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- PDB-6jk4: Ca2+-dependent type II antifreeze protein -

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Basic information

Entry
Database: PDB / ID: 6jk4
TitleCa2+-dependent type II antifreeze protein
ComponentsType II antifreeze protein
KeywordsANTIFREEZE PROTEIN / C-type lectin / ice-binding protein
Function / homology
Function and homology information


Type-2 ice-structuring protein / : / C-type lectin, conserved site / C-type lectin domain signature. / Mannose-Binding Protein A; Chain A / Mannose-Binding Protein A, subunit A / Lectin C-type domain / C-type lectin domain profile. / C-type lectin-like / C-type lectin (CTL) or carbohydrate-recognition domain (CRD) ...Type-2 ice-structuring protein / : / C-type lectin, conserved site / C-type lectin domain signature. / Mannose-Binding Protein A; Chain A / Mannose-Binding Protein A, subunit A / Lectin C-type domain / C-type lectin domain profile. / C-type lectin-like / C-type lectin (CTL) or carbohydrate-recognition domain (CRD) / C-type lectin-like/link domain superfamily / C-type lectin fold / Roll / Alpha Beta
Similarity search - Domain/homology
Type II antifreeze protein
Similarity search - Component
Biological speciesHypomesus nipponensis (Japanese smelt)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.06 Å
AuthorsArai, T. / Tsuda, S. / Kondo, H. / Nishimiya, Y.
CitationJournal: Biomolecules / Year: 2019
Title: Calcium-Binding Generates the Semi-Clathrate Waters on a Type II Antifreeze Protein to Adsorb onto an Ice Crystal Surface.
Authors: Arai, T. / Nishimiya, Y. / Ohyama, Y. / Kondo, H. / Tsuda, S.
History
DepositionFeb 27, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 26, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 23, 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: Type II antifreeze protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,3612
Polymers15,3211
Non-polymers401
Water5,206289
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-13 kcal/mol
Surface area6580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.952, 65.952, 49.794
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-353-

HOH

21A-475-

HOH

31A-586-

HOH

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Components

#1: Protein Type II antifreeze protein


Mass: 15321.056 Da / Num. of mol.: 1 / Mutation: N12D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hypomesus nipponensis (Japanese smelt) / Plasmid: pPICZalpha / Production host: Komagataella pastoris (fungus) / Strain (production host): X33 / References: UniProt: P84493
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 289 / 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.04 Å3/Da / Density % sol: 39.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 0.1 M sodium acetate, 0.25 M ammonium sulfate, 8% PEG 3350 The Crystal was soaked in crystallizaion solution containing 2mM CaCl2 and pH adjusted to 7.0 before data collection.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: May 29, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.06→21.567 Å / Num. obs: 56672 / % possible obs: 99.7 % / Redundancy: 10.5 % / Rmerge(I) obs: 0.045 / Rrim(I) all: 0.048 / Rsym value: 0.045 / Net I/σ(I): 10.1
Reflection shellResolution: 1.06→1.12 Å / Redundancy: 10.3 % / Rmerge(I) obs: 0.229 / Mean I/σ(I) obs: 3.4 / Num. unique obs: 8207 / Rrim(I) all: 0.241 / Rsym value: 0.229 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
HKL-20001.97.8data reduction
HKL-20001.97.8data scaling
MOLREP7.3.03phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ZIB

2zib


Resolution: 1.06→19.04 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.962 / SU B: 0.324 / SU ML: 0.017 / Cross valid method: THROUGHOUT / ESU R: 0.027 / ESU R Free: 0.029 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17418 2873 5.1 %RANDOM
Rwork0.15401 ---
obs0.15502 53860 99.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 9.774 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å2-0 Å2
3----0 Å2
Refinement stepCycle: 1 / Resolution: 1.06→19.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms983 0 1 289 1273
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0141029
X-RAY DIFFRACTIONr_bond_other_d0.0010.017859
X-RAY DIFFRACTIONr_angle_refined_deg1.9311.6481408
X-RAY DIFFRACTIONr_angle_other_deg2.4531.6452021
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3085127
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.84424.77344
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.00315161
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.983151
X-RAY DIFFRACTIONr_chiral_restr0.120.2137
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.021135
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02209
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9290.708505
X-RAY DIFFRACTIONr_mcbond_other0.9080.707504
X-RAY DIFFRACTIONr_mcangle_it1.3821.068630
X-RAY DIFFRACTIONr_mcangle_other1.3811.068631
X-RAY DIFFRACTIONr_scbond_it1.6670.867524
X-RAY DIFFRACTIONr_scbond_other1.6670.868525
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.3741.252778
X-RAY DIFFRACTIONr_long_range_B_refined4.18111.141339
X-RAY DIFFRACTIONr_long_range_B_other3.5719.5141252
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.06→1.087 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.227 198 -
Rwork0.213 3944 -
obs--100 %

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