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- PDB-6x7t: Allose-bound structure of Marinomonas primoryensis PA14 carbohydr... -

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Basic information

Entry
Database: PDB / ID: 6x7t
TitleAllose-bound structure of Marinomonas primoryensis PA14 carbohydrate-binding domain
ComponentsAntifreeze protein
KeywordsSUGAR BINDING PROTEIN / Allose-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-allofuranose / alpha-D-allofuranose / 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)
CitationJournal: 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.
History
DepositionMay 30, 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)21,2059
Polymers20,6041
Non-polymers6018
Water5,026279
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)45.470, 50.270, 79.010
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: 20603.902 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.: 6 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-VDS / beta-D-allofuranose


Mass: 180.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-VDV / alpha-D-allofuranose


Mass: 180.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H12O6
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 279 / 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: 2.19 Å3/Da / Density % sol: 43.87 %
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) Allose

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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: Feb 5, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 0.96→42.41 Å / Num. obs: 106122 / % possible obs: 95.55 % / Redundancy: 11.2 % / Biso Wilson estimate: 7.1 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 23.1
Reflection shellResolution: 0.96→0.99 Å / Rmerge(I) obs: 0.638 / Num. unique obs: 7281

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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→42.41 Å / SU ML: 0.065 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 9.556
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1302 4871 5 %
Rwork0.1271 92552 -
obs0.1272 97423 99.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 11.42 Å2
Refinement stepCycle: LAST / Resolution: 1→42.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1376 0 30 279 1685
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01131509
X-RAY DIFFRACTIONf_angle_d1.55842080
X-RAY DIFFRACTIONf_chiral_restr0.2208235
X-RAY DIFFRACTIONf_plane_restr0.0078276
X-RAY DIFFRACTIONf_dihedral_angle_d11.6847514
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1-1.010.21081470.1952789X-RAY DIFFRACTION89.57
1.01-1.020.16511510.15352876X-RAY DIFFRACTION94.39
1.02-1.040.15051560.11852961X-RAY DIFFRACTION96.59
1.04-1.050.12641590.10793018X-RAY DIFFRACTION97.63
1.05-1.060.11441600.10293038X-RAY DIFFRACTION98.8
1.06-1.080.11171600.10093036X-RAY DIFFRACTION98.76
1.08-1.090.11281600.10133057X-RAY DIFFRACTION98.83
1.09-1.110.11171610.10223058X-RAY DIFFRACTION98.92
1.11-1.130.10341600.09133055X-RAY DIFFRACTION99.2
1.13-1.140.10721620.09063063X-RAY DIFFRACTION99.29
1.14-1.160.09041610.093059X-RAY DIFFRACTION99.51
1.16-1.190.09721620.09493079X-RAY DIFFRACTION99.66
1.19-1.210.11061620.09713092X-RAY DIFFRACTION99.75
1.21-1.230.10531640.10043117X-RAY DIFFRACTION99.79
1.23-1.260.12351610.10083055X-RAY DIFFRACTION99.91
1.26-1.290.10131630.10133090X-RAY DIFFRACTION99.97
1.29-1.320.11751640.1053128X-RAY DIFFRACTION100
1.32-1.360.12471640.11093111X-RAY DIFFRACTION100
1.36-1.40.12021630.10993085X-RAY DIFFRACTION99.97
1.4-1.440.1271640.11273126X-RAY DIFFRACTION100
1.44-1.490.10841630.11213099X-RAY DIFFRACTION100
1.49-1.550.12111640.11333121X-RAY DIFFRACTION100
1.55-1.620.12371660.11783137X-RAY DIFFRACTION99.97
1.62-1.710.15111630.1243094X-RAY DIFFRACTION99.97
1.71-1.820.16311650.12943148X-RAY DIFFRACTION100
1.82-1.960.14091650.13253140X-RAY DIFFRACTION100
1.96-2.150.12761670.1233158X-RAY DIFFRACTION100
2.15-2.470.14651680.13953192X-RAY DIFFRACTION99.97
2.47-3.110.14481690.15253212X-RAY DIFFRACTION99.97
3.11-42.410.1351770.16683358X-RAY DIFFRACTION99.89

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