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- PDB-1wfb: WINTER FLOUNDER ANTIFREEZE PROTEIN ISOFORM HPLC6 AT-180 DEGREES C -

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Basic information

Entry
Database: PDB / ID: 1wfb
TitleWINTER FLOUNDER ANTIFREEZE PROTEIN ISOFORM HPLC6 AT-180 DEGREES C
ComponentsANTIFREEZE PROTEIN ISOFORM HPLC6
KeywordsANTIFREEZE POLYPEPTIDE / ICE BINDING PROTEIN / THERMAL HYSTERESIS PROTEIN
Function / homologyantifreeze activity / Antifreeze protein, type I / ice binding / extracellular space / identical protein binding / Ice-structuring protein A
Function and homology information
Biological speciesPseudopleuronectes americanus (winter flounder)
MethodX-RAY DIFFRACTION / Resolution: 1.5 Å
AuthorsYang, D.S.C. / Sicheri, F.
Citation
Journal: Nature / Year: 1995
Title: Ice-binding structure and mechanism of an antifreeze protein from winter flounder.
Authors: Sicheri, F. / Yang, D.S.
#1: Journal: To be Published
Title: Structure Determination of an Antifreeze Protein from Winter Flounder
Authors: Sicheri, F. / Yang, D.S.C.
History
DepositionApr 3, 1995Processing site: BNL
Revision 1.0Jun 3, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_conn / struct_site
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_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ANTIFREEZE PROTEIN ISOFORM HPLC6
B: ANTIFREEZE PROTEIN ISOFORM HPLC6


Theoretical massNumber of molelcules
Total (without water)6,4852
Polymers6,4852
Non-polymers00
Water2,342130
1
A: ANTIFREEZE PROTEIN ISOFORM HPLC6


Theoretical massNumber of molelcules
Total (without water)3,2421
Polymers3,2421
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ANTIFREEZE PROTEIN ISOFORM HPLC6


Theoretical massNumber of molelcules
Total (without water)3,2421
Polymers3,2421
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.409, 36.543, 21.360
Angle α, β, γ (deg.)90.00, 103.36, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein/peptide ANTIFREEZE PROTEIN ISOFORM HPLC6


Mass: 3242.490 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudopleuronectes americanus (winter flounder)
References: UniProt: P04002
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 130 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.19 Å3/Da / Density % sol: 43.85 %
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7.3 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
24 mg/mlprotein11
320 mMTris-HCl11
1acetone11

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Data collection

Diffraction sourceWavelength: 1.54
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Jul 1, 1993
RadiationScattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionNum. obs: 8329 / % possible obs: 89.2 % / Observed criterion σ(I): 1 / Redundancy: 3.4 % / Rmerge(I) obs: 0.054
Reflection
*PLUS
Highest resolution: 1.5 Å / Lowest resolution: 40 Å / Num. measured all: 28251 / Rmerge(I) obs: 0.054

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
RIGAKUdata reduction
X-PLORphasing
RefinementResolution: 1.5→8 Å / σ(F): 1
RfactorNum. reflection% reflection
Rfree0.196 --
Rwork0.177 --
obs0.177 8218 83.8 %
Refinement stepCycle: LAST / Resolution: 1.5→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms566 0 0 390 956
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
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_deg1.8
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
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
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 19.1 Å2

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