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Basic information

Entry
Database: PDB / ID: 5uyt
TitleCrystal structure of ice binding protein from an Antarctic bacterium Flavobacteriaceae
ComponentsIce-binding protein
KeywordsANTIFREEZE PROTEIN / ice binding protein / right-handed beta-helix / beta-solenoid
Function / homologyIce-binding protein / Ice-binding-like / Secretion system C-terminal sorting domain / Secretion system C-terminal sorting domain / NITRATE ION / Ice-binding protein
Function and homology information
Biological speciesFlavobacteriaceae bacterium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsWang, C. / Pakhomova, S. / Newcomer, M.E. / Christner, B.C. / Luo, B.-H.
CitationJournal: PLoS ONE / Year: 2017
Title: Structural basis of antifreeze activity of a bacterial multi-domain antifreeze protein.
Authors: Wang, C. / Pakhomova, S. / Newcomer, M.E. / Christner, B.C. / Luo, B.H.
History
DepositionFeb 24, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 25, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_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)105,6323
Polymers105,5702
Non-polymers621
Water12,322684
1
A: Ice-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,8472
Polymers52,7851
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Ice-binding protein


Theoretical massNumber of molelcules
Total (without water)52,7851
Polymers52,7851
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)119.826, 119.826, 367.764
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-978-

HOH

21A-980-

HOH

31A-1042-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: GLN / Beg label comp-ID: GLN / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: _ / Auth seq-ID: 23 - 444 / Label seq-ID: 2 - 423

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Ice-binding protein


Mass: 52785.129 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: A bacterial antifreeze protein / Source: (gene. exp.) Flavobacteriaceae bacterium (bacteria) / Strain: 3519-10 / Gene: FIC_00493 / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: B3GGB1
#2: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 684 / 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: 2.35 Å3/Da / Density % sol: 47.57 %
Crystal growTemperature: 295 K / Method: vapor diffusion / Details: 15-20% PEG 3350, 0.2 M ammonium nitrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Apr 2, 2012 / Details: Oxford Danfysik toroidal focusing mirror
RadiationMonochromator: Si(111) channel cut monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.75→36.08 Å / Num. obs: 101962 / % possible obs: 99.9 % / Redundancy: 8.6 % / Biso Wilson estimate: 20.6 Å2 / Rsym value: 0.09 / Net I/σ(I): 29.1
Reflection shellResolution: 1.75→1.81 Å / Redundancy: 8.5 % / Mean I/σ(I) obs: 3.2 / Num. unique obs: 10103 / Rsym value: 0.732 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→36.08 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.952 / SU B: 3.674 / SU ML: 0.062 / Cross valid method: THROUGHOUT / ESU R: 0.09 / ESU R Free: 0.087 / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.19051 2071 2 %RANDOM
Rwork0.16846 ---
obs0.16892 99891 99.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 28.613 Å2
Baniso -1Baniso -2Baniso -3
1--0.12 Å2-0.06 Å20 Å2
2---0.12 Å20 Å2
3---0.39 Å2
Refinement stepCycle: 1 / Resolution: 1.75→36.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5991 0 4 684 6679
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.026135
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4571.9498424
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5395863
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.5126.697218
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.3815886
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.182158
X-RAY DIFFRACTIONr_chiral_restr0.1010.21076
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214580
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.5321.1243404
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.7991.6814256
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.91.1922730
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined5.58710.9859670
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 619 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.1 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.751→1.796 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.25 135 -
Rwork0.235 7046 -
obs--95.59 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.71330.29820.64192.0622-0.25482.6636-0.18950.29870.4-0.18610.03130.1611-0.2419-0.02120.15820.15850.0059-0.07860.17840.12560.1782-6.925728.267561.8869
21.55920.53450.88092.72210.10460.9614-0.12680.58860.275-0.5921-0.03680.358-0.16440.13180.16360.30960.0399-0.08940.41590.09870.1536-12.696120.812746.5775
31.7547-0.01180.01871.49980.38781.0674-0.03190.33030.0411-0.2145-0.0390.2289-0.0581-0.00080.07090.15980.0446-0.08060.23670.05780.1473-15.641417.531354.6161
40.7323-0.01970.03580.7146-0.37111.8692-0.02360.1050.141-0.023-0.1017-0.165-0.18570.22090.12530.0432-0.0171-0.00060.08350.03780.108219.296813.468386.5496
51.0187-0.1982-0.01420.6942-0.3312.1225-0.03860.15040.1617-0.034-0.0354-0.0421-0.05590.03340.07390.0515-0.0137-0.01490.04910.03840.08215.219518.443179.5289
62.61040.2356-0.57232.8401-0.0414.1045-0.07180.18210.1536-0.0494-0.0671-0.24210.01120.310.13890.0208-0.005-0.00720.06470.03890.068715.160910.971887.9011
72.0386-0.74840.62421.98530.55062.8547-0.1189-0.28110.27330.36830.0893-0.207-0.1680.07030.02960.29940.0149-0.11680.2641-0.1320.159319.481123.0283146.8448
81.40180.41421.04462.7908-0.10331.84530.064-0.6301-0.26240.75020.0683-0.29840.2087-0.0343-0.13230.61520.0731-0.17280.65830.07850.141920.85733.7615161.5573
91.7586-0.00980.32431.2315-0.02841.85850.0167-0.3201-0.07220.37410.0355-0.21880.14580.1-0.05220.35620.0432-0.15890.3336-0.08140.13223.08579.6362150.897
101.00510.13840.13310.8680.52510.6759-0.0039-0.16760.15860.1156-0.05040.0673-0.035-0.06490.05440.1106-0.00310.02550.0491-0.04110.0714-7.177321.6244122.6982
110.7086-0.26810.17610.88480.29631.9096-0.0325-0.15450.06230.16710.0253-0.02330.04490.02840.00720.10860.0026-0.00640.0778-0.04370.06613.486917.4882126.7107
121.4385-0.6791-0.79993.23770.46173.22-0.0736-0.13540.0890.1721-0.02220.11040.048-0.15670.09580.0546-0.0005-0.0080.0604-0.03650.0603-8.291616.4544119.2628
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A23 - 71
2X-RAY DIFFRACTION2A72 - 117
3X-RAY DIFFRACTION3A118 - 223
4X-RAY DIFFRACTION4A224 - 308
5X-RAY DIFFRACTION5A309 - 419
6X-RAY DIFFRACTION6A420 - 445
7X-RAY DIFFRACTION7B23 - 86
8X-RAY DIFFRACTION8B87 - 141
9X-RAY DIFFRACTION9B142 - 222
10X-RAY DIFFRACTION10B223 - 323
11X-RAY DIFFRACTION11B324 - 418
12X-RAY DIFFRACTION12B419 - 446

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