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- PDB-6x9m: 3-O-methyl-glucose-bound structure of Marinomonas primoryensis PA... -

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Basic information

Entry
Database: PDB / ID: 6x9m
Title3-O-methyl-glucose-bound structure of Marinomonas primoryensis PA14 carbohydrate-binding domain
ComponentsAntifreeze protein
KeywordsSUGAR BINDING PROTEIN / 3-O-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
3-O-methyl-beta-D-glucopyranose / Antifreeze protein
Similarity search - Component
Biological speciesMarinomonas primoryensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1 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 3, 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

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Assembly

Deposited unit
A: Antifreeze protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,6269
Polymers20,1071
Non-polymers5198
Water5,350297
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)45.200, 50.330, 79.140
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: 20107.322 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.: 5 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Sugar ChemComp-3MG / 3-O-methyl-beta-D-glucopyranose / 3-O-methyl-beta-D-glucose / 3-O-methyl-D-glucose / 3-O-methyl-glucose


Type: D-saccharide, beta linking / Mass: 194.182 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H14O6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcp[3Me]bCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
3-methyl-b-D-glucopyranoseCOMMON NAMEGMML 1.0
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 297 / 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: 2.31 Å3/Da / Density % sol: 46.82 %
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) 3-O-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: Dec 7, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 0.97→42.47 Å / Num. obs: 101513 / % possible obs: 94.57 % / Redundancy: 11.1 % / Biso Wilson estimate: 7.53 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 19.9
Reflection shellResolution: 0.97→1 Å / Num. unique obs: 6335 / Rpim(I) all: 0.534

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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→42.47 Å / SU ML: 0.0802 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 13.5858
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1591 4807 5 %
Rwork0.1421 91318 -
obs0.143 96125 98.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 12.79 Å2
Refinement stepCycle: LAST / Resolution: 1→42.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1375 0 26 297 1698
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00941492
X-RAY DIFFRACTIONf_angle_d1.32082046
X-RAY DIFFRACTIONf_chiral_restr0.0933230
X-RAY DIFFRACTIONf_plane_restr0.0086270
X-RAY DIFFRACTIONf_dihedral_angle_d14.7257501
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1-1.010.29871210.2752323X-RAY DIFFRACTION75.27
1.01-1.020.26011310.24552471X-RAY DIFFRACTION81.31
1.02-1.040.22941460.21082770X-RAY DIFFRACTION90.59
1.04-1.050.15621590.16833019X-RAY DIFFRACTION97.57
1.05-1.060.19471600.15923027X-RAY DIFFRACTION99.19
1.06-1.080.17951590.14453027X-RAY DIFFRACTION97.79
1.08-1.090.15051590.14583020X-RAY DIFFRACTION98.82
1.09-1.110.16291610.14043063X-RAY DIFFRACTION99.91
1.11-1.130.15191620.13133072X-RAY DIFFRACTION100
1.13-1.140.17271640.12613121X-RAY DIFFRACTION100
1.14-1.160.14411610.12253053X-RAY DIFFRACTION100
1.16-1.190.1451620.12033075X-RAY DIFFRACTION100
1.19-1.210.12911610.11883076X-RAY DIFFRACTION100
1.21-1.230.15111630.11833095X-RAY DIFFRACTION100
1.23-1.260.14761630.1263086X-RAY DIFFRACTION100
1.26-1.290.14151620.12073085X-RAY DIFFRACTION99.97
1.29-1.320.14191630.12123093X-RAY DIFFRACTION100
1.32-1.360.13351630.12293090X-RAY DIFFRACTION100
1.36-1.40.1451620.12513095X-RAY DIFFRACTION99.97
1.4-1.440.15631640.12493105X-RAY DIFFRACTION100
1.44-1.490.1331630.1273101X-RAY DIFFRACTION100
1.49-1.550.15621640.12763116X-RAY DIFFRACTION100
1.55-1.620.15321640.12973109X-RAY DIFFRACTION99.94
1.62-1.710.17021630.13173103X-RAY DIFFRACTION100
1.71-1.820.1461650.13843133X-RAY DIFFRACTION99.82
1.82-1.960.15591640.14183128X-RAY DIFFRACTION99.73
1.96-2.150.12231660.13823135X-RAY DIFFRACTION99.88
2.15-2.470.1511670.14623176X-RAY DIFFRACTION99.88
2.47-3.110.19491680.15413200X-RAY DIFFRACTION99.94
3.11-42.470.17721770.16423351X-RAY DIFFRACTION99.92

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