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- PDB-4n13: Crystal Structure of PstS (BB_0215) from Borrelia burgdorferi -

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Basic information

Entry
Database: PDB / ID: 4n13
TitleCrystal Structure of PstS (BB_0215) from Borrelia burgdorferi
ComponentsPhosphate ABC transporter, periplasmic phosphate-binding protein
KeywordsTRANSPORT PROTEIN / Class II ligand-binding protein / Ligand-binding protein / phosphate-binding protein / ABC transporter
Function / homology
Function and homology information


phosphate transmembrane transporter activity / phosphate ion transport / ATP-binding cassette (ABC) transporter complex
Similarity search - Function
PBP superfamily domain / PBP domain / Bacterial extracellular solute-binding protein / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Phosphate-binding protein PstS
Similarity search - Component
Biological speciesBorrelia burgdorferi (Lyme disease spirochete)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsBrautigam, C.A. / Deka, R.K. / Norgard, M.V.
CitationJournal: Protein Sci. / Year: 2014
Title: Sequence, biophysical, and structural analyses of the PstS lipoprotein (BB0215) from Borrelia burgdorferi reveal a likely binding component of an ABC-type phosphate transporter.
Authors: Brautigam, C.A. / Ouyang, Z. / Deka, R.K. / Norgard, M.V.
History
DepositionOct 3, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 22, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 12, 2014Group: Database references
Revision 1.2Sep 20, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phosphate ABC transporter, periplasmic phosphate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7886
Polymers29,3421
Non-polymers4465
Water2,432135
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)32.307, 84.558, 42.947
Angle α, β, γ (deg.)90.000, 105.570, 90.000
Int Tables number4
Space group name H-MP1211
Detailsbiological unit is the same as asym.

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Components

#1: Protein Phosphate ABC transporter, periplasmic phosphate-binding protein


Mass: 29342.010 Da / Num. of mol.: 1 / Fragment: UNP residues 20-279 / Mutation: N30D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Borrelia burgdorferi (Lyme disease spirochete)
Strain: ATCC 35210 / B31 / CIP 102532 / DSM 4680 / Gene: BB_0215 / Production host: Escherichia coli (E. coli) / References: UniProt: O51233
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 135 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SEQUENCE DISCREPANCY AT RESIDUE 30 IS DUE TO AN AMPLIFICATION ARTIFACT.

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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: 1.93 Å3/Da / Density % sol: 36.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 3.5
Details: 2 M Ammonium sulfate 0.1 M citric acid, pH 3.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.95372 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 29, 2009
RadiationMonochromator: Silicon 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
ReflectionResolution: 1.3→42.3 Å / Num. all: 53905 / Num. obs: 53905 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 9.31 Å2
Reflection shellResolution: 1.3→1.32 Å / % possible all: 98.5

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Processing

Software
NameVersionClassificationNB
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.11data extraction
SBC-Collectdata collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1TWY

1twy


Resolution: 1.3→41.371 Å / Occupancy max: 1 / Occupancy min: 0.1 / SU ML: 0.1 / σ(F): 1.38 / Phase error: 14.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1606 2731 5.07 %
Rwork0.1369 --
obs0.1381 53871 98.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 14.1694 Å2
Refinement stepCycle: LAST / Resolution: 1.3→41.371 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1978 0 24 135 2137
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082278
X-RAY DIFFRACTIONf_angle_d1.2143092
X-RAY DIFFRACTIONf_dihedral_angle_d12.945853
X-RAY DIFFRACTIONf_chiral_restr0.072355
X-RAY DIFFRACTIONf_plane_restr0.006398
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2999-1.32230.16961470.14312491X-RAY DIFFRACTION98
1.3223-1.34640.17161100.13292535X-RAY DIFFRACTION96
1.3464-1.37230.16821240.13342532X-RAY DIFFRACTION99
1.3723-1.40030.19351430.12762512X-RAY DIFFRACTION97
1.4003-1.43080.18061410.12042516X-RAY DIFFRACTION99
1.4308-1.4640.17961300.11852538X-RAY DIFFRACTION98
1.464-1.50070.16161150.11082550X-RAY DIFFRACTION99
1.5007-1.54120.14441550.10682548X-RAY DIFFRACTION98
1.5412-1.58660.15241380.10562551X-RAY DIFFRACTION100
1.5866-1.63780.14591190.10862566X-RAY DIFFRACTION99
1.6378-1.69630.17141300.11042582X-RAY DIFFRACTION99
1.6963-1.76420.15811320.11482538X-RAY DIFFRACTION99
1.7642-1.84450.15361610.11712542X-RAY DIFFRACTION99
1.8445-1.94180.13261510.12162560X-RAY DIFFRACTION99
1.9418-2.06340.13891470.1232574X-RAY DIFFRACTION100
2.0634-2.22280.14991300.1252587X-RAY DIFFRACTION100
2.2228-2.44640.15671340.13552602X-RAY DIFFRACTION100
2.4464-2.80040.16131570.15322575X-RAY DIFFRACTION100
2.8004-3.52790.17141350.16692623X-RAY DIFFRACTION100
3.5279-41.39210.1721320.16462618X-RAY DIFFRACTION99

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