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- PDB-6xaq: Alpha-methyl-glucose-bound structure of Marinomonas primoryensis ... -

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Basic information

Entry
Database: PDB / ID: 6xaq
TitleAlpha-methyl-glucose-bound structure of Marinomonas primoryensis PA14 carbohydrate-binding domain
ComponentsAntifreeze protein
KeywordsSUGAR BINDING PROTEIN / Alpha-methyl-glucose-MpPA14 complex / PA14 domain / carbohydrate-binding protein
Function / homology
Function and homology information


Cadherin-like domain / : / : / Cadherin-like domain / Bacterial antifreeze protein repeat / : / Serralysin-like metalloprotease, C-terminal / Immunoglobulin-like fold
Similarity search - Domain/homology
methyl alpha-D-glucopyranoside / Antifreeze protein
Similarity search - Component
Biological speciesMarinomonas primoryensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsGuo, S. / Davies, P.L.
Funding support1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)
Citation
Journal: Mbio / Year: 2021
Title: Structural Basis of Ligand Selectivity by a Bacterial Adhesin Lectin Involved in Multispecies Biofilm Formation.
Authors: Guo, S. / Vance, T.D.R. / Zahiri, H. / Eves, R. / Stevens, C. / Hehemann, J.H. / Vidal-Melgosa, S. / Davies, P.L.
#1: Journal: To Be Published
Title: Molecular basis for a bacterial adhesins sugar-binding module
Authors: Guo, S.
History
DepositionJun 4, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 2, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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

Downloads & links

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Assembly

Deposited unit
A: Antifreeze protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,69310
Polymers20,1781
Non-polymers5159
Water4,666259
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.107, 50.477, 79.239
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Antifreeze protein


Mass: 20178.400 Da / Num. of mol.: 1 / Fragment: carbohydrate-binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Marinomonas primoryensis (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: A1YIY3
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#3: Sugar ChemComp-GYP / methyl alpha-D-glucopyranoside / METHYL-ALPHA-D-GLUCOPYRANOSIDE / ALPHA-METHYL-D-GLUCOPYRANOSIDE / methyl alpha-D-glucoside / methyl D-glucoside / methyl glucoside


Type: D-saccharide / Mass: 194.182 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H14O6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcp[1Me]aCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
1-methyl-a-D-glucopyranoseCOMMON NAMEGMML 1.0
methyl-a-D-glucopyranosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 259 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.32 Å3/Da / Density % sol: 46.93 %
Crystal growTemperature: 298 K / Method: microbatch / pH: 7
Details: 0.2 M calcium chloride, 0.1 M HEPES (pH 7), 20% (v/v) polyethylene glycol 3350 and 30 % (w/v) alpha-methyl-glucose

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Sep 23, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.18→42.57 Å / Num. obs: 60065 / % possible obs: 99.66 % / Redundancy: 12.6 % / Biso Wilson estimate: 8.63 Å2 / Rsym value: 0.019 / Net I/σ(I): 21.7
Reflection shellResolution: 1.18→1.22 Å / Num. unique obs: 5868 / Rpim(I) all: 0.11

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Processing

SoftwareName: PHENIX / Version: 1.17.1_3660 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5j6y

5j6y


Resolution: 1.2→42.57 Å / SU ML: 0.0771 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 15.13
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1665 2942 5.15 %
Rwork0.1627 54223 -
obs0.1629 57165 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 11.94 Å2
Refinement stepCycle: LAST / Resolution: 1.2→42.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1375 0 21 259 1655
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01281485
X-RAY DIFFRACTIONf_angle_d1.54582040
X-RAY DIFFRACTIONf_chiral_restr0.0898226
X-RAY DIFFRACTIONf_plane_restr0.01272
X-RAY DIFFRACTIONf_dihedral_angle_d15.3822509
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2-1.220.20161380.19182530X-RAY DIFFRACTION99.52
1.22-1.240.20351300.19692544X-RAY DIFFRACTION98.82
1.24-1.260.17531470.18522508X-RAY DIFFRACTION98.96
1.26-1.290.1871350.18632583X-RAY DIFFRACTION99.85
1.29-1.310.18611330.18432509X-RAY DIFFRACTION99.25
1.31-1.340.18411370.18012557X-RAY DIFFRACTION99.37
1.34-1.370.17391430.17792540X-RAY DIFFRACTION99.52
1.37-1.410.16721480.19142546X-RAY DIFFRACTION99.63
1.41-1.450.19161370.17432574X-RAY DIFFRACTION99.74
1.45-1.490.17721250.16822554X-RAY DIFFRACTION99.81
1.49-1.540.17111430.16142574X-RAY DIFFRACTION99.93
1.54-1.590.16551340.15172561X-RAY DIFFRACTION99.93
1.59-1.660.14521550.15432578X-RAY DIFFRACTION99.96
1.66-1.730.16771350.15722587X-RAY DIFFRACTION100
1.73-1.820.14721440.15122570X-RAY DIFFRACTION100
1.82-1.940.15541490.152604X-RAY DIFFRACTION100
1.94-2.090.17391310.14682608X-RAY DIFFRACTION100
2.09-2.30.1591270.14782626X-RAY DIFFRACTION99.96
2.3-2.630.15981410.15962633X-RAY DIFFRACTION100
2.63-3.310.14091430.16142656X-RAY DIFFRACTION100
3.31-42.570.17961670.16552781X-RAY DIFFRACTION99.97

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