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- PDB-9lhr: Crystal structure of Ice binding protein from Candidatus Cryoseri... -

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Basic information

Entry
Database: PDB / ID: 9lhr
TitleCrystal structure of Ice binding protein from Candidatus Cryosericum odellii SMC5
ComponentsDUF3494 domain-containing protein
KeywordsRECOMBINATION / Ice binding protein / Antifreeze protein / DUF3494 / Ice affinity / Candidatus Cryosericum odellii SMC5
Function / homology
Function and homology information


Large cysteine-rich periplasmic protein OmcB-like, DUF11 domain / : / Domain of unknown function DUF11 / Ice-binding protein / Ice-binding-like / : / S-layer homology domain / PKD domain / S-layer homology domain / S-layer homology (SLH) domain profile. ...Large cysteine-rich periplasmic protein OmcB-like, DUF11 domain / : / Domain of unknown function DUF11 / Ice-binding protein / Ice-binding-like / : / S-layer homology domain / PKD domain / S-layer homology domain / S-layer homology (SLH) domain profile. / Polycystic kidney disease (PKD) domain profile. / PKD domain / PKD domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
DUF3494 domain-containing protein
Similarity search - Component
Biological speciesCandidatus Cryosericum odellii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsHoang, T. / Do, H.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
Other governmentPN 24120 Korea, Republic Of
CitationJournal: Int.J.Biol.Macromol. / Year: 2025
Title: Ice affinity purification system for recombinant proteins using a DUF3494 ice-binding protein.
Authors: Hoang, T. / Nguyen, D.L. / Kim, B. / Choi, W. / Cho, S.M. / Kim, H.W. / Han, S.J. / Kim, K. / Lee, J.H. / Do, H.
History
DepositionJan 13, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 3, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DUF3494 domain-containing protein
B: DUF3494 domain-containing protein
C: DUF3494 domain-containing protein


Theoretical massNumber of molelcules
Total (without water)70,1533
Polymers70,1533
Non-polymers00
Water13,691760
1
A: DUF3494 domain-containing protein


Theoretical massNumber of molelcules
Total (without water)23,3841
Polymers23,3841
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: DUF3494 domain-containing protein


Theoretical massNumber of molelcules
Total (without water)23,3841
Polymers23,3841
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: DUF3494 domain-containing protein


Theoretical massNumber of molelcules
Total (without water)23,3841
Polymers23,3841
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)219.750, 47.560, 66.770
Angle α, β, γ (deg.)90.000, 92.222, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-393-

HOH

21A-488-

HOH

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Components

#1: Protein DUF3494 domain-containing protein / Ice binding domain


Mass: 23384.229 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: The Ice Binding Domain (DUF3494) region was truncated from CoIBP2 (WP_165844303.1)
Source: (gene. exp.) Candidatus Cryosericum odellii (bacteria)
Gene: SMC5_07020, SMC6_06280 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A398D577
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 760 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.32 Å3/Da / Density % sol: 47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M sodium cacodylate pH 5.0, 0.2 M Sodium acetate trihydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Dec 26, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→29.394 Å / Num. obs: 63299 / % possible obs: 98.6 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 25.6
Reflection shellResolution: 1.8→1.84 Å / Rmerge(I) obs: 0.18 / Num. unique obs: 3705

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→29.394 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.941 / SU B: 2.216 / SU ML: 0.07 / Cross valid method: FREE R-VALUE / ESU R: 0.115 / ESU R Free: 0.115
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2051 3189 5.038 %
Rwork0.1631 60109 -
all0.165 --
obs-63298 98.293 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 17.116 Å2
Baniso -1Baniso -2Baniso -3
1-0.002 Å2-0 Å2-0.003 Å2
2---0.001 Å2-0 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.8→29.394 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4802 0 0 760 5562
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0134901
X-RAY DIFFRACTIONr_bond_other_d0.0010.0154613
X-RAY DIFFRACTIONr_angle_refined_deg1.6741.646712
X-RAY DIFFRACTIONr_angle_other_deg1.4331.5710664
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3985670
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.70624.34159
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.07715708
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4159
X-RAY DIFFRACTIONr_chiral_restr0.0840.2712
X-RAY DIFFRACTIONr_gen_planes_refined0.010.025593
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02973
X-RAY DIFFRACTIONr_nbd_refined0.1890.2874
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1910.24185
X-RAY DIFFRACTIONr_nbtor_refined0.1570.22430
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0820.22161
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1320.2506
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1590.26
X-RAY DIFFRACTIONr_nbd_other0.150.241
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1080.227
X-RAY DIFFRACTIONr_mcbond_it1.3741.6822689
X-RAY DIFFRACTIONr_mcbond_other1.3631.6812688
X-RAY DIFFRACTIONr_mcangle_it1.8342.5133356
X-RAY DIFFRACTIONr_mcangle_other1.8342.5143357
X-RAY DIFFRACTIONr_scbond_it1.8711.8282212
X-RAY DIFFRACTIONr_scbond_other1.8711.8292213
X-RAY DIFFRACTIONr_scangle_it2.7772.6853356
X-RAY DIFFRACTIONr_scangle_other2.7762.6853357
X-RAY DIFFRACTIONr_lrange_it4.14221.4935428
X-RAY DIFFRACTIONr_lrange_other3.89720.8525250
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.8470.2592210.1874379X-RAY DIFFRACTION97.1079
1.847-1.8970.2322230.1764289X-RAY DIFFRACTION97.5357
1.897-1.9520.2431980.174155X-RAY DIFFRACTION97.8202
1.952-2.0120.2292120.1654055X-RAY DIFFRACTION97.867
2.012-2.0780.2261890.163975X-RAY DIFFRACTION98.115
2.078-2.1510.2151930.1613807X-RAY DIFFRACTION98.1595
2.151-2.2320.2092050.1593655X-RAY DIFFRACTION98.2688
2.232-2.3240.2041940.1493537X-RAY DIFFRACTION98.3136
2.324-2.4270.1921940.1523397X-RAY DIFFRACTION98.4105
2.427-2.5450.2151750.1513260X-RAY DIFFRACTION98.5936
2.545-2.6830.1841790.1533115X-RAY DIFFRACTION98.7706
2.683-2.8460.2371660.1682944X-RAY DIFFRACTION98.8243
2.846-3.0420.2061830.172758X-RAY DIFFRACTION98.7576
3.042-3.2850.2281410.182583X-RAY DIFFRACTION98.9826
3.285-3.5990.2091290.1862396X-RAY DIFFRACTION98.942
3.599-4.0230.141990.1532204X-RAY DIFFRACTION99.2672
4.023-4.6440.2910.1391940X-RAY DIFFRACTION99.1215
4.644-5.6850.192910.1531638X-RAY DIFFRACTION98.9697
5.685-8.0290.189660.1741299X-RAY DIFFRACTION99.2006
8.029-29.3940.148400.174723X-RAY DIFFRACTION96.2169

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