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- PDB-2spg: TYPE III ANTIFREEZE PROTEIN ISOFORM HPLC 12 T15S -

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Basic information

Entry
Database: PDB / ID: 2spg
TitleTYPE III ANTIFREEZE PROTEIN ISOFORM HPLC 12 T15S
ComponentsPROTEIN (ANTIFREEZE PROTEIN TYPE III)
KeywordsANTIFREEZE PROTEIN / MUTANT / ICE BINDING PROTEIN / THERMAL HYSTERESIS PROTEIN
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 / OTHER / Resolution: 1.75 Å
AuthorsGraether, S.P. / Deluca, C.I. / Baardsnes, J. / Hill, G.A. / Davies, P.L. / Jia, Z.
Citation
Journal: J.Biol.Chem. / Year: 1999
Title: Quantitative and qualitative analysis of type III antifreeze protein structure and function.
Authors: Graether, S.P. / DeLuca, C.I. / Baardsnes, J. / Hill, G.A. / Davies, P.L. / Jia, Z.
#1: Journal: J.Mol.Biol. / Year: 1998
Title: The effects of steric mutations on the structure of type III antifreeze protein and its interaction with ice.
Authors: DeLuca, C.I. / Davies, P.L. / Ye, Q. / Jia, Z.
#2: 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.
#3: 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.
#4: 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.
#5: 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
DepositionJan 21, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Apr 28, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 27, 2019Group: Database references / Category: citation / citation_author
Item: _citation.page_last / _citation.pdbx_database_id_DOI ..._citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.4Nov 3, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (ANTIFREEZE PROTEIN TYPE III)


Theoretical massNumber of molelcules
Total (without water)6,9651
Polymers6,9651
Non-polymers00
Water68538
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)33.276, 39.873, 44.670
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 PROTEIN (ANTIFREEZE PROTEIN TYPE III) / TYPE III ANTIFREEZE PROTEIN QAE ISOFORM


Mass: 6965.207 Da / Num. of mol.: 1 / Mutation: T15S, 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.: 38 / 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: 2.13 Å3/Da / Density % sol: 42.13 %
Crystal growpH: 5.5 / Details: pH 5.5
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, hanging drop / Details: Jia, Z., (1995) Protein Sci., 4, 1236. / 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: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.75→25 Å / Num. obs: 6388 / % possible obs: 98 % / Observed criterion σ(I): 1 / Redundancy: 3.5 % / Rsym value: 0.079 / Net I/σ(I): 15.4
Reflection shellResolution: 1.75→1.81 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 3.1 / Rsym value: 0.35 / % possible all: 99.5
Reflection
*PLUS
Num. measured all: 21851 / Rmerge(I) obs: 0.079

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: OTHER
Starting model: 1MSI

1msi


Resolution: 1.75→8 Å / Cross valid method: FREE R / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.249 350 5 %RANDOM
Rwork0.192 ---
obs-6227 98 %-
Displacement parametersBiso mean: 18.7 Å2
Refinement stepCycle: LAST / Resolution: 1.75→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms481 0 0 38 519
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_deg3.06
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d28.1
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.25
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: 1.75→1.83 Å / Rfactor Rfree error: 0.054
RfactorNum. reflection% reflection
Rfree0.348 41 5 %
Rwork0.29 705 -
obs--99.5 %
Xplor fileSerial no: 1 / Param file: PARAM19X.PRO / Topol file: TOPH19X.PRO
Software
*PLUS
Name: X-PLOR / Version: 3 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 8 Å / Rfactor obs: 0.183
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 18.7 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg28.1
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.25
LS refinement shell
*PLUS
Rfactor Rfree: 0.348 / Rfactor Rwork: 0.29

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