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- PDB-6x7x: mannose-bound structure of Marinomonas primoryensis PA14 carbohyd... -

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Basic information

Entry
Database: PDB / ID: 6x7x
Titlemannose-bound structure of Marinomonas primoryensis PA14 carbohydrate-binding domain
ComponentsAntifreeze protein
KeywordsSUGAR BINDING PROTEIN / mannose-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
beta-D-mannopyranose / alpha-D-mannopyranose / Antifreeze protein
Similarity search - Component
Biological speciesMarinomonas primoryensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 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
DepositionMay 31, 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)21,09514
Polymers20,2491
Non-polymers84513
Water4,756264
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)45.299, 50.358, 79.130
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

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Protein , 1 types, 1 molecules A

#1: Protein Antifreeze protein


Mass: 20249.479 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

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Sugars , 2 types, 2 molecules

#4: Sugar ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DManpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-mannopyranoseCOMMON NAMEGMML 1.0
a-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Sugar ChemComp-BMA / beta-D-mannopyranose / beta-D-mannose / D-mannose / mannose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DManpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-mannopyranoseCOMMON NAMEGMML 1.0
b-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 275 molecules

#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 9 / 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
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 264 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.26 Å3/Da / Density % sol: 45.47 %
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) mannose

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.03318 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: Apr 1, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03318 Å / Relative weight: 1
ReflectionResolution: 1.26→39.56 Å / Num. obs: 48977 / % possible obs: 98.66 % / Redundancy: 7.7 % / Biso Wilson estimate: 5.2 Å2 / Rmerge(I) obs: 0.302 / Net I/σ(I): 4.2
Reflection shellResolution: 1.26→1.31 Å / Rmerge(I) obs: 0.661 / Num. unique obs: 4287

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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: 1.3→39.56 Å / SU ML: 0.1052 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.1439
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1858 2325 5.15 %
Rwork0.158 42815 -
obs0.1595 45140 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 10.06 Å2
Refinement stepCycle: LAST / Resolution: 1.3→39.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1413 0 41 264 1718
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01441558
X-RAY DIFFRACTIONf_angle_d1.66632141
X-RAY DIFFRACTIONf_chiral_restr0.1195245
X-RAY DIFFRACTIONf_plane_restr0.0127283
X-RAY DIFFRACTIONf_dihedral_angle_d12.5939553
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3-1.330.22681370.22552363X-RAY DIFFRACTION96.23
1.33-1.360.23121250.19192512X-RAY DIFFRACTION99.96
1.36-1.390.19811590.17552467X-RAY DIFFRACTION100
1.39-1.420.21871410.17492494X-RAY DIFFRACTION100
1.42-1.460.19071200.15382493X-RAY DIFFRACTION100
1.46-1.50.19811290.15322496X-RAY DIFFRACTION99.96
1.5-1.550.2141320.1432511X-RAY DIFFRACTION100
1.55-1.610.21331350.1392498X-RAY DIFFRACTION100
1.61-1.670.18561330.1422515X-RAY DIFFRACTION99.96
1.67-1.750.17871430.14182493X-RAY DIFFRACTION100
1.75-1.840.15761560.13412498X-RAY DIFFRACTION100
1.84-1.950.15581250.13232540X-RAY DIFFRACTION100
1.95-2.110.14911510.13262514X-RAY DIFFRACTION100
2.11-2.320.17081350.14992543X-RAY DIFFRACTION99.96
2.32-2.650.20751200.1682585X-RAY DIFFRACTION99.96
2.65-3.340.18191300.17272602X-RAY DIFFRACTION100
3.34-39.560.18391540.1732691X-RAY DIFFRACTION99.51

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