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- PDB-6eio: Crystal structure of an ice binding protein from an Antarctic Bio... -

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Basic information

Entry
Database: PDB / ID: 6eio
TitleCrystal structure of an ice binding protein from an Antarctic Biological Consortium
ComponentsAntifreeze protein
KeywordsANTIFREEZE PROTEIN / antifreeze / ice-binding
Function / homologyIce-binding protein / Ice-binding-like / Prokaryotic membrane lipoprotein lipid attachment site profile. / Antifreeze protein
Function and homology information
Biological speciesuncultured bacterium (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.84 Å
AuthorsNardini, M. / Mangiagalli, M. / Nardone, V. / Bar Dolev, M. / Vena, V.F. / Sarusi, G. / Braslavsky, I. / Lotti, M.
CitationJournal: FEBS J. / Year: 2018
Title: Structure of a bacterial ice binding protein with two faces of interaction with ice.
Authors: Mangiagalli, M. / Sarusi, G. / Kaleda, A. / Bar Dolev, M. / Nardone, V. / Vena, V.F. / Braslavsky, I. / Lotti, M. / Nardini, M.
History
DepositionSep 19, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 28, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 25, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2May 16, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 17, 2024Group: 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)24,6626
Polymers24,1861
Non-polymers4765
Water7,404411
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area730 Å2
ΔGint-38 kcal/mol
Surface area8870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.482, 50.717, 92.452
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Antifreeze protein


Mass: 24185.994 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Ice-binding protein from the Antarctic ciliate Euplotes focardii and the associated bacterial consortium
Source: (gene. exp.) uncultured bacterium (environmental samples)
Production host: Escherichia coli (E. coli) / References: UniProt: A0A023J6X7
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 411 / Source method: isolated from a natural source / Formula: H2O

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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: 2.12 Å3/Da / Density % sol: 42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 2.2 M (NH4)2SO4, 0.1 M HEPES pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.82656 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 20, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.82656 Å / Relative weight: 1
ReflectionResolution: 0.84→46.23 Å / Num. obs: 183816 / % possible obs: 94.5 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 10
Reflection shellResolution: 0.84→0.89 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 19237 / % possible all: 68.8

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3WP9

3wp9


Resolution: 0.84→46.226 Å / SU ML: 0.06 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 11.26 / Details: anisotropic B-factors, H in protein atoms
RfactorNum. reflection% reflection
Rfree0.128 9278 5.05 %
Rwork0.1148 --
obs0.1155 183713 94.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 0.84→46.226 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1588 0 26 411 2025
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081776
X-RAY DIFFRACTIONf_angle_d1.1672467
X-RAY DIFFRACTIONf_dihedral_angle_d12.373626
X-RAY DIFFRACTIONf_chiral_restr0.091308
X-RAY DIFFRACTIONf_plane_restr0.007318
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.84-0.84960.28421700.27273377X-RAY DIFFRACTION55
0.8496-0.85950.24881950.25583865X-RAY DIFFRACTION63
0.8595-0.870.26282140.24074346X-RAY DIFFRACTION71
0.87-0.8810.24122560.22174750X-RAY DIFFRACTION78
0.881-0.89260.21632990.20575151X-RAY DIFFRACTION85
0.8926-0.90490.20873090.1875576X-RAY DIFFRACTION91
0.9049-0.91780.18393200.16085931X-RAY DIFFRACTION98
0.9178-0.93150.16493170.15086040X-RAY DIFFRACTION99
0.9315-0.94610.15653160.14276114X-RAY DIFFRACTION99
0.9461-0.96160.14693260.13456032X-RAY DIFFRACTION99
0.9616-0.97810.13583460.12896015X-RAY DIFFRACTION99
0.9781-0.99590.14583250.12216013X-RAY DIFFRACTION98
0.9959-1.01510.12723270.11116114X-RAY DIFFRACTION100
1.0151-1.03580.12762900.10756142X-RAY DIFFRACTION100
1.0358-1.05830.11063240.09986097X-RAY DIFFRACTION100
1.0583-1.0830.10583190.09796129X-RAY DIFFRACTION100
1.083-1.110.10963480.09386045X-RAY DIFFRACTION99
1.11-1.14010.10453170.09026099X-RAY DIFFRACTION99
1.1401-1.17360.13120.08836154X-RAY DIFFRACTION100
1.1736-1.21150.1022960.09176174X-RAY DIFFRACTION100
1.2115-1.25480.10173100.09376139X-RAY DIFFRACTION100
1.2548-1.3050.10843450.09356139X-RAY DIFFRACTION100
1.305-1.36440.10373500.09556100X-RAY DIFFRACTION100
1.3644-1.43640.11732970.09666190X-RAY DIFFRACTION100
1.4364-1.52640.11043300.09656213X-RAY DIFFRACTION100
1.5264-1.64420.10893450.09956174X-RAY DIFFRACTION100
1.6442-1.80970.11363520.10426213X-RAY DIFFRACTION100
1.8097-2.07160.11663460.1056227X-RAY DIFFRACTION100
2.0716-2.60990.12553360.1096312X-RAY DIFFRACTION100
2.6099-46.29610.14933410.13636564X-RAY DIFFRACTION100

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