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- PDB-4ke2: Crystal structure of the hyperactive Type I antifreeze from winte... -

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Basic information

Entry
Database: PDB / ID: 4ke2
TitleCrystal structure of the hyperactive Type I antifreeze from winter flounder
ComponentsType I hyperactive antifreeze protein
KeywordsANTIFREEZE PROTEIN / dimeric alpha-helical bundle
Function / homology
Function and homology information


ice binding / extracellular region / identical protein binding
Similarity search - Function
Helix Hairpins - #1860 / : / Antifreeze protein, type I / Helix Hairpins / Helix non-globular / Special
Similarity search - Domain/homology
Antifreeze protein Maxi
Similarity search - Component
Biological speciesPseudopleuronectes americanus (winter flounder)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.8 Å
AuthorsSun, T. / Lin, F.-H. / Campbell, R.L. / Allingham, J.S. / Davies, P.L.
Citation
Journal: Science / Year: 2014
Title: An antifreeze protein folds with an interior network of more than 400 semi-clathrate waters.
Authors: Sun, T. / Lin, F.H. / Campbell, R.L. / Allingham, J.S. / Davies, P.L.
#1: Journal: J.Biol.Chem. / Year: 2005
Title: Hyperactive antifreeze protein from winter flounder is a very long rod-like dimer of alpha-helices.
Authors: Marshall, C.B. / Chakrabartty, A. / Davies, P.L.
#2: Journal: Biochemistry / Year: 2008
Title: Hyperactive antifreeze protein from fish contains multiple ice-binding sites.
Authors: Graham, L.A. / Marshall, C.B. / Lin, F.H. / Campbell, R.L. / Davies, P.L.
History
DepositionApr 25, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 26, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 24, 2014Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Type I hyperactive antifreeze protein
B: Type I hyperactive antifreeze protein
C: Type I hyperactive antifreeze protein


Theoretical massNumber of molelcules
Total (without water)50,4773
Polymers50,4773
Non-polymers00
Water30,5531696
1
A: Type I hyperactive antifreeze protein

A: Type I hyperactive antifreeze protein


Theoretical massNumber of molelcules
Total (without water)33,6512
Polymers33,6512
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area3510 Å2
ΔGint-33 kcal/mol
Surface area24770 Å2
MethodPISA
2
B: Type I hyperactive antifreeze protein
C: Type I hyperactive antifreeze protein


Theoretical massNumber of molelcules
Total (without water)33,6512
Polymers33,6512
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3570 Å2
ΔGint-31 kcal/mol
Surface area24500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.820, 48.140, 182.540
Angle α, β, γ (deg.)90.00, 91.87, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-608-

HOH

21B-465-

HOH

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Components

#1: Protein Type I hyperactive antifreeze protein


Mass: 16825.670 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: deleted signal sequence
Source: (gene. exp.) Pseudopleuronectes americanus (winter flounder)
Plasmid: pET24 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B1P0S1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1696 / 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: 4.17 Å3/Da / Density % sol: 70.49 %
Crystal growTemperature: 277 K / pH: 9.6
Details: 0.2 M NaSCN, 12.5% PEG 3350, 100mM Arginine, pH 9.6, vapor diffusion, hanging drop, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.9788
DetectorType: ADSC Q270 / Detector: CCD / Date: Jul 11, 2011 / Details: MIRRORS
RadiationMonochromator: SI 111 CHANNEL / Protocol: MIR / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9788 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 77118 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 5.6 % / Biso Wilson estimate: 21.9 Å2 / Rmerge(I) obs: 0.126 / Net I/σ(I): 11.64
Reflection shellResolution: 1.8→1.85 Å / Redundancy: 5.5 % / Rmerge(I) obs: 1.225 / Mean I/σ(I) obs: 1.77 / % possible all: 98.6

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Phasing

PhasingMethod: MIR

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
SHARPphasing
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.11data extraction
XDSdata reduction
autoSHARPphasing
RefinementMethod to determine structure: MIR / Resolution: 1.8→47.88 Å / Occupancy max: 1 / Occupancy min: 0.2 / SU ML: 0.23 / Isotropic thermal model: isotropic / σ(F): 0 / Phase error: 28.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.253 3872 5.02 %
Rwork0.196 --
obs0.199 77118 99 %
all-77118 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.06 Å2
Baniso -1Baniso -2Baniso -3
1-0.3486 Å2-1.3682 Å23.2968 Å2
2---1.531 Å20.7032 Å2
3----0.1541 Å2
Refinement stepCycle: LAST / Resolution: 1.8→47.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3528 0 0 1696 5224
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113709
X-RAY DIFFRACTIONf_angle_d0.9495156
X-RAY DIFFRACTIONf_dihedral_angle_d9.0341101
X-RAY DIFFRACTIONf_chiral_restr0.051726
X-RAY DIFFRACTIONf_plane_restr0.004686
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.82190.39311630.34512468X-RAY DIFFRACTION98
1.8219-1.8450.38131540.31662670X-RAY DIFFRACTION99
1.845-1.86930.3391340.28382503X-RAY DIFFRACTION99
1.8693-1.89490.31611170.26812604X-RAY DIFFRACTION99
1.8949-1.9220.37251310.26872657X-RAY DIFFRACTION99
1.922-1.95060.29411480.23632487X-RAY DIFFRACTION99
1.9506-1.98110.27431410.232607X-RAY DIFFRACTION99
1.9811-2.01360.27861240.20852608X-RAY DIFFRACTION99
2.0136-2.04830.23541210.19492581X-RAY DIFFRACTION99
2.0483-2.08560.23031390.19852623X-RAY DIFFRACTION99
2.0856-2.12570.27591240.19122587X-RAY DIFFRACTION99
2.1257-2.16910.23371450.18522621X-RAY DIFFRACTION99
2.1691-2.21620.22861470.18282574X-RAY DIFFRACTION99
2.2162-2.26780.24861520.18352577X-RAY DIFFRACTION99
2.2678-2.32450.27461440.18312618X-RAY DIFFRACTION99
2.3245-2.38740.27711200.19022588X-RAY DIFFRACTION99
2.3874-2.45760.25971350.19262620X-RAY DIFFRACTION99
2.4576-2.53690.25961350.18722651X-RAY DIFFRACTION99
2.5369-2.62760.24061320.1782579X-RAY DIFFRACTION99
2.6276-2.73280.22751320.17092620X-RAY DIFFRACTION99
2.7328-2.85710.2411360.16752653X-RAY DIFFRACTION99
2.8571-3.00770.21251310.16622652X-RAY DIFFRACTION100
3.0077-3.19620.20881460.15912614X-RAY DIFFRACTION99
3.1962-3.44290.20251460.15882627X-RAY DIFFRACTION100
3.4429-3.78920.20491530.17182642X-RAY DIFFRACTION100
3.7892-4.33720.2511340.18582655X-RAY DIFFRACTION99
4.3372-5.46320.30941420.22672650X-RAY DIFFRACTION99
5.4632-47.90140.31591320.26932710X-RAY DIFFRACTION97

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