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- PDB-1ucs: Type III Antifreeze Protein RD1 from an Antarctic Eel Pout -

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Basic information

Entry
Database: PDB / ID: 1ucs
TitleType III Antifreeze Protein RD1 from an Antarctic Eel Pout
ComponentsAntifreeze peptide RD1
KeywordsANTIFREEZE PROTEIN / Small Beta Barrel / Pretzel Fold
Function / homology
Function and homology information


extracellular region
Similarity search - Function
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 RD1
Similarity search - Component
Biological speciesLycodichthys dearborni (Antarctic eel pout)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.62 Å
AuthorsKo, T.-P. / Robinson, H. / Gao, Y.-G. / Cheng, C.-H.C. / DeVries, A.L. / Wang, A.H.-J.
CitationJournal: Biophys.J. / Year: 2003
Title: The refined crystal structure of an eel pout type III antifreeze protein RD1 at 0.62-A resolution reveals structural microheterogeneity of protein and solvation.
Authors: Ko, T.P. / Robinson, H. / Gao, Y.G. / Cheng, C.H. / DeVries, A.L. / Wang, A.H.
History
DepositionApr 21, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 6, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 6, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_DOI ..._citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Antifreeze peptide RD1


Theoretical massNumber of molelcules
Total (without water)6,9111
Polymers6,9111
Non-polymers00
Water4,324240
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)32.501, 39.502, 44.640
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 Antifreeze peptide RD1 / Type III Antifreeze Protein RD1


Mass: 6911.279 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Lycodichthys dearborni (Antarctic eel pout)
References: UniProt: P35751
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 240 / 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: 1.4 Å3/Da / Density % sol: 11.58 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Ammonium Sulfate, Tris-HCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
140 mg/mlprotein1drop
24 mMTris1droppH7.5
320 %ammonium sulfate1drop
450 %ammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.6668 Å
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Jan 23, 2000
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.6668 Å / Relative weight: 1
ReflectionResolution: 0.62→50 Å / Num. all: 127366 / Num. obs: 118502 / % possible obs: 94 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 3.3 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 21.5
Reflection shellResolution: 0.62→0.64 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.653 / Mean I/σ(I) obs: 1.2 / Num. unique all: 10198 / % possible all: 91.8
Reflection
*PLUS
Lowest resolution: 1.2 Å / Num. obs: 108526 / % possible obs: 97 % / Num. measured all: 256420 / Rmerge(I) obs: 0.073
Reflection shell
*PLUS
% possible obs: 91.8 % / Num. unique obs: 10198 / Num. measured obs: 18801

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
SHELXL-97refinement
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: A polypeptide model derived from NMR experiments

Resolution: 0.62→22.32 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: anisotropic model was used in refinement and then the converted to isotropic B values
RfactorNum. reflection% reflectionSelection details
Rfree0.155 5902 -random
Rwork0.133 ---
all0.139 127291 --
obs0.137 118101 92.8 %-
Displacement parametersBiso mean: 8.91 Å2
Refinement stepCycle: LAST / Resolution: 0.62→22.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1020 0 0 240 1260
Refine LS restraintsType: s_bond_d / Dev ideal: 0.012
LS refinement shellResolution: 0.62→0.65 Å / Rfactor Rfree error: 0.015
RfactorNum. reflection% reflection
Rfree0.291 582 -
Rwork0.265 --
obs-11845 69.4 %
Software
*PLUS
Name: SHELXL / Version: 97 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 50 Å / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_angle_d
X-RAY DIFFRACTIONs_angle_deg2.1

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