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

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Basic information

Entry
Database: PDB / ID: 5xqp
TitleCrystal structure of Notched-fin eelpout type III antifreeze protein (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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)28,4098
Polymers28,0254
Non-polymers3844
Water9,368520
1
A: Ice-structuring protein
B: Ice-structuring protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,2054
Polymers14,0132
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1330 Å2
ΔGint-41 kcal/mol
Surface area6340 Å2
MethodPISA
2
C: Ice-structuring protein
hetero molecules

D: Ice-structuring protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,2054
Polymers14,0132
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x+1/2,-y+1/2,-z1
Buried area1310 Å2
ΔGint-43 kcal/mol
Surface area6260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.553, 75.950, 108.575
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: 7006.291 Da / Num. of mol.: 4 / 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


Mass: 96.063 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 520 / 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: 2.79 Å3/Da / Density % sol: 55.91 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: 2.5M Ammonium sulfate, 0.1M Na-Citrate pH5.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.905 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 24, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.905 Å / Relative weight: 1
ReflectionResolution: 1→50 Å / Num. obs: 167949 / % possible obs: 99.9 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.036 / Net I/σ(I): 36.3
Reflection shellResolution: 1→1.04 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 2.5 / % 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→44.17 Å / SU ML: 0.08 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 8.53
RfactorNum. reflection% reflection
Rfree0.125 8390 5 %
Rwork0.111 --
obs0.112 167830 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1→44.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1867 0 20 520 2407
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092138
X-RAY DIFFRACTIONf_angle_d1.4952947
X-RAY DIFFRACTIONf_dihedral_angle_d12.768821
X-RAY DIFFRACTIONf_chiral_restr0.083355
X-RAY DIFFRACTIONf_plane_restr0.009380
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1-1.01140.21922740.19745210X-RAY DIFFRACTION99
1.0114-1.02330.1972750.17695237X-RAY DIFFRACTION100
1.0233-1.03580.16462780.15735260X-RAY DIFFRACTION100
1.0358-1.04890.16682750.1425239X-RAY DIFFRACTION100
1.0489-1.06270.14042760.12395238X-RAY DIFFRACTION100
1.0627-1.07720.12462770.11065261X-RAY DIFFRACTION100
1.0772-1.09260.12352770.10165261X-RAY DIFFRACTION100
1.0926-1.10890.11282770.09515271X-RAY DIFFRACTION100
1.1089-1.12630.09622780.08765267X-RAY DIFFRACTION100
1.1263-1.14470.09142790.08475304X-RAY DIFFRACTION100
1.1447-1.16450.09752760.08545243X-RAY DIFFRACTION100
1.1645-1.18570.09062790.0865309X-RAY DIFFRACTION100
1.1857-1.20850.10422780.08525288X-RAY DIFFRACTION100
1.2085-1.23310.09212770.08165257X-RAY DIFFRACTION100
1.2331-1.260.09652780.08115297X-RAY DIFFRACTION100
1.26-1.28930.10162800.07985307X-RAY DIFFRACTION100
1.2893-1.32150.08932780.07725273X-RAY DIFFRACTION100
1.3215-1.35720.09212780.07475296X-RAY DIFFRACTION100
1.3572-1.39720.08562800.07725315X-RAY DIFFRACTION100
1.3972-1.44230.10242790.07955311X-RAY DIFFRACTION100
1.4423-1.49380.09412810.08285323X-RAY DIFFRACTION100
1.4938-1.55360.09612810.07955326X-RAY DIFFRACTION100
1.5536-1.62440.11222800.0865335X-RAY DIFFRACTION100
1.6244-1.710.11172810.08995329X-RAY DIFFRACTION100
1.71-1.81710.10482820.09455355X-RAY DIFFRACTION100
1.8171-1.95740.10122820.09795360X-RAY DIFFRACTION100
1.9574-2.15440.10942830.10165393X-RAY DIFFRACTION100
2.1544-2.46620.12832850.11335417X-RAY DIFFRACTION100
2.4662-3.1070.15262900.14155492X-RAY DIFFRACTION100
3.107-44.20840.17132960.15635666X-RAY DIFFRACTION99

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