PDB-6kxk: BON1 - Yorodumi

ID or keywords:

Entry

Database: PDB / ID: 6kxk

Title

BON1

Components

(Protein BONZAI ...) x 5

Keywords

LIPID BINDING PROTEIN /

Copines / BON1 /

C2 domain / vWA domain /

Phospholipid /

Membrane.

Function / homology

Function and homology information

response to humidity /

plasmodesma / calcium-dependent phospholipid binding /

plastid / response to temperature stimulus / positive regulation of cell size / defense response /

metal ion binding /

plasma membrane
Similarity search - Function

Biological species

Arabidopsis thaliana (thale cress)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.5 Å

Authors

Wang, Q.C. / Jiang, M.Q. / Isupov, M.N. / Sun, L.F. / Wu, Y.K.

Citation

Journal: To be published
Title: Crystal Structure of an Arabidopsis Copine providing insights into this protein family
Authors: Wang, Q.C. / Jiang, M.Q. / Isupov, M.N. / Sun, L.F. / Wu, Y.K.

History

Deposition	Sep 12, 2019	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Sep 16, 2020	Provider: repository / Type: Initial release
Revision 1.1	Mar 27, 2024	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6kxk.cif.gz	884.5 KB	Display	PDBx/mmCIF format
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Validation report

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

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Related structure data

Related structure data	6kxtC 6kxuC C: citing same article (ref.)
Similar structure data	6kxu-1 6kxu-3 6kxu-6 6kxu-4 6kxu-8 6kxu-5 1e57-d 1wrl-d 3bb5-d 6sur-3 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) 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) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

Related structure data

6kxtC

6kxuC

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#196 - Apr 2016 Lead Poisoning similarity (5) #134 - Feb 2011 Integrin similarity (4) #148 - Apr 2012 Ras Protein similarity (5) #239 - Nov 2019 Phospholipase A2 similarity (5) #55 - Jul 2004 DNA Ligase similarity (3) #166 - Oct 2013 Proteasome similarity (3)

Deposited unit

A: Protein BONZAI 1

B: Protein BONZAI 1

C: Protein BONZAI 1

D: Protein BONZAI 1

E: Protein BONZAI 1

F: Protein BONZAI 1

G: Protein BONZAI 1

H: Protein BONZAI 1

hetero molecules

494 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Protein BONZAI 1

hetero molecules

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

2

B: Protein BONZAI 1

hetero molecules

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

3

C: Protein BONZAI 1

hetero molecules

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

4

D: Protein BONZAI 1

hetero molecules

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

5

E: Protein BONZAI 1

hetero molecules

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

6

F: Protein BONZAI 1

hetero molecules

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

7

G: Protein BONZAI 1

hetero molecules

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

8

H: Protein BONZAI 1

hetero molecules

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

Unit cell

Length a, b, c (Å)	122.284, 118.716, 222.253
Angle α, β, γ (deg.)	90.000, 90.200, 90.000
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	GLY	GLY	ARG	ARG	A	A	16 - 542	26 - 552
2	1	GLY	GLY	ARG	ARG	B	B	16 - 542	1 - 527
1	2	GLY	GLY	ASN	ASN	A	A	-9 - 543	1 - 553
2	2	GLY	GLY	ASN	ASN	C	C	-9 - 543	1 - 553
1	3	GLY	GLY	ASN	ASN	A	A	-9 - 543	1 - 553
2	3	GLY	GLY	ASN	ASN	D	D	-9 - 543	1 - 553
1	4	SER	SER	ASN	ASN	A	A	-6 - 543	4 - 553
2	4	SER	SER	ASN	ASN	E	E	-6 - 543	1 - 550
1	5	GLY	GLY	ASN	ASN	A	A	-9 - 543	1 - 553
2	5	GLY	GLY	ASN	ASN	F	F	-9 - 543	1 - 553
1	6	LEU	LEU	ARG	ARG	A	A	17 - 542	27 - 552
2	6	LEU	LEU	ARG	ARG	G	G	17 - 542	1 - 526
1	7	GLY	GLY	ASN	ASN	A	A	-9 - 543	1 - 553
2	7	GLY	GLY	ASN	ASN	H	H	-9 - 543	1 - 553
1	8	GLY	GLY	ARG	ARG	B	B	16 - 542	1 - 527
2	8	GLY	GLY	ARG	ARG	C	C	16 - 542	26 - 552
1	9	GLY	GLY	ARG	ARG	B	B	16 - 542	1 - 527
2	9	GLY	GLY	ARG	ARG	D	D	16 - 542	26 - 552
1	10	GLY	GLY	ARG	ARG	B	B	16 - 542	1 - 527
2	10	GLY	GLY	ARG	ARG	E	E	16 - 542	23 - 549
1	11	GLY	GLY	ARG	ARG	B	B	16 - 542	1 - 527
2	11	GLY	GLY	ARG	ARG	F	F	16 - 542	26 - 552
1	12	LEU	LEU	ARG	ARG	B	B	17 - 542	2 - 527
2	12	LEU	LEU	ARG	ARG	G	G	17 - 542	1 - 526
1	13	GLY	GLY	ARG	ARG	B	B	16 - 542	1 - 527
2	13	GLY	GLY	ARG	ARG	H	H	13 - 542	23 - 552
1	14	GLY	GLY	ASN	ASN	C	C	-9 - 543	1 - 553
2	14	GLY	GLY	ASN	ASN	D	D	-9 - 543	1 - 553
1	15	SER	SER	ASN	ASN	C	C	-6 - 543	4 - 553
2	15	SER	SER	ASN	ASN	E	E	-6 - 543	1 - 550
1	16	GLY	GLY	ASN	ASN	C	C	-9 - 543	1 - 553
2	16	GLY	GLY	ASN	ASN	F	F	-9 - 543	1 - 553
1	17	LEU	LEU	ARG	ARG	C	C	17 - 542	27 - 552
2	17	LEU	LEU	ARG	ARG	G	G	17 - 542	1 - 526
1	18	GLY	GLY	ASN	ASN	C	C	-9 - 543	1 - 553
2	18	GLY	GLY	ASN	ASN	H	H	-9 - 543	1 - 553
1	19	SER	SER	ASN	ASN	D	D	-6 - 543	4 - 553
2	19	SER	SER	ASN	ASN	E	E	-6 - 543	1 - 550
1	20	GLY	GLY	ASN	ASN	D	D	-9 - 543	1 - 553
2	20	GLY	GLY	ASN	ASN	F	F	-9 - 543	1 - 553
1	21	LEU	LEU	ARG	ARG	D	D	17 - 542	27 - 552
2	21	LEU	LEU	ARG	ARG	G	G	17 - 542	1 - 526
1	22	GLY	GLY	ASN	ASN	D	D	-9 - 543	1 - 553
2	22	GLY	GLY	ASN	ASN	H	H	-9 - 543	1 - 553
1	23	SER	SER	ASN	ASN	E	E	-6 - 543	1 - 550
2	23	SER	SER	ASN	ASN	F	F	-6 - 543	4 - 553
1	24	LEU	LEU	ARG	ARG	E	E	17 - 542	24 - 549
2	24	LEU	LEU	ARG	ARG	G	G	17 - 542	1 - 526
1	25	SER	SER	ARG	ARG	E	E	-6 - 542	1 - 549
2	25	SER	SER	ARG	ARG	H	H	-6 - 542	4 - 552
1	26	LEU	LEU	ARG	ARG	F	F	17 - 542	27 - 552
2	26	LEU	LEU	ARG	ARG	G	G	17 - 542	1 - 526
1	27	GLY	GLY	ASN	ASN	F	F	-9 - 543	1 - 553
2	27	GLY	GLY	ASN	ASN	H	H	-9 - 543	1 - 553
1	28	LEU	LEU	ARG	ARG	G	G	17 - 542	1 - 526
2	28	LEU	LEU	ARG	ARG	H	H	17 - 542	27 - 552

NCS ensembles :

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Protein BONZAI ... , 5 types, 8 molecules ACDFBEGH

#1: Protein	Protein BONZAI 1 / COPINE 1 Mass: 61060.125 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: BON1, CPN1, At5g61900, K22G18.2 / Plasmid: pET32a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q941L3
#2: Protein	Protein BONZAI 1 / COPINE 1 Mass: 58420.270 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: BON1, CPN1, At5g61900, K22G18.2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q941L3
#3: Protein	Protein BONZAI 1 / COPINE 1 Mass: 60814.898 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: BON1, CPN1, At5g61900, K22G18.2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q941L3
#4: Protein	Protein BONZAI 1 / COPINE 1 Mass: 58363.223 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: BON1, CPN1, At5g61900, K22G18.2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q941L3
#5: Protein	Protein BONZAI 1 / COPINE 1 Mass: 61074.156 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: BON1, CPN1, At5g61900, K22G18.2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q941L3

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Non-polymers , 8 types, 739 molecules

#6: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol Mass: 106.120 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#7: Chemical	... ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol Mass: 62.068 Da / Num. of mol.: 81 / Source method: obtained synthetically / Formula: C₂H₆O₂
#8: Chemical	... ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 27 / Source method: obtained synthetically / Formula: C₃H₈O₃
#9: Chemical	ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol Mass: 150.173 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₆H₁₄O₄
#10: Chemical	ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₈H₁₈O₅ / Comment: precipitant*YM
#11: Chemical	ChemComp-CL / CHLORIDE ION / Chloride Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#12: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#13: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 603 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 3.36 Å³/Da / Density % sol: 63.39 % / Mosaicity: 0.13 °
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.05 M MES (PH 7.0), 0.05 M HEPES (PH 7.5), 7% PEG 8000

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

SSRF

/ Beamline: BL17U1 / Wavelength: 0.9789 Å

Detector

Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 1, 2017

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.9789 Å / Relative weight: 1

Reflection

Resolution: 2.5→48.21 Å / Num. obs: 215443 / % possible obs: 98.2 % / Redundancy: 4 % / CC_1/2: 0.997 / R_merge(I) obs: 0.116 / R_pim(I) all: 0.065 / R_rim(I) all: 0.134 / Net I/σ(I): 8.2

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. measured all	Num. unique obs	CC_1/2	R_pim(I) all	R_rim(I) all	Net I/σ(I) obs	% possible all
2.5-2.54	4.1	0.2442	44256	10744	0.249	0.1364	0.2804	0.7	98.9
13.69-48.16	3.7	0.029	5063	1370	0.999	0.017	0.033	33.3	96.1

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Processing

Software

Name	Version	Classification
Aimless	0.7.4	data scaling
REFMAC	5.8.0238	refinement
PDB_EXTRACT	3.25	data extraction
XDS		data reduction
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.5→48.21 Å / Cor.coef. F_o:F_c: 0.949 / Cor.coef. F_o:F_c free: 0.927 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.43 / ESU R Free: 0.282 / Details: U VALUES : REFINED INDIVIDUALLY

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2662	10856	5 %	RANDOM
R_work	0.2271	-	-	-
obs	0.229	204561	98.03 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å

Displacement parameters

B_iso max: 228.1 Å² / B_iso mean: 68.067 Å² / B_iso min: 18.62 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.75 Å²	0 Å²	0 Å²
2-	-	5.31 Å²	0 Å²
3-	-	-	-3.56 Å²

Refinement step

Cycle: final / Resolution: 2.5→48.21 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	33809	0	685	603	35097
B_iso mean	-	-	75.51	48.5	-
Num. residues	-	-	-	-	4345

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.012	35009
X-RAY DIFFRACTION	r_angle_refined_deg	1.533	1.629	47071
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.476	5	4331
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	39.093	23.155	1667
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	18.958	15	6056
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	22.447	15	168
X-RAY DIFFRACTION	r_chiral_restr	0.118	0.2	4559
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	25890

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-ID	Dom-ID	Auth asym-ID	Number	Rms dev position (Å)
1	1	A	15663	0.11
1	2	B	15663	0.11
2	1	A	16958	0.09
2	2	C	16958	0.09
3	1	A	16737	0.1
3	2	D	16737	0.1
4	1	A	16338	0.11
4	2	E	16338	0.11
5	1	A	16758	0.1
5	2	F	16758	0.1
6	1	A	15383	0.09
6	2	G	15383	0.09
7	1	A	16596	0.1
7	2	H	16596	0.1
8	1	B	15651	0.11
8	2	C	15651	0.11
9	1	B	15506	0.11
9	2	D	15506	0.11
10	1	B	15780	0.11
10	2	E	15780	0.11
11	1	B	15555	0.11
11	2	F	15555	0.11
12	1	B	15459	0.09
12	2	G	15459	0.09
13	1	B	15834	0.11
13	2	H	15834	0.11
14	1	C	16754	0.09
14	2	D	16754	0.09
15	1	C	16307	0.11
15	2	E	16307	0.11
16	1	C	16829	0.1
16	2	F	16829	0.1
17	1	C	15382	0.09
17	2	G	15382	0.09
18	1	C	16554	0.1
18	2	H	16554	0.1
19	1	D	16165	0.11
19	2	E	16165	0.11
20	1	D	16946	0.09
20	2	F	16946	0.09
21	1	D	15190	0.1
21	2	G	15190	0.1
22	1	D	16389	0.11
22	2	H	16389	0.11
23	1	E	16270	0.11
23	2	F	16270	0.11
24	1	E	15445	0.09
24	2	G	15445	0.09
25	1	E	16623	0.1
25	2	H	16623	0.1
26	1	F	15320	0.1
26	2	G	15320	0.1
27	1	F	16485	0.11
27	2	H	16485	0.11
28	1	G	15500	0.09
28	2	H	15500	0.09

LS refinement shell

Resolution: 2.5→2.565 Å / R_factor R_free error: 0

	R_factor	Num. reflection	% reflection
R_free	0.426	859	-
R_work	0.35	15064	-
obs	-	-	98.52 %

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Protein BONZAI ... , 5 types, 8 molecules ACDFBEGH

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Non-polymers , 8 types, 739 molecules

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-Protein BONZAI ... , 5 types, 8 molecules ACDFBEGH

-Non-polymers , 8 types, 739 molecules

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Protein BONZAI ... , 5 types, 8 molecules ACDFBEGH

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Non-polymers , 8 types, 739 molecules

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