PDB-6xnr: Crystal structure of Rhagium Mordax antifreeze protein

ID or keywords:

Entry

Database: PDB / ID: 6xnr

Title

Crystal structure of Rhagium Mordax antifreeze protein

Components

Antifreeze protein

Keywords

ANTIFREEZE PROTEIN / Ice-binding protein

Biological species

Rhagium mordax (beetle)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.05 Å

Authors

Ye, Q. / Eves, R. / Campbell, R.L. / Davies, P.L.

Funding support

Canada, 1items

Citation

Journal: Biochem.J. / Year: 2020
Title: Crystal structure of an insect antifreeze protein reveals ordered waters on the ice-binding surface.
Authors: Ye, Q. / Eves, R. / Campbell, R.L. / Davies, P.L.

History

Deposition	Jul 4, 2020	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 26, 2020	Provider: repository / Type: Initial release
Revision 1.1	Sep 30, 2020	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2	Oct 18, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	6xnr.cif.gz	222.8 KB	Display	PDBx/mmCIF format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/xn/6xnr ftp://data.pdbj.org/pub/pdb/validation_reports/xn/6xnr	HTTPS FTP

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Related structure data

Related structure data	4dt5S S: Starting model for refinement
Similar structure data	6tlt-d 2agm-d 2b7j-2 6a22-4 6sal-d 1rqc-1 6t4x-d 5x8x-4 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details)

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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

AAA: Antifreeze protein

BBB: Antifreeze protein

CCC: Antifreeze protein

DDD: Antifreeze protein

EEE: Antifreeze protein

hetero molecules

68.3 kDa, 5 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

AAA: Antifreeze protein

defined by author&software
Evidence: gel filtration, Analytical ultracentrifugation
27.2 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

BBB: Antifreeze protein

CCC: Antifreeze protein

hetero molecules

defined by author&software
27.4 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

DDD: Antifreeze protein

EEE: Antifreeze protein

hetero molecules

defined by author&software
27.3 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	66.457, 91.143, 117.447
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	18
Space group name H-M	P2₁22₁

#1: Protein	Antifreeze protein / Mass: 13622.429 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhagium mordax (beetle) / Plasmid: pET24a / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₂H₆O₂
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 514 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	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: 2.67 Å³/Da / Density % sol: 53.9 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4 Details: PEG monomethyl ether 5000, sodium acetate, magnesium chloride

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9795 Å
Detector	Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 14, 2018
Radiation	Monochromator: DCM, Si-111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9795 Å / Relative weight: 1
Reflection	Resolution: 2.05→50 Å / Num. obs: 45419 / % possible obs: 99.7 % / Redundancy: 13.3 % / CC_1/2: 0.998 / R_pim(I) all: 0.068 / Χ²: 1 / Net I/σ(I): 9
Reflection shell	Resolution: 2.05→2.11 Å / Redundancy: 13.7 % / Mean I/σ(I) obs: 2 / Num. unique obs: 3463 / CC_1/2: 0.835 / R_pim(I) all: 0.519 / Χ²: 1.02 / % possible all: 99.4

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0258	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4DT5

4dt5

Resolution: 2.05→49.413 Å / Cor.coef. F_o:F_c: 0.961 / Cor.coef. F_o:F_c free: 0.942 / SU B: 10.866 / SU ML: 0.147 / Cross valid method: THROUGHOUT / ESU R: 0.204 / ESU R Free: 0.177
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2509	2230	4.914 %
R_work	0.2131	43150	-
all	0.215	-	-
obs	-	45380	99.666 %

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: 32.012 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-3.624 Å²	0 Å²	-0 Å²
2-	-	1.162 Å²	0 Å²
3-	-	-	2.463 Å²

Refinement step

Cycle: LAST / Resolution: 2.05→49.413 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4393	0	12	514	4919

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.013	4431
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.018	3929
X-RAY DIFFRACTION	r_angle_refined_deg	1.471	1.671	6099
X-RAY DIFFRACTION	r_angle_other_deg	1.516	1.56	9126
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.32	5	686
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	37.032	24.186	86
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	11.898	15	553
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	23.754	15	10
X-RAY DIFFRACTION	r_chiral_restr	0.054	0.2	820
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	5164
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	750
X-RAY DIFFRACTION	r_nbd_refined	0.173	0.2	700
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.214	0.2	3469
X-RAY DIFFRACTION	r_nbtor_refined	0.127	0.2	2187
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.082	0.2	2444
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.166	0.2	380
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.272	0.2	26
X-RAY DIFFRACTION	r_nbd_other	0.25	0.2	120
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.147	0.2	13
X-RAY DIFFRACTION	r_mcbond_it	0.581	0.366	2753
X-RAY DIFFRACTION	r_mcbond_other	0.581	0.366	2752
X-RAY DIFFRACTION	r_mcangle_it	1.071	0.546	3433
X-RAY DIFFRACTION	r_mcangle_other	1.071	0.546	3434
X-RAY DIFFRACTION	r_scbond_it	0.412	0.428	1678
X-RAY DIFFRACTION	r_scbond_other	0.417	0.431	1679
X-RAY DIFFRACTION	r_scangle_it	0.677	0.602	2665
X-RAY DIFFRACTION	r_scangle_other	0.677	0.605	2666
X-RAY DIFFRACTION	r_lrange_it	9.633	6.752	4513
X-RAY DIFFRACTION	r_lrange_other	9.66	5.614	4422
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.096	0.05	3753
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.099	0.05	3740
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.097	0.05	3712
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.093	0.05	3772
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.103	0.05	3726
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.086	0.05	3685
X-RAY DIFFRACTION	r_ncsr_local_group_7	0.09	0.05	3755
X-RAY DIFFRACTION	r_ncsr_local_group_8	0.084	0.05	3712
X-RAY DIFFRACTION	r_ncsr_local_group_9	0.096	0.05	3756
X-RAY DIFFRACTION	r_ncsr_local_group_10	0.074	0.05	3721

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.05-2.103	0.286	177	0.29	3115	X-RAY DIFFRACTION	99.1268
2.103-2.161	0.342	176	0.28	3038	X-RAY DIFFRACTION	99.3509
2.161-2.223	0.284	145	0.273	2990	X-RAY DIFFRACTION	99.2717
2.223-2.292	0.309	147	0.268	2908	X-RAY DIFFRACTION	99.4143
2.292-2.367	0.278	150	0.255	2796	X-RAY DIFFRACTION	99.8306
2.367-2.45	0.273	126	0.241	2731	X-RAY DIFFRACTION	99.5124
2.45-2.542	0.245	130	0.232	2644	X-RAY DIFFRACTION	99.6766
2.542-2.646	0.241	140	0.204	2511	X-RAY DIFFRACTION	99.7742
2.646-2.764	0.272	113	0.203	2484	X-RAY DIFFRACTION	99.8462
2.764-2.898	0.245	115	0.191	2327	X-RAY DIFFRACTION	99.7957
2.898-3.055	0.25	117	0.193	2230	X-RAY DIFFRACTION	99.8299
3.055-3.24	0.204	114	0.218	2101	X-RAY DIFFRACTION	99.8197
3.24-3.464	0.273	107	0.223	2014	X-RAY DIFFRACTION	100
3.464-3.741	0.248	98	0.194	1841	X-RAY DIFFRACTION	100
3.741-4.097	0.239	80	0.194	1734	X-RAY DIFFRACTION	99.9449
4.097-4.579	0.216	83	0.173	1565	X-RAY DIFFRACTION	99.9394
4.579-5.286	0.208	77	0.186	1392	X-RAY DIFFRACTION	99.864
5.286-6.468	0.268	66	0.225	1200	X-RAY DIFFRACTION	100
6.468-9.124	0.213	47	0.167	953	X-RAY DIFFRACTION	100
9.124-9.14	0.305	22	0.231	576	X-RAY DIFFRACTION	99.0066

Refinement TLS params.

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

ID	L11 (°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)
1	3.3172	-0.3006	0.1975	1.838	0.2722	1.4135	-0.0598	-0.0381	0.2846	0.0144	0.061	-0.1065	-0.0834	0.0116	-0.0012	0.3458	-0.0118	0.0066	0.3856	0.0036	0.0287	8.3876	-27.4536	-5.485
2	4.7318	-0.1783	0.1249	1.926	-0.3395	1.4994	0.0161	-0.1983	0.043	-0.0446	-0.024	-0.0267	-0.0184	-0.0542	0.0079	0.2599	0.0031	0.0109	0.4685	-0.0567	0.0078	-1.3227	-47.4248	-32.8938
3	3.9781	-0.5745	0.6697	2.2931	-0.2243	1.2964	0.0149	0.0862	0.1694	0.001	0.0088	-0.1292	-0.0697	0.09	-0.0237	0.3487	-0.0088	0.0477	0.4155	-0.0302	0.0226	3.6697	-46.58	-47.3987
4	4.0609	0.7024	0.1698	3.2296	0.4113	1.5806	0.0866	0.0862	-0.2923	-0.0482	-0.0256	-0.0314	-0.0286	-0.0378	-0.0611	0.2641	0.0043	0.0019	0.434	0.1577	0.3224	13.0408	-0.2216	-33.4245
5	3.6464	0.5676	-0.2301	3.4349	0.1111	1.7678	-0.0507	0.1883	-0.4293	-0.236	0.0362	-0.0167	0.1218	-0.0749	0.0146	0.492	-0.0303	0.0131	0.4352	0.0574	0.2587	16.4359	6.2792	-47.0427

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	ALL	AAA	1 - 139
2	X-RAY DIFFRACTION	2	ALL	BBB	1 - 24
3	X-RAY DIFFRACTION	2	ALL	BBB	27 - 92
4	X-RAY DIFFRACTION	2	ALL	BBB	95 - 138
5	X-RAY DIFFRACTION	3	ALL	CCC	1 - 138
6	X-RAY DIFFRACTION	4	ALL	DDD	2 - 92
7	X-RAY DIFFRACTION	4	ALL	DDD	95 - 137
8	X-RAY DIFFRACTION	5	ALL	EEE	1 - 138

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