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- PDB-1hg7: High resolution structure of HPLC-12 type III antifreeze protein ... -

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Basic information

Entry
Database: PDB / ID: 1hg7
TitleHigh resolution structure of HPLC-12 type III antifreeze protein from Ocean Pout Macrozoarces americanus
ComponentsHPLC-12 TYPE III ANTIFREEZE PROTEIN
KeywordsANTIFREEZE PROTEIN / OCEAN POUT / MACROZOARCES AMERICANUS / ICE-BINDING 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.15 Å
AuthorsAntson, A.A. / Smith, D.J. / Roper, D.I. / Lewis, S. / Caves, L.S.D. / Verma, C.S. / Buckley, S.L. / Lillford, P.J. / Hubbard, R.E.
CitationJournal: J.Mol.Biol. / Year: 2001
Title: Understanding the Mechanism of Ice Binding by Type III Antifreeze Protein
Authors: Antson, A.A. / Smith, D.J. / Roper, D.I. / Lewis, S. / Caves, L.S.D. / Verma, C.S. / Buckley, S.L. / Lillford, P.J. / Hubbard, R.E.
History
DepositionDec 13, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 31, 2001Provider: repository / Type: Initial release
Revision 1.1Dec 7, 2011Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Version format compliance
Revision 1.2Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HPLC-12 TYPE III ANTIFREEZE PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,1352
Polymers7,0391
Non-polymers961
Water2,774154
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)32.218, 39.127, 44.694
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: 7039.351 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MACROZOARCES AMERICANUS (ocean pout) / Tissue: BLOOD SERUM / Gene: RECOMBINANT TYPE III AFP HPURCE 10 FRACTION 12 / Variant: HPLC-12 COMPONENT / Plasmid: PET22B
Gene (production host): RECOMBINANT TYPE III AFP HPURCE 10 FRACTION 12
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P19614
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 154 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCHAIN A ENGINEERED MUTATION PRO64ALA, PRO65ALA, ALA66 DELETION MUTATNT ANTIFREEZE PROTEINS LOWER ...CHAIN A ENGINEERED MUTATION PRO64ALA, PRO65ALA, ALA66 DELETION MUTATNT ANTIFREEZE PROTEINS LOWER THE BLOOD FREEZING POINT BY DISRUPTING THE ICE STRUCTURE

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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: 4.6 / Details: 50% AMMONIUM SULFATE, 0.1M SODIUM ACETATE, PH 4.6
Crystal
*PLUS
Density % sol: 40.2 %
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, hanging drop / PH range low: 5 / PH range high: 4.6
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 mg/mlprotein1drop
245 %(w/v)ammonium sulfate1reservoir
30.1 Msodium acetate1reservoir

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 0.91
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 15, 1996
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91 Å / Relative weight: 1
ReflectionResolution: 1.15→45 Å / Num. obs: 20883 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 6.7 % / Rmerge(I) obs: 0.108 / Net I/σ(I): 5.2
Reflection shellResolution: 1.15→1.17 Å / Redundancy: 5 % / Rmerge(I) obs: 0.493 / Mean I/σ(I) obs: 3.7 / % possible all: 100
Reflection
*PLUS
Lowest resolution: 45 Å
Reflection shell
*PLUS
% possible obs: 100 %

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Processing

Software
NameClassification
SHELXL-97refinement
DENZOdata reduction
CCP4data scaling
SHELXLphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GZI

1gzi


Resolution: 1.15→40 Å / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.169 -10 %
all0.12 20679 -
obs0.12 --
Refinement stepCycle: LAST / Resolution: 1.15→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms488 0 5 154 647
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.015
X-RAY DIFFRACTIONs_angle_d0.031
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes
X-RAY DIFFRACTIONs_zero_chiral_vol
X-RAY DIFFRACTIONs_non_zero_chiral_vol
X-RAY DIFFRACTIONs_anti_bump_dis_restr
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt
X-RAY DIFFRACTIONs_similar_adp_cmpnt
X-RAY DIFFRACTIONs_approx_iso_adps
Software
*PLUS
Name: SHELXL / Classification: refinement
Refinement
*PLUS
σ(F): 4 / Num. reflection Rfree: 2066 / Rfactor all: 0.12 / Rfactor obs: 0.104 / Rfactor Rwork: 0.12
Solvent computation
*PLUS
Displacement parameters
*PLUS

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