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- PDB-6sw4: The structure of AraP, an arabinose binding protein from Geobacil... -

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Basic information

Entry
Database: PDB / ID: 6sw4
TitleThe structure of AraP, an arabinose binding protein from Geobacillus stearothermophilus
ComponentsArabinose binding protein
KeywordsSUGAR BINDING PROTEIN / Geobacillus stearothermophilus / binding protein / arabinose / three component sensing system
Function / homologyPeriplasmic binding protein / Periplasmic binding protein domain / Periplasmic binding protein-like I / carbohydrate binding / Arabinose binding protein
Function and homology information
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.845 Å
AuthorsLansky, S. / Salama, R. / Lavid, N. / Shoham, Y. / Shoham, G.
CitationJournal: To Be Published
Title: The structure of AraP, an arabinose binding protein from Geobacillus stearothermophilus
Authors: Lansky, S. / Salama, R. / Lavid, N. / Shoham, Y. / Shoham, G.
History
DepositionSep 19, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 14, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 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: Arabinose binding protein
B: Arabinose binding protein


Theoretical massNumber of molelcules
Total (without water)74,0782
Polymers74,0782
Non-polymers00
Water3,477193
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2950 Å2
ΔGint-14 kcal/mol
Surface area24360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.790, 95.600, 128.940
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Arabinose binding protein


Mass: 37039.055 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Gene: araP / Production host: Escherichia coli (E. coli) / References: UniProt: B3EYL5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 193 / 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: 2.25 Å3/Da / Density % sol: 45.24 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 23% PEG 8K, 0.1 M acetate buffer pH 4.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 15, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.84→50 Å / Num. obs: 50563 / % possible obs: 99.6 % / Redundancy: 14.1 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 22.8
Reflection shellResolution: 1.84→1.96 Å / Rmerge(I) obs: 1.357 / Num. unique obs: 7925

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.15.2_3472refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3G1W

3g1w


Resolution: 1.845→43.984 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 30.92
RfactorNum. reflection% reflection
Rfree0.276 2517 4.99 %
Rwork0.2341 --
obs0.2362 50436 99.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 96.69 Å2 / Biso mean: 47.0996 Å2 / Biso min: 17.54 Å2
Refinement stepCycle: final / Resolution: 1.845→43.984 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4517 0 0 193 4710
Biso mean---45.78 -
Num. residues----587
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.845-1.88030.42781250.4073244092
1.8803-1.91870.39331380.34822627100
1.9187-1.96050.34811390.29882653100
1.9605-2.00610.32781390.27332626100
2.0061-2.05620.30121390.27992639100
2.0562-2.11180.33551390.27242648100
2.1118-2.1740.341390.2712644100
2.174-2.24410.28991390.27112643100
2.2441-2.32430.28681410.26992682100
2.3243-2.41740.35161390.28472625100
2.4174-2.52740.29491400.27232665100
2.5274-2.66060.33041400.2682664100
2.6606-2.82730.29811400.25932667100
2.8273-3.04550.31831420.26222695100
3.0455-3.35190.31791430.24572705100
3.3519-3.83670.24711420.21682699100
3.8367-4.83290.22331440.1872752100
4.8329-43.9840.22231490.1885284599

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