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- PDB-1ame: CRYSTAL STRUCTURE OF TYPE III ANTIFREEZE PROTEIN AT 4 C -

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Basic information

Entry
Database: PDB / ID: 1ame
TitleCRYSTAL STRUCTURE OF TYPE III ANTIFREEZE PROTEIN AT 4 C
ComponentsTYPE III ANTIFREEZE PROTEIN ISOFORM HPLC 12
KeywordsANTIFREEZE PROTEIN / CRYO-CRYSTALLOGRAPHY / COLD-ADAPTATION / CRYSTALLIZATION / FREEZING POINT
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 (ROOM TEMPERATURE STARTING MODEL) / Resolution: 1.65 Å
AuthorsJia, Z. / Leinala, E. / Ye, Q.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 1998
Title: Structure of type III antifreeze protein at 277 K.
Authors: Ye, Q. / Leinala, E. / Jia, Z.
#1: 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.
History
DepositionJun 13, 1997Processing site: BNL
Revision 1.0Jun 17, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 2, 2023Group: Database references / Other / Refinement description
Category: database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site
Revision 1.4May 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)7,0501
Polymers7,0501
Non-polymers00
Water81145
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)32.690, 38.840, 47.510
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


Mass: 7050.310 Da / Num. of mol.: 1 / Mutation: INS(0), 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.: 45 / 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: 2.11 Å3/Da / Density % sol: 31 % / Description: DATA COLLECTED AT 4 DEGREES C
Crystal growTemperature: 277 K / pH: 4.5
Details: 53% AMMONIUM SULFATE 100 MM SODIUM ACETATE PH 4.5 CRYSTALLIZED AT 4 DEGREES C, temperature 277K
Crystal grow
*PLUS
Temperature: 277 K / Method: vapor diffusion, hanging drop
Details: drop was mixed with an equal volume of reservoir solution
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
16 mg/mlprotein1drop
253-55 %ammonium sulfate1reservoir
30.1 Msodium acetate1reservoir

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 1, 1997
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. obs: 6600 / % possible obs: 86.6 % / Observed criterion σ(I): 2 / Redundancy: 4.07 % / Biso Wilson estimate: 17.16 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 15.13
Reflection shellResolution: 1.65→1.71 Å / Redundancy: 4.03 % / Rmerge(I) obs: 0.397 / Mean I/σ(I) obs: 2.29 / % possible all: 85.8
Reflection
*PLUS
Num. measured all: 27105 / Rmerge(I) obs: 0.061
Reflection shell
*PLUS
% possible obs: 85.8 %

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: ISOMORPHOUS (ROOM TEMPERATURE STARTING MODEL)
Starting model: PDB ENTRY 1MSI

1msi


Resolution: 1.65→8 Å / Rfactor Rfree error: 0.0147 / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.282 368 5 %RANDOM
Rwork0.199 ---
obs0.199 6636 86.47 %-
Displacement parametersBiso mean: 16.7 Å2
Refinement stepCycle: LAST / Resolution: 1.65→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms482 0 0 43 525
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.019
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_deg2.718
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d26.97
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.418
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: 1.65→1.72 Å / Rfactor Rfree error: 0.044 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.324 54 5 %
Rwork0.307 670 -
obs--83.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARAM19X.PROTOPH19X.PRO
X-RAY DIFFRACTION2PARAM11.WAT
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26.97
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.418

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