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- PDB-1msi: STRUCTURE OF ANTIFREEZE GLYCOPROTEIN QAE(HPLC 12) -

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Basic information

Entry
Database: PDB / ID: 1msi
TitleSTRUCTURE OF ANTIFREEZE GLYCOPROTEIN QAE(HPLC 12)
ComponentsTYPE III ANTIFREEZE PROTEIN ISOFORM HPLC 12
KeywordsANTIFREEZE PROTEIN / MULTIGENE FAMILY / THERMAL HYSTERESIS
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
Type-3 ice-structuring protein HPLC 12
Similarity search - Component
Biological speciesMacrozoarces americanus (ocean pout)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.25 Å
AuthorsJia, Z. / Deluca, C.I. / Chao, H. / Davies, P.L.
Citation
Journal: Nature / Year: 1996
Title: Structural basis for the binding of a globular antifreeze protein to ice.
Authors: Jia, Z. / DeLuca, C.I. / Chao, H. / Davies, P.L.
#1: Journal: Nature / Year: 1997
Title: Erratum. Structural Basis for the Binding of a Globular Antifreeze Protein to Ice
Authors: Jia, Z. / Deluca, C.I. / Chao, H. / Davies, P.L.
#2: Journal: Protein Sci. / Year: 1995
Title: Crystallization and Preliminary X-Ray Crystallographic Studies on Type III Antifreeze Protein
Authors: Jia, Z. / Deluca, C.I. / Davies, P.L.
#3: Journal: Protein Sci. / Year: 1993
Title: Use of Proline Mutants to Help Solve the NMR Solution Structure of Type III Antifreeze Protein
Authors: Chao, H. / Davies, P.L. / Sykes, B.D. / Sonnichsen, F.D.
#4: Journal: J.Biol.Chem. / Year: 1988
Title: Multiple Genes Provide the Basis for Antifreeze Protein Diversity and Dosage in the Ocean Pout, Macrozoarces Americanus
Authors: Hew, C.L. / Wang, N.C. / Joshi, S. / Fletcher, G.L. / Scott, G.K. / Hayes, P.H. / Buettner, B. / Davies, P.L.
History
DepositionOct 8, 1996Processing site: BNL
Revision 1.0Dec 24, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Data collection / Database references / Other
Category: database_2 / diffrn_source ...database_2 / diffrn_source / 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 / _diffrn_source.pdbx_synchrotron_site / _pdbx_database_status.process_site / _struct_ref_seq_dif.details
Revision 1.4Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TYPE III ANTIFREEZE PROTEIN ISOFORM HPLC 12


Theoretical massNumber of molelcules
Total (without water)7,4231
Polymers7,4231
Non-polymers00
Water1,62190
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)32.328, 38.893, 45.483
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 TYPE III ANTIFREEZE PROTEIN ISOFORM HPLC 12 / TYPE III ANTIFREEZE PROTEIN QAE ISOFORM


Mass: 7422.746 Da / Num. of mol.: 1 / Mutation: P64A, P65A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macrozoarces americanus (ocean pout) / Plasmid: PT7-7F / Production host: Escherichia coli (E. coli) / References: UniProt: P19614
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 90 / 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: 1.92 Å3/Da / Density % sol: 30 %
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, hanging drop / PH range low: 4.5 / PH range high: 4
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
13-3.5 mg/mlprotein1drop
225-27.5 %satammonium sulfate1drop
30.05 Msodium acetate1drop
450-55 %satammonium sulfate1reservoir
50.1 Msodium acetate1reservoir

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.927
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 30, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.927 Å / Relative weight: 1
ReflectionResolution: 1.25→50 Å / Num. obs: 16529 / % possible obs: 96.6 % / Observed criterion σ(I): 1 / Redundancy: 2.8 % / Biso Wilson estimate: 15.46 Å2 / Rmerge(I) obs: 0.049 / Rsym value: 0.049 / Net I/σ(I): 24.1
Reflection shellResolution: 1.25→1.31 Å / Rmerge(I) obs: 0.557 / Mean I/σ(I) obs: 1.64 / Rsym value: 0.557 / % possible all: 98.1
Reflection
*PLUS
Num. measured all: 46873
Reflection shell
*PLUS
% possible obs: 98.1 %

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Processing

Software
NameVersionClassification
X-PLOR3model building
X-PLOR3refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3phasing
RefinementResolution: 1.25→8 Å / Cross valid method: FREE R / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.225 779 5 %RANDOM
Rwork0.198 ---
obs0.198 46873 96.6 %-
Displacement parametersBiso mean: 18.5 Å2
Refinement stepCycle: LAST / Resolution: 1.25→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms482 0 0 90 572
Refine LS restraints
Refine-IDTypeDev ideal
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_deg3.045
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d26.33
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.642
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 1.25→1.31 Å
RfactorNum. reflection% reflection
Rfree0.3425 90 5 %
Rwork0.3109 1876 -
obs--98.01 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARAM19X.PROTOPH19X.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26.33
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.642
LS refinement shell
*PLUS
Rfactor obs: 0.3109

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