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- PDB-5msi: TYPE III ANTIFREEZE PROTEIN ISOFORM HPLC 12 -

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Basic information

Entry
Database: PDB / ID: 5msi
TitleTYPE III ANTIFREEZE PROTEIN ISOFORM HPLC 12
ComponentsTYPE III ANTIFREEZE PROTEIN ISOFORM HPLC 12
KeywordsANTIFREEZE / ANTIFREEZE POLYPEPTIDE / MUTANT / ICE BINDING PROTEIN / THERMAL HYSTERESIS PROTEIN / GLYCOPROTEIN
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 / ISOMORPHOUS / Resolution: 1.6 Å
AuthorsDeluca, C.I. / Davies, P.L. / Ye, Q. / Jia, Z.
CitationJournal: 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.
History
DepositionSep 17, 1997Processing site: BNL
Revision 1.0Oct 21, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Other
Category: 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 1.4Aug 9, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.5May 22, 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)7,0281
Polymers7,0281
Non-polymers00
Water1,26170
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)32.650, 39.096, 46.260
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: 7028.391 Da / Num. of mol.: 1 / Mutation: A16C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macrozoarces americanus (ocean pout) / Plasmid: PT7-7F-PGP1-2 / Production host: Escherichia coli (E. coli) / Strain (production host): JM 83 / References: UniProt: P19614
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 70 / 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: 2.1 Å3/Da / Density % sol: 30 %
Crystal growpH: 4.5
Details: PROTEIN WAS CRYSTALLIZED IN 50-55% AMMONIUM SULFATE, 0.1 M SODIUM ACETATE PH 4-4.5
PH range: 4-4.5
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: 295 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 26, 1996
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 7177 / % possible obs: 84.5 % / Observed criterion σ(I): 1 / Redundancy: 2.7 % / Rsym value: 0.066 / Net I/σ(I): 17
Reflection shellResolution: 1.6→1.67 Å / Mean I/σ(I) obs: 2.8 / Rsym value: 0.254 / % possible all: 67.9
Reflection
*PLUS
Num. measured all: 19644 / Rmerge(I) obs: 0.062

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Processing

Software
NameVersionClassification
X-PLOR3model building
X-PLOR3refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3phasing
RefinementMethod to determine structure: ISOMORPHOUS
Starting model: 1MSI

1msi


Resolution: 1.6→50 Å / Cross valid method: FREE-R REFINEMENT / σ(F): 1
RfactorNum. reflection% reflectionSelection details
Rfree0.199 -5 %RANDOM
Rwork0.226 ---
obs0.226 19230 96.4 %-
Refinement stepCycle: LAST / Resolution: 1.6→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms485 0 0 82 567
LS refinement shellResolution: 1.6→1.67 Å / Total num. of bins used: 8 / % reflection obs: 93.94 %
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
Lowest resolution: 8 Å / Num. reflection obs: 7177 / Rfactor obs: 0.194 / Rfactor Rfree: 0.268
Solvent computation
*PLUS
Displacement parameters
*PLUS

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