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- PDB-1gzi: CRYSTAL STRUCTURE OF TYPE III ANTIFREEZE PROTEIN FROM OCEAN POUT,... -

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Basic information

Entry
Database: PDB / ID: 1gzi
TitleCRYSTAL STRUCTURE OF TYPE III ANTIFREEZE PROTEIN FROM OCEAN POUT, AT 1.8 ANGSTROM RESOLUTION
ComponentsHPLC-12 TYPE III ANTIFREEZE PROTEIN
KeywordsICE-BINDING PROTEIN / ANTIFREEZE PROTEIN / OCEAN POUT / GLYCOPROTEIN / MACROZOARCES AMERICANUS / MULTIGENE FAMILY
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 / MIR / Resolution: 1.8 Å
AuthorsAntson, A.A. / Lewis, S. / Roper, D.I. / Smith, D.J. / Hubbard, R.E.
Citation
Journal: To be Published
Title: The Structure of Type III Antifreeze Protein from Ocean Pout
Authors: Antson, A.A. / Lewis, S. / Roper, D.I. / Smith, D.J. / Hubbard, R.E.
#1: 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.
#2: 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.
History
DepositionOct 25, 1996Processing site: BNL
Revision 1.0Sep 17, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 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 1.4Feb 7, 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: HPLC-12 TYPE III ANTIFREEZE PROTEIN


Theoretical massNumber of molelcules
Total (without water)6,9081
Polymers6,9081
Non-polymers00
Water97354
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)32.550, 39.300, 45.520
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 HPLC-12 TYPE III ANTIFREEZE PROTEIN


Mass: 6908.155 Da / Num. of mol.: 1 / Mutation: P64A, P65A, DEL(A66)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macrozoarces americanus (ocean pout) / Tissue: BLOOD SERUM / Cell line: BL21 / Gene: RECOMBINANT TYPE III AFP HPLC / Organ: BLOOD / Variant: HPLC-12 COMPONENT / Plasmid: PET22B / Species (production host): Escherichia coli
Gene (production host): RECOMBINANT TYPE III AFP HPLC FRACTION 12
Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P19614
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 54 / 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: 2.06 Å3/Da / Density % sol: 39.8 %
Crystal growpH: 5.6 / Details: 50% AMMONIUM SULFATE, 0.1M SODIUM ACETATE, PH 5.6

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 18, 1996
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→15 Å / Num. obs: 5155 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 21.2 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 6.3
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.208 / Mean I/σ(I) obs: 3.2 / % possible all: 100

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Processing

Software
NameClassification
CCP4model building
REFMACrefinement
DENZOdata reduction
CCP4data scaling
CCP4phasing
RefinementMethod to determine structure: MIR / Resolution: 1.8→15 Å / σ(F): 0
Details: THE FOLLOWING RESIDUES WERE MODELED IN TWO CONFORMATIONS: VAL A 20 - SIDE CHAIN ATOMS. SER A 42 - TWO CONFORMATIONS FOR THE SIDE CHAIN HYDROXYL.
RfactorNum. reflection% reflectionSelection details
Rfree0.233 -9.7 %RANDOM
Rwork0.174 ---
obs-5709 99.7 %-
Displacement parametersBiso mean: 25.3 Å2
Refinement stepCycle: LAST / Resolution: 1.8→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms483 0 0 54 537
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0110.02
X-RAY DIFFRACTIONp_angle_d0.0290.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0350.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.352
X-RAY DIFFRACTIONp_mcangle_it2.022.5
X-RAY DIFFRACTIONp_scbond_it4.014
X-RAY DIFFRACTIONp_scangle_it6.026
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr0.1720.2
X-RAY DIFFRACTIONp_singtor_nbd0.190.3
X-RAY DIFFRACTIONp_multtor_nbd0.2550.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor5.17
X-RAY DIFFRACTIONp_staggered_tor17.615
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor7.225
X-RAY DIFFRACTIONp_special_tor

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