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- PDB-6x95: 2-deoxy-glucose-bound structure of Marinomonas primoryensis PA14 ... -

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Basic information

Entry
Database: PDB / ID: 6x95
Title2-deoxy-glucose-bound structure of Marinomonas primoryensis PA14 carbohydrate-binding domain
ComponentsAntifreeze protein
KeywordsSUGAR BINDING PROTEIN / 2-deoxy-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
2-deoxy-alpha-D-arabino-hexopyranose / Antifreeze protein
Similarity search - Component
Biological speciesMarinomonas primoryensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 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 2, 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)20,99011
Polymers20,3781
Non-polymers61310
Water5,152286
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)45.190, 50.030, 77.790
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: 20377.607 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: Sugar ChemComp-Z61 / 2-deoxy-alpha-D-arabino-hexopyranose / 2-deoxy-alpha-D-glucopyranose / 2-deoxy-alpha-D-mannopyranose


Type: D-saccharide, alpha linking / Mass: 164.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H12O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 286 / 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: 2.26 Å3/Da / Density % sol: 45.63 %
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) 2-deoxy 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: 0.96→42.08 Å / Num. obs: 103370 / % possible obs: 96.25 % / Redundancy: 10.9 % / Biso Wilson estimate: 10.08 Å2 / Rrim(I) all: 0.058 / Net I/σ(I): 17.1
Reflection shellResolution: 0.96→1 Å / Num. unique obs: 7163 / Rpim(I) all: 3.13 / % possible all: 67.7

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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: 1.1→42.08 Å / SU ML: 0.0867 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 14.5883
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1691 3615 5 %
Rwork0.1563 68669 -
obs0.1569 72284 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 14.08 Å2
Refinement stepCycle: LAST / Resolution: 1.1→42.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1375 0 32 286 1693
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00831451
X-RAY DIFFRACTIONf_angle_d1.18891979
X-RAY DIFFRACTIONf_chiral_restr0.1418219
X-RAY DIFFRACTIONf_plane_restr0.0069261
X-RAY DIFFRACTIONf_dihedral_angle_d17.2817489
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1-1.110.23131370.23662606X-RAY DIFFRACTION99.89
1.11-1.130.20991380.19952611X-RAY DIFFRACTION100
1.13-1.150.1831370.19142611X-RAY DIFFRACTION100
1.15-1.160.2051380.17962605X-RAY DIFFRACTION99.96
1.16-1.180.17161370.17672611X-RAY DIFFRACTION100
1.18-1.20.16341370.17652605X-RAY DIFFRACTION100
1.2-1.220.16231390.16962640X-RAY DIFFRACTION100
1.22-1.240.20431360.16772588X-RAY DIFFRACTION100
1.24-1.270.18061380.16262612X-RAY DIFFRACTION100
1.27-1.290.16121370.16532617X-RAY DIFFRACTION100
1.29-1.320.15871390.16332629X-RAY DIFFRACTION100
1.32-1.350.16891370.15852598X-RAY DIFFRACTION100
1.35-1.390.1941380.16242624X-RAY DIFFRACTION100
1.39-1.420.18141380.1672637X-RAY DIFFRACTION100
1.42-1.470.14691390.15732631X-RAY DIFFRACTION100
1.47-1.510.14761380.14992623X-RAY DIFFRACTION99.93
1.51-1.570.15411390.14392646X-RAY DIFFRACTION99.96
1.57-1.630.15631380.14542609X-RAY DIFFRACTION100
1.63-1.70.18071390.14712646X-RAY DIFFRACTION100
1.7-1.790.16591390.15122650X-RAY DIFFRACTION100
1.79-1.910.16221400.15122657X-RAY DIFFRACTION100
1.91-2.050.15471410.14592670X-RAY DIFFRACTION100
2.05-2.260.16041400.13922673X-RAY DIFFRACTION100
2.26-2.590.14081420.15212691X-RAY DIFFRACTION100
2.59-3.260.17671430.15562724X-RAY DIFFRACTION100
3.26-42.080.1851510.1592855X-RAY DIFFRACTION100

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