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- PDB-9i1m: Structure of AauA, a sugar-binding protein with its substrate -

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Basic information

Entry
Database: PDB / ID: 9i1m
TitleStructure of AauA, a sugar-binding protein with its substrate
ComponentsSugar-binding protein
KeywordsSUGAR BINDING PROTEIN / sugar / transporter / E.coli / substrate-binding protein
Function / homology: / Periplasmic binding protein / Periplasmic binding protein domain / Periplasmic binding protein-like I / transmembrane transport / outer membrane-bounded periplasmic space / carbohydrate binding / : / Sugar-binding protein
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsJosts, I. / Cottam, C. / Connolly, J.P.R.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
UK Research and Innovation (UKRI) United Kingdom
CitationJournal: To Be Published
Title: Structure of AauA, a sugar-binding protein with its substrate
Authors: Josts, I. / Cottam, C. / Connolly, J.P.R.
History
DepositionJan 16, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 16, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sugar-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,2364
Polymers35,6971
Non-polymers5393
Water3,873215
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area560 Å2
ΔGint6 kcal/mol
Surface area12800 Å2
Unit cell
Length a, b, c (Å)76.380, 66.940, 57.850
Angle α, β, γ (deg.)90.00, 94.45, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Sugar-binding protein


Mass: 35697.199 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ECs_0374 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8X6A6
#2: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#3: Sugar ChemComp-A1IZL / (2~{S},3~{R},4~{R})-2-(hydroxymethyl)oxolane-2,3,4-triol


Type: saccharide / Mass: 150.130 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H10O5
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 215 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.07 Å3/Da / Density % sol: 40.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 10% PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9686 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Sep 9, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 1.35→38.9 Å / Num. obs: 50386 / % possible obs: 79.1 % / Redundancy: 6.2 % / CC1/2: 1 / Rmerge(I) obs: 0.028 / Net I/σ(I): 29.8
Reflection shellResolution: 1.35→1.37 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 7.5 / Num. unique obs: 574 / CC1/2: 0.98 / % possible all: 18.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
xia2data reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.35→38.9 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.969 / SU B: 1.039 / SU ML: 0.02 / Cross valid method: THROUGHOUT / ESU R: 0.059 / ESU R Free: 0.049 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.1435 2594 5.1 %RANDOM
Rwork0.12632 ---
obs0.1272 47791 79.05 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.456 Å2
Baniso -1Baniso -2Baniso -3
1--0.36 Å20 Å20.24 Å2
2--0.58 Å2-0 Å2
3----0.26 Å2
Refinement stepCycle: 1 / Resolution: 1.35→38.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2233 0 36 215 2484
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0122306
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162269
X-RAY DIFFRACTIONr_angle_refined_deg2.0221.823112
X-RAY DIFFRACTIONr_angle_other_deg0.691.7645239
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.255290
X-RAY DIFFRACTIONr_dihedral_angle_2_deg12.476512
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.84710402
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.3790.2354
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022646
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02476
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_it3.8881.0151166
X-RAY DIFFRACTIONr_mcbond_other3.8711.0151166
X-RAY DIFFRACTIONr_mcangle_it5.5781.821454
X-RAY DIFFRACTIONr_mcangle_other5.5791.8231455
X-RAY DIFFRACTIONr_scbond_it7.0141.3971140
X-RAY DIFFRACTIONr_scbond_other7.0121.3981141
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other9.492.3661659
X-RAY DIFFRACTIONr_long_range_B_refined15.32819.752679
X-RAY DIFFRACTIONr_long_range_B_other14.38718.632626
X-RAY DIFFRACTIONr_rigid_bond_restr4.81934575
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.35→1.385 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.174 41 -
Rwork0.099 877 -
obs--19.51 %

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