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- PDB-6ame: TYPE III ANTIFREEZE PROTEIN ISOFORM HPLC 12 M21A -

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Basic information

Entry
Database: PDB / ID: 6ame
TitleTYPE III ANTIFREEZE PROTEIN ISOFORM HPLC 12 M21A
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: 2.1 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 24, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Apr 29, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 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 1.4Sep 20, 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

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Assembly

Deposited unit
A: PROTEIN (ANTIFREEZE PROTEIN TYPE III)


Theoretical massNumber of molelcules
Total (without water)6,9191
Polymers6,9191
Non-polymers00
Water1,29772
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)32.592, 39.525, 45.932
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: 6919.115 Da / Num. of mol.: 1 / Mutation: M21A, 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.: 72 / 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: 2.14 Å3/Da / Density % sol: 42.42 %
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: 2.1→50 Å / Num. obs: 3554 / % possible obs: 94.7 % / Observed criterion σ(I): 1 / Redundancy: 3.6 % / Rsym value: 0.075 / Net I/σ(I): 15.9
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 7.2 / Rsym value: 0.155 / % possible all: 91.5
Reflection
*PLUS
Num. measured all: 11961 / Rmerge(I) obs: 0.075

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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: 2.1→8 Å / Rfactor Rfree error: 0.017 / Cross valid method: FREE R / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.237 190 5 %RANDOM
Rwork0.171 ---
obs-3530 94.9 %-
Displacement parametersBiso mean: 14.4 Å2
Refinement stepCycle: LAST / Resolution: 2.1→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms580 0 0 216 796
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.016
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_deg2.92
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d27.66
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.37
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: 2.1→2.19 Å / Rfactor Rfree error: 0.04
RfactorNum. reflection% reflection
Rfree0.193 22 5 %
Rwork0.194 376 -
obs--89.7 %
Xplor fileSerial no: 1 / Param file: PARAM19X.PRO / Topol file: TOPH19X.PRO
Software
*PLUS
Name: X-PLOR / Version: 3 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 8 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.166
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 14.4 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg27.66
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.37
LS refinement shell
*PLUS
Highest resolution: 2.1 Å / Rfactor Rfree: 0.193 / % reflection Rfree: 5 % / Rfactor Rwork: 0.194

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