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- PDB-6x8d: Arabinose-bound structure of Marinomonas primoryensis PA14 carboh... -

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Basic information

Entry
Database: PDB / ID: 6x8d
TitleArabinose-bound structure of Marinomonas primoryensis PA14 carbohydrate-binding domain
ComponentsAntifreeze protein
KeywordsSUGAR BINDING PROTEIN / Arabinose-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
alpha-L-arabinopyranose / 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 1, 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)20,88311
Polymers20,3071
Non-polymers57710
Water5,062281
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)45.120, 50.710, 79.620
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: 20306.529 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: Sugar ChemComp-ARA / alpha-L-arabinopyranose / alpha-L-arabinose / L-arabinose / arabinose


Type: L-saccharide, alpha linking / Mass: 150.130 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H10O5 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
LArapaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-L-arabinopyranoseCOMMON NAMEGMML 1.0
a-L-ArapIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
AraSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 281 / 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: 2.24 Å3/Da / Density % sol: 45.16 %
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) arabinose

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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→42.77 Å / Num. obs: 106425 / % possible obs: 95.17 % / Redundancy: 11 % / Biso Wilson estimate: 7.31 Å2 / Rrim(I) all: 0.067 / Net I/σ(I): 19.1
Reflection shellResolution: 0.96→0.99 Å / Num. unique obs: 6942 / Rpim(I) all: 0.685

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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→42.77 Å / SU ML: 0.0899 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 13.7632
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1659 4912 5 %
Rwork0.1461 93327 -
obs0.1471 98239 99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 13.96 Å2
Refinement stepCycle: LAST / Resolution: 1→42.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1361 0 28 281 1670
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01711494
X-RAY DIFFRACTIONf_angle_d1.67222049
X-RAY DIFFRACTIONf_chiral_restr0.1203225
X-RAY DIFFRACTIONf_plane_restr0.0133275
X-RAY DIFFRACTIONf_dihedral_angle_d14.6042511
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1-1.010.35341340.312556X-RAY DIFFRACTION82.92
1.01-1.020.25051460.23822764X-RAY DIFFRACTION89.62
1.02-1.040.20981630.17613102X-RAY DIFFRACTION98.64
1.04-1.050.15071640.15073103X-RAY DIFFRACTION99.94
1.05-1.060.17151620.14273095X-RAY DIFFRACTION99.97
1.06-1.080.16751670.143162X-RAY DIFFRACTION100
1.08-1.090.15841610.14153062X-RAY DIFFRACTION99.88
1.09-1.110.13921630.14073100X-RAY DIFFRACTION99.82
1.11-1.130.13571640.12873118X-RAY DIFFRACTION99.94
1.13-1.140.18681630.12173099X-RAY DIFFRACTION99.97
1.14-1.160.15281630.12263104X-RAY DIFFRACTION99.91
1.16-1.190.141650.12243139X-RAY DIFFRACTION100
1.19-1.210.15571650.11713124X-RAY DIFFRACTION100
1.21-1.230.14071630.12653108X-RAY DIFFRACTION100
1.23-1.260.16371650.12363133X-RAY DIFFRACTION100
1.26-1.290.16221650.12683132X-RAY DIFFRACTION100
1.29-1.320.15541630.12623099X-RAY DIFFRACTION100
1.32-1.360.15191660.12713146X-RAY DIFFRACTION99.94
1.36-1.40.15731630.1293110X-RAY DIFFRACTION99.97
1.4-1.440.15241660.13343150X-RAY DIFFRACTION100
1.44-1.490.15671660.12613143X-RAY DIFFRACTION99.97
1.49-1.550.14941640.12453132X-RAY DIFFRACTION99.97
1.55-1.620.14961660.13063155X-RAY DIFFRACTION99.97
1.62-1.710.16771660.13483140X-RAY DIFFRACTION99.94
1.71-1.820.14711670.14223180X-RAY DIFFRACTION99.91
1.82-1.960.16061670.14453161X-RAY DIFFRACTION99.76
1.96-2.150.16231670.1453181X-RAY DIFFRACTION99.91
2.15-2.470.14771690.15233204X-RAY DIFFRACTION99.88
2.47-3.110.17671700.16513231X-RAY DIFFRACTION99.91
3.11-42.770.20011790.17323394X-RAY DIFFRACTION99.89

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