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- PDB-5z6c: Crystal structure of Bacillus subtilis sugar-binding protein YesO... -

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Basic information

Entry
Database: PDB / ID: 5z6c
TitleCrystal structure of Bacillus subtilis sugar-binding protein YesO involved in import of rhamnogalacturonan
ComponentsPutative ABC transporter substrate-binding protein YesO
KeywordsTRANSPORT PROTEIN / ABC transporter substrate-binding protein / sugar transport
Function / homology: / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta / Putative ABC transporter substrate-binding protein YesO
Function and homology information
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 Å
AuthorsSugiura, H. / Oiki, S. / Mikami, B. / Murata, K. / Hashimoto, W.
Funding support Japan, 1items
OrganizationGrant numberCountry
Fuji Foundation for Protein Research Japan
CitationJournal: To Be Published
Title: Crystal structure of Bacillus subtilis sugar-binding protein YesO involved in import of rhamnogalacturonan
Authors: Sugiura, H. / Oiki, S. / Mikami, B. / Murata, K. / Hashimoto, W.
History
DepositionJan 22, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 23, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: 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: Putative ABC transporter substrate-binding protein YesO


Theoretical massNumber of molelcules
Total (without water)48,3911
Polymers48,3911
Non-polymers00
Water2,090116
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area16880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.184, 108.578, 40.494
Angle α, β, γ (deg.)90.00, 101.58, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Putative ABC transporter substrate-binding protein YesO


Mass: 48390.648 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Strain: 168 / Gene: yesO, BSU06970 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O31518
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 116 / 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: 1.61 Å3/Da / Density % sol: 23.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1M MIB (sodium malonate, imidazole, boric acid) buffer (pH 6.0), 25% (w/v) PEG-1500

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 22, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.97→50 Å / Num. obs: 42265 / % possible obs: 98.9 % / Redundancy: 2.2 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 12.1
Reflection shellResolution: 1.97→2 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.278 / Mean I/σ(I) obs: 3.06 / % possible all: 98.3

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4R6K

4r6k


Resolution: 1.97→37.261 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.42 / Phase error: 26.89
RfactorNum. reflection% reflection
Rfree0.2575 1095 5.1 %
Rwork0.1994 --
obs0.2025 21481 98.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.97→37.261 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3029 0 0 116 3145
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073098
X-RAY DIFFRACTIONf_angle_d0.974193
X-RAY DIFFRACTIONf_dihedral_angle_d7.8351875
X-RAY DIFFRACTIONf_chiral_restr0.054451
X-RAY DIFFRACTIONf_plane_restr0.006541
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9659-2.05530.27311100.19872446X-RAY DIFFRACTION94
2.0553-2.16370.30151280.21592595X-RAY DIFFRACTION100
2.1637-2.29920.30421480.22532557X-RAY DIFFRACTION100
2.2992-2.47670.32081380.21892558X-RAY DIFFRACTION100
2.4767-2.72590.2631390.22142578X-RAY DIFFRACTION99
2.7259-3.12020.26521270.22252556X-RAY DIFFRACTION99
3.1202-3.93040.26651590.18842542X-RAY DIFFRACTION99
3.9304-37.26780.2021460.17072554X-RAY DIFFRACTION98

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