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

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Basic information

Entry
Database: PDB / ID: 5xqu
TitleCrystal structure of Notched-fin eelpout type III antifreeze protein A20I mutant (NFE6, AFP), P212121 form
ComponentsIce-structuring protein
KeywordsANTIFREEZE PROTEIN
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
Ice-structuring protein
Similarity search - Component
Biological speciesZoarces elongatus (fish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1 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

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Assembly

Deposited unit
A: Ice-structuring protein


Theoretical massNumber of molelcules
Total (without water)7,0481
Polymers7,0481
Non-polymers00
Water3,099172
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area3710 Å2
Unit cell
Length a, b, c (Å)22.892, 45.384, 57.910
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 Ice-structuring protein / Antifreeze protein


Mass: 7048.371 Da / Num. of mol.: 1 / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 172 / 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: 2.17 Å3/Da / Density % sol: 43.42 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 26% MPD, 15% PEG8K, 0.1 M NaAcetate pH5.5, 0.1M CaCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: May 7, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1→50 Å / Num. obs: 33453 / % possible obs: 99.9 % / Redundancy: 8.4 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 54.3
Reflection shellResolution: 1→1.04 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.268 / Mean I/σ(I) obs: 8.6 / % possible all: 99.5

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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→35.72 Å / SU ML: 0.07 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 10.93
RfactorNum. reflection% reflection
Rfree0.133 1670 5 %
Rwork0.12 --
obs0.121 33393 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1→35.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms471 0 0 172 643
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01527
X-RAY DIFFRACTIONf_angle_d1.539725
X-RAY DIFFRACTIONf_dihedral_angle_d12.313207
X-RAY DIFFRACTIONf_chiral_restr0.09288
X-RAY DIFFRACTIONf_plane_restr0.00896
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.9999-1.02930.1811360.16122571X-RAY DIFFRACTION99
1.0293-1.06250.14191350.11662574X-RAY DIFFRACTION100
1.0625-1.10050.11551380.10442624X-RAY DIFFRACTION100
1.1005-1.14460.1321380.10412607X-RAY DIFFRACTION100
1.1446-1.19670.12911370.09152612X-RAY DIFFRACTION100
1.1967-1.25980.12091380.09142621X-RAY DIFFRACTION100
1.2598-1.33870.11441380.09142632X-RAY DIFFRACTION100
1.3387-1.44210.12011390.09422637X-RAY DIFFRACTION100
1.4421-1.58720.11391380.10192631X-RAY DIFFRACTION100
1.5872-1.81680.12911420.11312676X-RAY DIFFRACTION100
1.8168-2.2890.12241420.12062715X-RAY DIFFRACTION100
2.289-35.7440.15461490.14862823X-RAY DIFFRACTION100

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