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- PDB-4nu2: Crystal structure of an ice-binding protein (FfIBP) from the Anta... -

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Basic information

Entry
Database: PDB / ID: 4nu2
TitleCrystal structure of an ice-binding protein (FfIBP) from the Antarctic bacterium, Flavobacterium frigoris PS1
ComponentsAntifreeze protein
KeywordsANTIFREEZE PROTEIN / Beta-helical / antifreeze activity / ice crystal
Function / homologyIce-binding protein / Ice-binding-like / extracellular region / Ice-binding protein
Function and homology information
Biological speciesFlavobacterium frigoris PS1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsDo, H. / Kim, S.J. / Lee, S.G. / Park, H. / Kim, H.J. / Lee, J.H.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Structure-based characterization and antifreeze properties of a hyperactive ice-binding protein from the Antarctic bacterium Flavobacterium frigoris PS1
Authors: Do, H. / Kim, S.J. / Kim, H.J. / Lee, J.H.
History
DepositionDec 3, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 16, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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 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


Theoretical massNumber of molelcules
Total (without water)25,4621
Polymers25,4621
Non-polymers00
Water1,02757
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)69.171, 69.171, 178.764
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number91
Space group name H-MP4122

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Components

#1: Protein Antifreeze protein


Mass: 25461.578 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Flavobacterium frigoris PS1 (bacteria) / Gene: HJ01_03463 / Production host: Escherichia coli (E. coli) / References: UniProt: H7FWB6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / 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: 4.2 Å3/Da / Density % sol: 70.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.4
Details: 0.1M sodium acetate, 3M sodium chloride, pH 4.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 6, 2012
RadiationMonochromator: DCM Si (111) Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.1→37.81 Å / Num. all: 25048 / Num. obs: 24497 / % possible obs: 97.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 2.1→2.14 Å / % possible all: 99.1

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.8.0049refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3UYU

3uyu


Resolution: 2.1→37.81 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.939 / SU B: 3.741 / SU ML: 0.097 / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R: 0.134 / ESU R Free: 0.132 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23901 1309 5.1 %RANDOM
Rwork0.20848 ---
all0.2193 25048 --
obs0.21005 24497 97.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.85 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0 Å20 Å2
2---0.01 Å20 Å2
3---0.03 Å2
Refinement stepCycle: LAST / Resolution: 2.1→37.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1554 0 0 57 1611
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.021585
X-RAY DIFFRACTIONr_bond_other_d0.0010.021538
X-RAY DIFFRACTIONr_angle_refined_deg2.0471.9482164
X-RAY DIFFRACTIONr_angle_other_deg0.9733528
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5825217
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.29325.96252
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.07915252
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.66154
X-RAY DIFFRACTIONr_chiral_restr0.1290.2272
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021831
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02335
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_it4.1513.984868
X-RAY DIFFRACTIONr_mcbond_other4.1273.979867
X-RAY DIFFRACTIONr_mcangle_it4.8645.9231085
X-RAY DIFFRACTIONr_mcangle_other4.8795.9281086
X-RAY DIFFRACTIONr_scbond_it4.7294.363717
X-RAY DIFFRACTIONr_scbond_other4.7264.367718
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.8056.3751080
X-RAY DIFFRACTIONr_long_range_B_refined7.43832.0671697
X-RAY DIFFRACTIONr_long_range_B_other7.41432.0621693
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.151 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.313 80 -
Rwork0.281 1759 -
obs--96.89 %

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