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- PDB-4nu3: Crystal structure of mFfIBP, a capping head region swapped mutant... -

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Basic information

Entry
Database: PDB / ID: 4nu3
TitleCrystal structure of mFfIBP, a capping head region swapped mutant of ice-binding protein
Componentsice-binding 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: 1.399 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _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

Downloads & links

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Assembly

Deposited unit
A: ice-binding protein
B: ice-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,0867
Polymers52,6792
Non-polymers4075
Water11,187621
1
A: ice-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,5313
Polymers26,3391
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ice-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,5544
Polymers26,3391
Non-polymers2153
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: ice-binding protein
hetero molecules

A: ice-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,0867
Polymers52,6792
Non-polymers4075
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_554x,y,z-11
Buried area1970 Å2
ΔGint-66 kcal/mol
Surface area17000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)31.681, 51.459, 75.230
Angle α, β, γ (deg.)104.41, 96.85, 97.67
Int Tables number1
Space group name H-MP1

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Components

#1: Protein ice-binding protein


Mass: 26339.299 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Flavobacterium frigoris PS1 (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: H7FWB6*PLUS
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 621 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE DATABASE (UNIPROTKB) AT ...THE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE DATABASE (UNIPROTKB) AT THE TIME OF DEPOSITION.

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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: 2.21 Å3/Da / Density % sol: 44.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 30%(w/v) PEG4000, 0.19M ammonium sulfate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 10, 2013
RadiationMonochromator: DCM Si (111) Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.39→49.11 Å / Num. all: 84562 / Num. obs: 78787 / % possible obs: 93.17 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 1.39→1.42 Å / % possible all: 93.3

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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: 4NU2

4nu2


Resolution: 1.399→49.11 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.91 / SU B: 1.243 / SU ML: 0.051 / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R: 0.081 / ESU R Free: 0.081 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25016 4133 5 %RANDOM
Rwork0.22319 ---
obs0.22454 78787 93.17 %-
all-84562 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 9.724 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å20.01 Å2
2--0.01 Å2-0.01 Å2
3----0 Å2
Refinement stepCycle: LAST / Resolution: 1.399→49.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3269 0 21 621 3911
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.023363
X-RAY DIFFRACTIONr_bond_other_d0.0010.023180
X-RAY DIFFRACTIONr_angle_refined_deg2.2341.9524607
X-RAY DIFFRACTIONr_angle_other_deg0.99537299
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9775455
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.12425.495111
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.14615509
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.102158
X-RAY DIFFRACTIONr_chiral_restr0.1410.2575
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.023879
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02725
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_it0.9640.8021817
X-RAY DIFFRACTIONr_mcbond_other0.9630.8021816
X-RAY DIFFRACTIONr_mcangle_it1.4511.2032273
X-RAY DIFFRACTIONr_mcangle_other1.4511.2032274
X-RAY DIFFRACTIONr_scbond_it1.4510.9441546
X-RAY DIFFRACTIONr_scbond_other1.4150.931531
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.0921.3462311
X-RAY DIFFRACTIONr_long_range_B_refined4.5948.5214250
X-RAY DIFFRACTIONr_long_range_B_other4.1247.2663829
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.399→1.435 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.354 255 -
Rwork0.285 4924 -
obs--78.62 %

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