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- PDB-6a8k: Crystal structure of Ice-binding Protein from a Sea-Ice Microalga -

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Basic information

Entry
Database: PDB / ID: 6a8k
TitleCrystal structure of Ice-binding Protein from a Sea-Ice Microalga
ComponentsIce binding protein 1
KeywordsANTIFREEZE PROTEIN / beta-solenoid right-handed beta-helix
Function / homologyIce-binding protein / Ice-binding-like / Ice binding protein 1
Function and homology information
Biological speciesFragilariopsis cylindrus (Diatom)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsKondo, H. / Bayer-Giraldi, M.
CitationJournal: Phys Chem Chem Phys / Year: 2018
Title: Multiple binding modes of a moderate ice-binding protein from a polar microalga
Authors: Kondo, H. / Mochizuki, K. / Bayer-Giraldi, M.
History
DepositionJul 9, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 7, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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: Ice binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,0482
Polymers25,9561
Non-polymers921
Water5,026279
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area160 Å2
ΔGint0 kcal/mol
Surface area9970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.054, 47.586, 134.517
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number17
Space group name H-MP2221
Components on special symmetry positions
IDModelComponents
11A-460-

HOH

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Components

#1: Protein Ice binding protein 1


Mass: 25956.189 Da / Num. of mol.: 1 / Fragment: UNP residues 42-298
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Fragilariopsis cylindrus (Diatom) / Production host: Escherichia coli (E. coli) / References: UniProt: D0FHA3
#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 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 279 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsAUTHORS STATE THAT THE GENEBANK ACCESSION NUMBER IS DR026070 FOR THIS SEQUENCE.

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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: 2.22 Å3/Da / Density % sol: 44.7 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1M Tris-HCl pH8.5, 2.0M Ammonium dihydrogen phosphate

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 17, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.4→47.6 Å / Num. obs: 46394 / % possible obs: 99.7 % / Redundancy: 12.3 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 24.1
Reflection shellResolution: 1.4→1.48 Å / Redundancy: 11.6 % / Rmerge(I) obs: 0.434 / Mean I/σ(I) obs: 6.3 / % possible all: 98.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3VN3

3vn3


Resolution: 1.4→47.59 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.972 / SU B: 0.789 / SU ML: 0.031 / Cross valid method: FREE R-VALUE / ESU R: 0.047 / ESU R Free: 0.05 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1622 2319 5 %RANDOM
Rwork0.1368 ---
obs0.13806 44028 99.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 15.013 Å2
Baniso -1Baniso -2Baniso -3
1-1.09 Å20 Å2-0 Å2
2---0.92 Å20 Å2
3----0.17 Å2
Refinement stepCycle: 1 / Resolution: 1.4→47.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1725 0 6 279 2010
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0290.021800
X-RAY DIFFRACTIONr_bond_other_d0.0020.021716
X-RAY DIFFRACTIONr_angle_refined_deg2.4781.962467
X-RAY DIFFRACTIONr_angle_other_deg1.15333969
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0455257
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.5125.63655
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.91315268
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.792153
X-RAY DIFFRACTIONr_chiral_restr0.1390.2307
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0212075
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02364
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.721.285992
X-RAY DIFFRACTIONr_mcbond_other1.721.282991
X-RAY DIFFRACTIONr_mcangle_it2.5061.921243
X-RAY DIFFRACTIONr_mcangle_other2.5061.9241244
X-RAY DIFFRACTIONr_scbond_it2.8561.473808
X-RAY DIFFRACTIONr_scbond_other2.8441.473808
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.0522.1191219
X-RAY DIFFRACTIONr_long_range_B_refined5.74812.1912155
X-RAY DIFFRACTIONr_long_range_B_other5.74912.1932155
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.401→1.437 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2 166 -
Rwork0.192 3161 -
obs--97.74 %

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