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- PDB-3wp9: Crystal structure of antifreeze protein from an Antarctic sea ice... -

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Basic information

Entry
Database: PDB / ID: 3wp9
TitleCrystal structure of antifreeze protein from an Antarctic sea ice bacterium Colwellia sp.
ComponentsIce-binding protein
KeywordsANTIFREEZE PROTEIN / Right-handed Beta-helix
Function / homologyIce-binding protein / Ice-binding-like / extracellular region / Ice-binding protein
Function and homology information
Biological speciesColwellia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsHanada, Y. / Nishimiya, Y. / Miura, A. / Tsuda, S. / Kondo, H.
CitationJournal: Febs J. / Year: 2014
Title: Hyperactive antifreeze protein from an Antarctic sea ice bacterium Colwellia sp. has a compound ice-binding site without repetitive sequences.
Authors: Hanada, Y. / Nishimiya, Y. / Miura, A. / Tsuda, S. / Kondo, H.
History
DepositionJan 10, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 2, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2022Group: Database references / Category: citation / database_2
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 8, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ice-binding protein


Theoretical massNumber of molelcules
Total (without water)23,5001
Polymers23,5001
Non-polymers00
Water3,693205
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)90.250, 106.950, 44.075
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-324-

HOH

21A-352-

HOH

31A-374-

HOH

41A-414-

HOH

51A-494-

HOH

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Components

#1: Protein Ice-binding protein / antifreeze protein


Mass: 23500.225 Da / Num. of mol.: 1 / Fragment: UNP residues 28-253
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Colwellia (bacteria) / Strain: SLW05 / Plasmid: pET20b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A5XB26
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 205 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.26 Å3/Da / Density % sol: 45.64 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1M Tris-HCl, 0.2M sodium acetate, 30% polypolyethylene glycol 4000, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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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 210 / Detector: CCD / Date: Jun 11, 2010
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→37.17 Å / Num. all: 28529 / Num. obs: 28529 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 21.2 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 7.5
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 13.8 % / Rmerge(I) obs: 0.218 / Mean I/σ(I) obs: 3.5 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIXmodel building
REFMAC5.7.0032refinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3VN3

3vn3


Resolution: 1.6→37.17 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.935 / SU B: 2.147 / SU ML: 0.074 / Cross valid method: THROUGHOUT / ESU R: 0.099 / ESU R Free: 0.103 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2425 1442 5.1 %RANDOM
Rwork0.19819 ---
obs0.20045 27057 99.64 %-
all-27057 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.057 Å2
Baniso -1Baniso -2Baniso -3
1--1.29 Å2-0 Å2-0 Å2
2--0.02 Å20 Å2
3---1.27 Å2
Refinement stepCycle: LAST / Resolution: 1.6→37.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1635 0 0 205 1840
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.021664
X-RAY DIFFRACTIONr_angle_refined_deg2.1241.9612279
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9765223
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.34126.2361
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.28515250
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.517153
X-RAY DIFFRACTIONr_chiral_restr0.1520.2278
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0211243
X-RAY DIFFRACTIONr_mcbond_it2.2412.071895
X-RAY DIFFRACTIONr_mcangle_it2.9373.1031117
X-RAY DIFFRACTIONr_scbond_it3.7982.413768
X-RAY DIFFRACTIONr_long_range_B_refined6.95719.8022655
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.366 92 -
Rwork0.282 1977 -
obs--99.95 %

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