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- PDB-5ulb: Crystal structure of sugar ABC transporter from Yersinia enteroco... -

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Basic information

Entry
Database: PDB / ID: 5ulb
TitleCrystal structure of sugar ABC transporter from Yersinia enterocolitica subsp. enterocolitica 8081
ComponentsPutative sugar ABC transporter
KeywordsSUGAR BINDING PROTEIN / ABC transporter / Methylthioribose-binding protein / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homologyPeriplasmic binding protein / Periplasmic binding protein domain / Periplasmic binding protein-like I / 5-Se-methyl-5-seleno-alpha-D-ribofuranose / 5-Se-methyl-5-seleno-beta-D-ribofuranose / Putative sugar ABC transporter / Putative sugar ABC transporter
Function and homology information
Biological speciesYersinia enterocolitica subsp. enterocolitica 8081 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.28 Å
AuthorsNocek, B. / Bigelow, L. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To Be Published
Title: Crystal structure of sugar ABC transporter from Yersinia enterocolitica subsp. enterocolitica 8081
Authors: Nocek, B. / Bigelow, L. / Joachimiak, A.
History
DepositionJan 24, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 12, 2018Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection / Derived calculations
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _chem_comp.type
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative sugar ABC transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,8333
Polymers36,3791
Non-polymers4542
Water7,008389
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.993, 55.856, 119.573
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Putative sugar ABC transporter


Mass: 36378.641 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia enterocolitica subsp. enterocolitica 8081 (bacteria)
Production host: Escherichia coli (E. coli) / References: UniProt: A0A0T9SS21, UniProt: A1JTX8*PLUS
#2: Sugar ChemComp-8GA / 5-Se-methyl-5-seleno-alpha-D-ribofuranose


Type: D-saccharide, alpha linking / Mass: 227.117 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O4Se
#3: Sugar ChemComp-8GG / 5-Se-methyl-5-seleno-beta-D-ribofuranose


Type: D-saccharide, beta linking / Mass: 227.117 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O4Se
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 389 / 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: 2.12 Å3/Da / Density % sol: 41.88 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1 M Bis-Tris pH 6.5, 28% w/v PEG MME 2000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 7, 2013 / Details: double crystal
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.28→40 Å / Num. obs: 78779 / % possible obs: 99.2 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 20
Reflection shellResolution: 1.28→1.3 Å / Rmerge(I) obs: 0.8 / % possible all: 92.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementResolution: 1.28→40 Å / Cor.coef. Fo:Fc: 0.985 / Cor.coef. Fo:Fc free: 0.975 / SU B: 1.625 / SU ML: 0.03 / Cross valid method: THROUGHOUT / ESU R: 0.044 / ESU R Free: 0.047 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.153 3342 5 %RANDOM
Rwork0.11 ---
obs0.112 63186 93.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 18.48 Å2
Baniso -1Baniso -2Baniso -3
1--0.64 Å20 Å20 Å2
2--0.51 Å20 Å2
3---0.12 Å2
Refinement stepCycle: LAST / Resolution: 1.28→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2531 0 22 389 2942
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.022710
X-RAY DIFFRACTIONr_bond_other_d0.0020.022559
X-RAY DIFFRACTIONr_angle_refined_deg2.2211.9643706
X-RAY DIFFRACTIONr_angle_other_deg1.1912.9975983
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7635367
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.53425.678118
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.88915458
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6381512
X-RAY DIFFRACTIONr_chiral_restr0.1520.2426
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0213058
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02514
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_it3.1181.4661370
X-RAY DIFFRACTIONr_mcbond_other3.0511.4651369
X-RAY DIFFRACTIONr_mcangle_it3.4632.2091721
X-RAY DIFFRACTIONr_mcangle_other3.4642.2131722
X-RAY DIFFRACTIONr_scbond_it5.0961.8481340
X-RAY DIFFRACTIONr_scbond_other5.0941.8471341
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.6232.6071970
X-RAY DIFFRACTIONr_long_range_B_refined6.26530.74612302
X-RAY DIFFRACTIONr_long_range_B_other4.82229.60211913
X-RAY DIFFRACTIONr_rigid_bond_restr5.09535269
X-RAY DIFFRACTIONr_sphericity_free36.859553
X-RAY DIFFRACTIONr_sphericity_bonded16.00855542
LS refinement shellResolution: 1.28→1.32 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.321 18 -
Rwork0.234 388 -
obs--6.98 %

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