phosphate-binding protein (PfluDING) bound with phosphate at pH 4.5
ComponentsPutative alkaline phosphatase
KeywordsPHOSPHATE-BINDING PROTEIN / venus flytrap / phosphate binding protein / pstS / DING
Function / homology
Function and homology information


phosphate ion transmembrane transport / phosphate ion binding / ATP-binding cassette (ABC) transporter complex
Similarity search - Function
Phosphate ABC transporter, substrate-binding protein PstS / : / PBP domain / PBP superfamily domain / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
HYDROGENPHOSPHATE ION / Phosphate-binding protein PstS
Similarity search - Component
Biological speciesPseudomonas fluorescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.98 Å
AuthorsLiebschner, D. / Elias, M. / Tawfik, D.S. / Moniot, S. / Fournier, B. / Scott, K. / Jelsch, C. / Guillot, B. / Lecomte, C. / Chabriere, E.
Citation
Journal: Nature / Year: 2012
Title: The molecular basis of phosphate discrimination in arsenate-rich environments.
Authors: Elias, M. / Wellner, A. / Goldin-Azulay, K. / Chabriere, E. / Vorholt, J.A. / Erb, T.J. / Tawfik, D.S.
#1: Journal: J.Am.Chem.Soc. / Year: 2009
Title: Elucidation of the phosphate binding mode of DING proteins revealed by subangstrom X-ray crystallography.
Authors: Liebschner, D. / Elias, M. / Moniot, S. / Fournier, B. / Scott, K. / Jelsch, C. / Guillot, B. / Lecomte, C. / Chabriere, E.
History
DepositionMay 7, 2012Deposition site: RCSB / Processing site: RCSB
SupersessionMay 23, 2012ID: 3G62
Revision 1.0May 23, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 5, 2012Group: Database references
Revision 1.2Oct 3, 2012Group: Database references
Revision 1.3Oct 17, 2012Group: Database references
Revision 1.4Nov 21, 2012Group: Database references
Revision 1.5Sep 13, 2023Group: 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 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative alkaline phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,5607
Polymers39,1191
Non-polymers4406
Water22,2311234
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)36.960, 124.370, 41.010
Angle α, β, γ (deg.)90.00, 116.55, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Putative alkaline phosphatase


Mass: 39119.289 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas fluorescens (bacteria) / Strain: SBW25 / Gene: PFLU_2427 / Production host: Escherichia coli (E. coli) / References: UniProt: C3K8K1
#2: Chemical ChemComp-PI / HYDROGENPHOSPHATE ION


Mass: 95.979 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: HO4P
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1234 / 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: 2.16 Å3/Da / Density % sol: 42.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 4% PEG 8000, 100 mM acetate buffer pH 4.5, 200 mM Li2SO4, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.953 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 5, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953 Å / Relative weight: 1
ReflectionResolution: 0.98→36.69 Å / Num. obs: 185558 / % possible obs: 98.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2

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Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.6.0117refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3G62

3g62
PDB Unreleased entry


Resolution: 0.98→36.69 Å / Cor.coef. Fo:Fc: 0.987 / Cor.coef. Fo:Fc free: 0.983 / SU B: 0.338 / SU ML: 0.009 / Cross valid method: THROUGHOUT / ESU R: 0.016 / ESU R Free: 0.015 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.09591 9308 5 %RANDOM
Rwork0.08773 ---
obs0.08814 176838 98.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 8.948 Å2
Baniso -1Baniso -2Baniso -3
1--0.25 Å20 Å2-0.1 Å2
2--0.06 Å2-0 Å2
3---0.09 Å2
Refinement stepCycle: LAST / Resolution: 0.98→36.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2698 0 26 1234 3958
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.023475
X-RAY DIFFRACTIONr_bond_other_d0.0080.023272
X-RAY DIFFRACTIONr_angle_refined_deg2.2161.944835
X-RAY DIFFRACTIONr_angle_other_deg1.07437441
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5385523
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.79125.344131
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.19315489
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6691512
X-RAY DIFFRACTIONr_chiral_restr0.110.2553
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0214336
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02814
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr10.13836747
X-RAY DIFFRACTIONr_sphericity_free16.4475375
X-RAY DIFFRACTIONr_sphericity_bonded7.51657486
LS refinement shellResolution: 0.98→1.005 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.136 582 -
Rwork0.125 11013 -
obs--83.77 %

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