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- PDB-5xqr: Crystal structure of Notched-fin eelpout type III antifreeze prot... -

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Basic information

Entry
Database: PDB / ID: 5xqr
TitleCrystal structure of Notched-fin eelpout type III antifreeze protein A20V mutant (NFE6, AFP), C2221 form
ComponentsIce-structuring protein
KeywordsANTIFREEZE PROTEIN / Type III / Notched-fin eelpout
Function / homology
Function and homology information


extracellular region
Similarity search - Function
SAF domain / SAF / SAF domain / Antifreeze, type III / Type Iii Antifreeze Protein Isoform Hplc 12 / Antifreeze-like/N-acetylneuraminic acid synthase C-terminal domain / Antifreeze-like/N-acetylneuraminic acid synthase C-terminal / Antifreeze protein-like domain profile. / Antifreeze-like/N-acetylneuraminic acid synthase C-terminal domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Ice-structuring protein
Similarity search - Component
Biological speciesZoarces elongatus (fish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsAdachi, M. / Shimizu, R. / Shibazaki, C. / Kondo, H. / Tsuda, S.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Polypentagonal ice-like water networks emerge solely in an activity-improved variant of ice-binding protein
Authors: Mahatabuddin, S. / Fukami, D. / Arai, T. / Nishimiya, Y. / Shimizu, R. / Shibazaki, C. / Kondo, H. / Adachi, M. / Tsuda, S.
History
DepositionJun 7, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 16, 2018Provider: repository / Type: Initial release
Revision 1.1May 23, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed
Revision 1.2Jun 6, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 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

Downloads & links

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Assembly

Deposited unit
A: Ice-structuring protein
B: Ice-structuring protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1874
Polymers14,0692
Non-polymers1182
Water4,161231
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area700 Å2
ΔGint-7 kcal/mol
Surface area6830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.460, 108.699, 38.055
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-281-

HOH

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Components

#1: Protein Ice-structuring protein / Antifreeze protein


Mass: 7034.344 Da / Num. of mol.: 2 / Fragment: UNP residues 23-88 / Mutation: A20V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zoarces elongatus (fish) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q53UJ4
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 231 / 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: 2.88 Å3/Da / Density % sol: 57.31 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 26% MPD, 15% PEG8K, 0.1M NaAcetate pH5.5, 0.1M CaCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 3, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.3→100 Å / Num. obs: 38950 / % possible obs: 100 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 34.6
Reflection shellResolution: 1.3→1.35 Å / Redundancy: 7 % / Rmerge(I) obs: 0.104 / Mean I/σ(I) obs: 1.9 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
SCALEPACKdata scaling
Cootmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5XQN

5xqn


Resolution: 1.3→26.79 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 14.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.156 1947 5 %
Rwork0.132 --
obs0.133 38935 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.3→26.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms904 0 8 231 1143
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011986
X-RAY DIFFRACTIONf_angle_d1.4311350
X-RAY DIFFRACTIONf_dihedral_angle_d13.252381
X-RAY DIFFRACTIONf_chiral_restr0.089169
X-RAY DIFFRACTIONf_plane_restr0.008174
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3003-1.33290.25971360.21432588X-RAY DIFFRACTION100
1.3329-1.36890.21311370.18582613X-RAY DIFFRACTION100
1.3689-1.40920.22331390.16312642X-RAY DIFFRACTION100
1.4092-1.45470.1911360.14832584X-RAY DIFFRACTION100
1.4547-1.50670.17611390.12572627X-RAY DIFFRACTION100
1.5067-1.5670.13741360.10772589X-RAY DIFFRACTION100
1.567-1.63830.14511390.10212625X-RAY DIFFRACTION100
1.6383-1.72460.14371380.10142641X-RAY DIFFRACTION100
1.7246-1.83270.13271390.10152625X-RAY DIFFRACTION100
1.8327-1.97410.13331380.10032636X-RAY DIFFRACTION100
1.9741-2.17270.13541390.10792650X-RAY DIFFRACTION100
2.1727-2.48690.13951410.12032657X-RAY DIFFRACTION100
2.4869-3.13250.15481420.15292703X-RAY DIFFRACTION100
3.1325-26.7990.16641480.14632808X-RAY DIFFRACTION100

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