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- PDB-6bg8: Shewanella frigidimarina ice-binding protein_1 DUF3494 Domain -

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Basic information

Entry
Database: PDB / ID: 6bg8
TitleShewanella frigidimarina ice-binding protein_1 DUF3494 Domain
ComponentsIg domain protein, group 2 domain protein
KeywordsANTIFREEZE PROTEIN / Ice Adhesin / DUF3494 Domain / C-terminal Domain
Function / homology
Function and homology information


cell outer membrane
Similarity search - Function
Ice-binding protein / Ice-binding-like / Bacterial Ig-like domain (group 2) / Invasin/intimin cell-adhesion fragments / Bacterial Ig-like domain 2 / Bacterial Ig-like domain, group 2 / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
PHOSPHATE ION / Ice-binding protein 1
Similarity search - Component
Biological speciesShewanella frigidimarina (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.59712947109 Å
AuthorsVance, T.D.R. / Davies, P.L.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)353755 Canada
CitationJournal: FEBS J. / Year: 2018
Title: An ice-binding and tandem beta-sandwich domain-containing protein in Shewanella frigidimarina is a potential new type of ice adhesin.
Authors: Vance, T.D.R. / Graham, L.A. / Davies, P.L.
History
DepositionOct 27, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 7, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 14, 2018Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2May 2, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 2.0Feb 20, 2019Group: Atomic model / Author supporting evidence ...Atomic model / Author supporting evidence / Data collection / Derived calculations
Category: atom_site / pdbx_audit_support ...atom_site / pdbx_audit_support / pdbx_nonpoly_scheme / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_audit_support.funding_organization / _pdbx_nonpoly_scheme.auth_seq_num / _struct_site.details / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id / _struct_site.pdbx_num_residues
Revision 2.1Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.2Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ig domain protein, group 2 domain protein
B: Ig domain protein, group 2 domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,53213
Polymers51,6152
Non-polymers91711
Water13,980776
1
A: Ig domain protein, group 2 domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2547
Polymers25,8081
Non-polymers4466
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ig domain protein, group 2 domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2796
Polymers25,8081
Non-polymers4715
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Ig domain protein, group 2 domain protein
hetero molecules

B: Ig domain protein, group 2 domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,53213
Polymers51,6152
Non-polymers91711
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,y-1/2,-z1
Buried area2450 Å2
ΔGint-85 kcal/mol
Surface area18660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.288, 80.278, 72.736
Angle α, β, γ (deg.)90.000, 105.519, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Ig domain protein, group 2 domain protein


Mass: 25807.529 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Density for C-terminal His tag was too unreliable to model.
Source: (gene. exp.) Shewanella frigidimarina (strain NCIMB 400) (bacteria)
Strain: NCIMB 400 / Gene: Sfri_1018 / Production host: Escherichia coli (E. coli) / References: UniProt: Q086E4

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Non-polymers , 5 types, 787 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 776 / 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: 2.5 Å3/Da / Density % sol: 50.88 %
Crystal growTemperature: 277.15 K / Method: microbatch / Details: 2.4 M Ammonium Sulfate, 0.1 M citric acid (pH 5)

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Data collection

DiffractionMean temperature: 101.2 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 0.98 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: May 27, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.597→42.67334 Å / Num. obs: 64562 / % possible obs: 99.14 % / Redundancy: 3.8 % / Biso Wilson estimate: 8.72197289856 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.1775 / Net I/σ(I): 5.94

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Phyre2 Model

Resolution: 1.59712947109→42.6733383803 Å / SU ML: 0.181687045676 / Cross valid method: FREE R-VALUE / σ(F): 1.34762305288 / Phase error: 25.3923917528
RfactorNum. reflection% reflection
Rfree0.216840600662 2010 3.11768081773 %
Rwork0.184375182423 --
obs0.185402565195 64471 99.1388722302 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 11.6712645205 Å2
Refinement stepCycle: LAST / Resolution: 1.59712947109→42.6733383803 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3497 0 51 776 4324
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005318648851993673
X-RAY DIFFRACTIONf_angle_d0.8345231307425039
X-RAY DIFFRACTIONf_chiral_restr0.0562346199529593
X-RAY DIFFRACTIONf_plane_restr0.00502863734331664
X-RAY DIFFRACTIONf_dihedral_angle_d6.611962954862840
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5971-1.63710.3290714552781290.3179651938134178X-RAY DIFFRACTION92.0889459055
1.6371-1.68130.2970702809741480.2799386028014424X-RAY DIFFRACTION99.7382198953
1.6813-1.73080.290057782291450.2469090161124478X-RAY DIFFRACTION99.6336206897
1.7308-1.78670.2482832784491430.2361115949724475X-RAY DIFFRACTION99.7408207343
1.7867-1.85050.2178250249841480.2146689397564461X-RAY DIFFRACTION99.7403159489
1.8505-1.92460.2639546290081430.2038041316024471X-RAY DIFFRACTION99.41822883
1.9246-2.01220.2075913102971430.1860794017254479X-RAY DIFFRACTION99.741044454
2.0122-2.11830.2305921344121420.1789673289964454X-RAY DIFFRACTION99.6314762627
2.1183-2.2510.2095054742431420.1753199449154469X-RAY DIFFRACTION99.7188581315
2.251-2.42480.2160684062131450.1677188213294511X-RAY DIFFRACTION99.807073955
2.4248-2.66880.2248832375711480.1735254164074474X-RAY DIFFRACTION99.8272138229
2.6688-3.05490.2119543232731430.1610820901024503X-RAY DIFFRACTION99.7637964355
3.0549-3.84840.1584421012131410.1475094101354517X-RAY DIFFRACTION99.8285469353
3.8484-42.68860.1809094666641500.1503231883324567X-RAY DIFFRACTION99.3261739314

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