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- PDB-1ops: ICE-BINDING SURFACE ON A TYPE III ANTIFREEZE PROTEIN FROM OCEAN POUT -

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Basic information

Entry
Database: PDB / ID: 1ops
TitleICE-BINDING SURFACE ON A TYPE III ANTIFREEZE PROTEIN FROM OCEAN POUT
ComponentsTYPE III ANTIFREEZE PROTEIN
KeywordsANTIFREEZE PROTEIN / ICE CRYSTAL GROWTH INHIBITION / PRETZEL FOLD / GLYCOPROTEIN
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 SP2(HPLC 1)
Similarity search - Component
Biological speciesMacrozoarces americanus (ocean pout)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsYang, D.S.C. / Hon, W.-C. / Bubanko, S. / Xue, Y. / Seetharaman, J. / Hew, C.L. / Sicheri, F.
CitationJournal: Biophys.J. / Year: 1998
Title: Identification of the ice-binding surface on a type III antifreeze protein with a "flatness function" algorithm.
Authors: Yang, D.S. / Hon, W.C. / Bubanko, S. / Xue, Y. / Seetharaman, J. / Hew, C.L. / Sicheri, F.
History
DepositionNov 17, 1997Processing site: BNL
Revision 1.0May 20, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_ref_seq_dif.details
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TYPE III ANTIFREEZE PROTEIN


Theoretical massNumber of molelcules
Total (without water)6,7511
Polymers6,7511
Non-polymers00
Water59433
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)23.060, 40.790, 29.990
Angle α, β, γ (deg.)90.00, 100.60, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein TYPE III ANTIFREEZE PROTEIN / TYPE III AFP


Mass: 6750.958 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: ISOFORM HPLC-3 / Source: (natural) Macrozoarces americanus (ocean pout) / Tissue: SERUM / References: UniProt: P19608
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / 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: 2.05 Å3/Da / Density % sol: 40.05 %
Description: THE STRUCTURE WAS SOLVED BY THE METHOD OF ITERATIVE SINGLE ANOMALOUS SCATTERING (B.C. WANG, (1985), METHODS ENZYMOL., 114, P90-117).
Crystal growpH: 8 / Details: pH 8.0
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
18 mg/mlprotein1drop
268 mMTris-HCl1reservoir
32.72 Mammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: May 1, 1993 / Details: SUPPER DOUBLE FOCUSING MIRRORS
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→40 Å / Num. obs: 3107 / % possible obs: 82.4 % / Observed criterion σ(I): 2 / Biso Wilson estimate: 19.3 Å2 / Rsym value: 0.066
Reflection
*PLUS
Rmerge(I) obs: 0.066
Reflection shell
*PLUS
% possible obs: 54.9 %

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Processing

Software
NameVersionClassification
X-PLOR3.843model building
X-PLOR3.843refinement
R-AXISdata reduction
R-AXISdata scaling
X-PLOR3.843phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: THE STARTING STRUCTURAL MODEL WAS DETERMINED FROM A CRYSTAL GROWN WITH THE RECOMBINANT, SINGLY-IODINATED PROTEIN, ISOFORM HPLC-6. THIS MODEL IS NOT YET AVAILABLE.

Resolution: 2→40 Å / Rfactor Rfree error: 0.016 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Details: BULK ENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.259 304 9.8 %RANDOM
Rwork0.204 ---
obs0.204 3107 82.6 %-
Displacement parametersBiso mean: 17.4 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.26 Å
Luzzati d res low-40 Å
Luzzati sigma a0.29 Å0.26 Å
Refinement stepCycle: LAST / Resolution: 2→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms445 0 0 33 478
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.014
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.7
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d27.2
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.71
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it2.971.5
X-RAY DIFFRACTIONx_mcangle_it3.862
X-RAY DIFFRACTIONx_scbond_it4.92
X-RAY DIFFRACTIONx_scangle_it6.152.5
LS refinement shellResolution: 2→2.07 Å / Rfactor Rfree error: 0.06 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.287 23 11.6 %
Rwork0.318 175 -
obs--52.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3.843 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 40 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg27.2
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.71
LS refinement shell
*PLUS
Rfactor obs: 0.318

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