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

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Basic information

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


extracellular region
Similarity search - Function
SAF domain / SAF domain / SAF / 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
Ice-structuring protein
Similarity search - Component
Biological speciesZoarces elongatus (fish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.19 Å
AuthorsAdachi, M. / 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 1.3Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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-structuring protein
B: Ice-structuring protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,2054
Polymers14,0132
Non-polymers1922
Water5,368298
1
A: Ice-structuring protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,1022
Polymers7,0061
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ice-structuring protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,1022
Polymers7,0061
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.651, 108.248, 38.041
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
11A-198-

HOH

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Components

#1: Protein Ice-structuring protein / Antifreeze protein / Antifreeze protein


Mass: 7006.291 Da / Num. of mol.: 2 / Fragment: UNP residues 23-88
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-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 298 / 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: 2.83 Å3/Da / Density % sol: 56.55 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: 2.5 M Ammonium sulfate, 0.1 M Na-Citrate pH5.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Date: Nov 3, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.19→50 Å / Num. obs: 48626 / % possible obs: 96.3 % / Redundancy: 15 % / Biso Wilson estimate: 14.15 Å2 / Net I/σ(I): 88.4
Reflection shellResolution: 1.19→1.23 Å / Num. unique obs: 4581 / % possible all: 92.2

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
SCALEPACKdata scaling
Cootmodel building
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.19→26.823 Å / SU ML: 0.08 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 14.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1618 2425 5 %
Rwork0.1339 --
obs0.1353 48468 95.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.19→26.823 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms913 0 10 298 1221
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006970
X-RAY DIFFRACTIONf_angle_d1.2321328
X-RAY DIFFRACTIONf_dihedral_angle_d12.344371
X-RAY DIFFRACTIONf_chiral_restr0.077164
X-RAY DIFFRACTIONf_plane_restr0.006169
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1899-1.21420.22321270.18092446X-RAY DIFFRACTION88
1.2142-1.24060.19221400.16322640X-RAY DIFFRACTION95
1.2406-1.26940.16871410.15132679X-RAY DIFFRACTION95
1.2694-1.30120.17821390.14432649X-RAY DIFFRACTION96
1.3012-1.33640.15571410.13382674X-RAY DIFFRACTION96
1.3364-1.37570.17761410.12922664X-RAY DIFFRACTION96
1.3757-1.42010.15741410.1162678X-RAY DIFFRACTION96
1.4201-1.47080.14151430.12142729X-RAY DIFFRACTION97
1.4708-1.52970.14411440.11282721X-RAY DIFFRACTION97
1.5297-1.59930.1421430.10772702X-RAY DIFFRACTION97
1.5993-1.68360.13271420.10972725X-RAY DIFFRACTION97
1.6836-1.78910.14791460.12332760X-RAY DIFFRACTION98
1.7891-1.92720.18041460.13242753X-RAY DIFFRACTION98
1.9272-2.12110.14261480.12732803X-RAY DIFFRACTION98
2.1211-2.42780.17651470.13532809X-RAY DIFFRACTION99
2.4278-3.05810.18441510.14962865X-RAY DIFFRACTION99
3.0581-26.82930.15231450.13692746X-RAY DIFFRACTION91

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