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- PDB-6xa5: Trehalose-bound structure of Marinomonas primoryensis PA14 carboh... -

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Basic information

Entry
Database: PDB / ID: 6xa5
TitleTrehalose-bound structure of Marinomonas primoryensis PA14 carbohydrate-binding domain
ComponentsAntifreeze protein
KeywordsSUGAR BINDING PROTEIN / Trehalose-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
trehalose / Antifreeze protein
Similarity search - Component
Biological speciesMarinomonas primoryensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.03 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)20,7009
Polymers20,0771
Non-polymers6238
Water5,206289
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)45.270, 50.640, 79.430
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: 20077.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Marinomonas primoryensis (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: A1YIY3
#2: Polysaccharide alpha-D-glucopyranose-(1-1)-alpha-D-glucopyranose / trehalose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: trehalose
DescriptorTypeProgram
DGlcpa1-1DGlcpaGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a1-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(1+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 289 / 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: 2.27 Å3/Da / Density % sol: 45.75 %
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) trehalose

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97934 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Sep 19, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.03→42.7 Å / Num. obs: 75689 / % possible obs: 84.2 % / Redundancy: 7.5 % / Biso Wilson estimate: 6.94 Å2 / CC1/2: 0.99 / Net I/σ(I): 27.95
Reflection shellResolution: 1.03→1.06 Å / Num. unique obs: 4536 / CC1/2: 0.88

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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: 1.03→42.7 Å / SU ML: 0.043 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 10.3427
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1308 3785 5 %
Rwork0.1184 71901 -
obs0.119 75686 84.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 10.72 Å2
Refinement stepCycle: LAST / Resolution: 1.03→42.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1411 0 30 289 1730
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00821503
X-RAY DIFFRACTIONf_angle_d1.22432065
X-RAY DIFFRACTIONf_chiral_restr0.0918233
X-RAY DIFFRACTIONf_plane_restr0.0088274
X-RAY DIFFRACTIONf_dihedral_angle_d12.3939504
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.03-1.050.2566140.2334261X-RAY DIFFRACTION8.36
1.05-1.060.1708370.179711X-RAY DIFFRACTION22.92
1.06-1.080.1656590.13181107X-RAY DIFFRACTION35.17
1.08-1.090.1268760.10841448X-RAY DIFFRACTION47.02
1.09-1.110.1114940.09411789X-RAY DIFFRACTION56.55
1.11-1.120.11831060.08782013X-RAY DIFFRACTION64.98
1.12-1.140.09851190.08352271X-RAY DIFFRACTION72.91
1.14-1.160.1081320.08352493X-RAY DIFFRACTION79.47
1.16-1.180.10241450.08222764X-RAY DIFFRACTION88.07
1.18-1.210.10381600.07963042X-RAY DIFFRACTION96.33
1.21-1.230.11561620.08013083X-RAY DIFFRACTION99.08
1.23-1.260.10681660.08243153X-RAY DIFFRACTION99.46
1.26-1.290.12361630.08323090X-RAY DIFFRACTION100
1.29-1.320.09471650.0873137X-RAY DIFFRACTION99.64
1.32-1.350.10611670.08653160X-RAY DIFFRACTION99.73
1.35-1.390.09811640.08683122X-RAY DIFFRACTION99.79
1.39-1.440.10431660.09013155X-RAY DIFFRACTION99.91
1.44-1.490.1141660.08983150X-RAY DIFFRACTION100
1.49-1.550.09831660.09173160X-RAY DIFFRACTION100
1.55-1.620.11711670.10083183X-RAY DIFFRACTION99.97
1.62-1.710.12161670.10843154X-RAY DIFFRACTION100
1.71-1.810.12251670.1153191X-RAY DIFFRACTION100
1.81-1.950.13461680.11863184X-RAY DIFFRACTION100
1.95-2.150.13311680.1233198X-RAY DIFFRACTION100
2.15-2.460.15651700.13543218X-RAY DIFFRACTION100
2.46-3.10.14631710.15983256X-RAY DIFFRACTION99.97
3.1-42.70.16261800.15933408X-RAY DIFFRACTION99.89

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