PDB-9li0: Crystal structure of engineered ice-binding protein (M74I and A97...

ID or keywords:

Entry

Database: PDB / ID: 9li0

Title

Crystal structure of engineered ice-binding protein (M74I and A97V) from Candidatus Cryosericum odellii strain SMC5_169

Components

DUF3494 domain-containing protein

Keywords

PROTEIN BINDING / Ice binding protein / Antifreeze protein / DUF3494 / Ice affinity / Candidatus Cryosericum odellii SMC5

Function / homology

Ice-binding protein / Ice-binding-like / DUF3494 domain-containing protein

Function and homology information

Biological species

Candidatus Cryosericum odellii (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.453 Å

Authors

Hoang, T. / Do, H.

Funding support

Korea, Republic Of, 1items

Citation

Journal: 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

Deposition	Jan 13, 2025	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Sep 3, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9li0.cif.gz	105 KB	Display	PDBx/mmCIF format
PDB format	pdb9li0.ent.gz	75.1 KB	Display	PDB format
PDBx/mmJSON format	9li0.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9li0_validation.pdf.gz	421.2 KB	Display	wwPDB validaton report
Full document	9li0_full_validation.pdf.gz	422.3 KB	Display
Data in XML	9li0_validation.xml.gz	24.9 KB	Display
Data in CIF	9li0_validation.cif.gz	36.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/li/9li0 ftp://data.pdbj.org/pub/pdb/validation_reports/li/9li0	HTTPS FTP

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Related structure data

Related structure data	9lhnC 9lhrC 9lhsC C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#120 - Dec 2009 Antifreeze Proteins similarity (1)

Deposited unit

A: DUF3494 domain-containing protein

B: DUF3494 domain-containing protein

45.1 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: DUF3494 domain-containing protein

defined by author
Evidence: gel filtration
22.6 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: DUF3494 domain-containing protein

defined by author
22.6 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	31.150, 61.920, 92.540
Angle α, β, γ (deg.)	90.000, 94.260, 90.000
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	DUF3494 domain-containing protein / Ice binding domain Mass: 22573.094 Da / Num. of mol.: 2 / Mutation: M74I,A97V Source method: isolated from a genetically manipulated source Details: CoIBP1 (WP_119120131.1) with M74I and A97V mutations Source: (gene. exp.) Candidatus Cryosericum odellii (bacteria) Gene: SMC6_07610 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A398CWR6
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 482 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	N

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 1.97 Å³/Da / Density % sol: 37.61 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 90% of precipitant (35% PEG 2000 MME), 10% of mixture(6 M Ammonium nitrate, 0.1M Tris pH 8.5)

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1 Å
Detector	Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: May 22, 2024
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.453→29.352 Å / Num. obs: 61537 / % possible obs: 99.51 % / Redundancy: 6.6 % / CC_1/2: 0.999 / R_merge(I) obs: 0.03924 / R_pim(I) all: 0.01636 / Net I/σ(I): 28.83
Reflection shell	Resolution: 1.453→1.505 Å / Redundancy: 5.6 % / R_merge(I) obs: 0.1599 / Mean I/σ(I) obs: 8.53 / Num. unique obs: 5966 / CC_1/2: 0.988 / R_pim(I) all: 0.07278 / % possible all: 96.95

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0267	refinement
XDS		data reduction
XDS		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.453→29.352 Å / Cor.coef. F_o:F_c: 0.967 / Cor.coef. F_o:F_c free: 0.955 / SU B: 1.024 / SU ML: 0.04 / Cross valid method: FREE R-VALUE / ESU R: 0.065 / ESU R Free: 0.067
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.1816	3077	5 %
R_work	0.1535	58460	-
all	0.155	-	-
obs	-	61537	99.521 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 10.438 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.001 Å²	-0 Å²	-0.001 Å²
2-	-	-0.001 Å²	-0 Å²
3-	-	-	0 Å²

Refinement step

Cycle: LAST / Resolution: 1.453→29.352 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3117	0	0	482	3599

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.014	0.013	3169
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.015	2978
X-RAY DIFFRACTION	r_angle_refined_deg	1.839	1.634	4361
X-RAY DIFFRACTION	r_angle_other_deg	1.602	1.563	6830
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.545	5	446
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	42.501	26.042	96
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	9.617	15	425
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	15.454	15	2
X-RAY DIFFRACTION	r_chiral_restr	0.093	0.2	490
X-RAY DIFFRACTION	r_gen_planes_refined	0.012	0.02	3710
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	654
X-RAY DIFFRACTION	r_nbd_refined	0.212	0.2	546
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.191	0.2	2742
X-RAY DIFFRACTION	r_nbtor_refined	0.164	0.2	1617
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.088	0.2	1540
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.114	0.2	256
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.291	0.2	19
X-RAY DIFFRACTION	r_nbd_other	0.211	0.2	60
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.168	0.2	40
X-RAY DIFFRACTION	r_mcbond_it	0.951	0.988	1790
X-RAY DIFFRACTION	r_mcbond_other	0.951	0.987	1789
X-RAY DIFFRACTION	r_mcangle_it	1.357	1.484	2234
X-RAY DIFFRACTION	r_mcangle_other	1.357	1.485	2235
X-RAY DIFFRACTION	r_scbond_it	1.607	1.08	1379
X-RAY DIFFRACTION	r_scbond_other	1.601	1.08	1379
X-RAY DIFFRACTION	r_scangle_it	2.256	1.581	2127
X-RAY DIFFRACTION	r_scangle_other	2.258	1.582	2128
X-RAY DIFFRACTION	r_lrange_it	3.529	13.393	3425
X-RAY DIFFRACTION	r_lrange_other	3.313	12.815	3325

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
1.453-1.491	0.237	220	0.2	4183	0.202	4577	0.936	0.94	96.1984	0.166
1.491-1.532	0.221	218	0.176	4139	0.178	4392	0.94	0.948	99.2031	0.149
1.532-1.576	0.204	215	0.162	4093	0.164	4329	0.948	0.955	99.5149	0.141
1.576-1.624	0.198	209	0.161	3973	0.163	4195	0.942	0.954	99.6901	0.141
1.624-1.677	0.218	201	0.163	3812	0.166	4023	0.94	0.952	99.7514	0.145
1.677-1.736	0.184	197	0.154	3751	0.155	3954	0.953	0.957	99.8483	0.139
1.736-1.801	0.201	188	0.155	3564	0.157	3754	0.944	0.957	99.9467	0.142
1.801-1.875	0.188	184	0.153	3490	0.154	3675	0.954	0.961	99.9728	0.142
1.875-1.958	0.175	175	0.151	3341	0.153	3519	0.955	0.962	99.9147	0.146
1.958-2.053	0.176	166	0.154	3154	0.155	3321	0.962	0.968	99.9699	0.152
2.053-2.163	0.168	159	0.145	3020	0.146	3181	0.965	0.971	99.9371	0.146
2.163-2.294	0.162	152	0.138	2880	0.14	3032	0.961	0.97	100	0.143
2.294-2.451	0.185	142	0.138	2697	0.14	2840	0.959	0.968	99.9648	0.144
2.451-2.646	0.175	132	0.143	2519	0.145	2652	0.962	0.966	99.9623	0.153
2.646-2.896	0.186	123	0.146	2325	0.148	2450	0.955	0.966	99.9184	0.159
2.896-3.234	0.177	110	0.154	2084	0.155	2196	0.956	0.965	99.9089	0.17
3.234-3.726	0.167	98	0.151	1870	0.152	1970	0.969	0.971	99.8985	0.178
3.726-4.546	0.162	84	0.14	1599	0.141	1685	0.972	0.979	99.8813	0.173
4.546-6.353	0.186	66	0.176	1246	0.177	1313	0.976	0.979	99.9238	0.206
6.353-29.352	0.147	38	0.198	720	0.195	767	0.983	0.969	98.8266	0.236

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