PDB-6kxu: BON1

Basic information

• Entry: Database: PDB / ID: 6kxu
• Title: BON1
• Components: (Protein BONZAI ...) x 5
• Keywords: LIPID BINDING PROTEIN / Copines / BON1 / C2 domain / vWA domain / Phospholipid / Membrane.

Function / homology

Function:

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

Domain/homology:

Copine, C2B domain / Copine / Copine, C-terminal / Copine / C2 domain / Protein kinase C conserved region 2 (CalB) / C2 domain / C2 domain / C2 domain profile. / VWFA domain profile. / von Willebrand factor (vWF) type A domain / von Willebrand factor, type A / C2 domain superfamily / von Willebrand factor A-like domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta

Component:

: / Protein BONZAI 1

• Biological species: Arabidopsis thaliana (thale cress)
• Method: X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.83 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 / database_2 / struct_ncs_dom_lim Item: _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

Assembly

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

Summary:

• 484 kDa, 8 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	484,162	35
Polymers	482,581	8
Non-polymers	1,581	27
Water	414	23

1

A: Protein BONZAI 1

hetero molecules

Summary:

• defined by author&software
• 61.4 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	61,393	6
Polymers	61,060	1
Non-polymers	333	5
Water	18	1

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

Calculated values:

Buried area	0 Å2
ΔGint	0 kcal/mol
Surface area	26290 Å2
Method	PISA

2

B: Protein BONZAI 1

hetero molecules

Summary:

• defined by author&software
• 58.5 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	58,537	3
Polymers	58,420	1
Non-polymers	117	2
Water	18	1

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

Calculated values:

Buried area	0 Å2
ΔGint	0 kcal/mol
Surface area	24120 Å2
Method	PISA

3

C: Protein BONZAI 1

hetero molecules

Summary:

• defined by author&software
• 61.4 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	61,399	7
Polymers	61,060	1
Non-polymers	339	6
Water	18	1

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

Calculated values:

Buried area	140 Å2
ΔGint	-9 kcal/mol
Surface area	26760 Å2
Method	PISA

4

D: Protein BONZAI 1

hetero molecules

Summary:

• defined by author&software
• 61.3 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	61,268	5
Polymers	61,060	1
Non-polymers	207	4
Water	18	1

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

Calculated values:

Buried area	130 Å2
ΔGint	-8 kcal/mol
Surface area	26670 Å2
Method	PISA

5

E: Protein BONZAI 1

hetero molecules

Summary:

• defined by author&software
• 60.7 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	60,652	2
Polymers	60,597	1
Non-polymers	55	1
Water	18	1

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

Calculated values:

Buried area	0 Å2
ΔGint	0 kcal/mol
Surface area	25980 Å2
Method	PISA

6

F: Protein BONZAI 1

hetero molecules

Summary:

• defined by author&software
• 61.3 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	61,294	5
Polymers	61,060	1
Non-polymers	234	4
Water	0

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

Calculated values:

Buried area	0 Å2
ΔGint	0 kcal/mol
Surface area	27290 Å2
Method	PISA

7

G: Protein BONZAI 1

hetero molecules

Summary:

• defined by author&software
• 58.4 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	58,366	3
Polymers	58,249	1
Non-polymers	117	2
Water	0

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

Calculated values:

Buried area	0 Å2
ΔGint	0 kcal/mol
Surface area	24410 Å2
Method	PISA

8

H: Protein BONZAI 1

hetero molecules

Summary:

• defined by author&software
• 61.3 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	61,253	4
Polymers	61,074	1
Non-polymers	179	3
Water	18	1

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

Calculated values:

Buried area	0 Å2
ΔGint	0 kcal/mol
Surface area	26940 Å2
Method	PISA

Unit cell

Length a, b, c (Å)	122.406, 118.705, 222.317
Angle α, β, γ (deg.)	90.000, 90.030, 90.000
Int Tables number	4
Space group name H-M	P1211

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
1	2	A
2	2	C
1	3	A
2	3	D
1	4	A
2	4	E
1	5	A
2	5	F
1	6	A
2	6	G
1	7	A
2	7	H
1	8	B
2	8	C
1	9	B
2	9	D
1	10	B
2	10	E
1	11	B
2	11	F
1	12	B
2	12	G
1	13	B
2	13	H
1	14	C
2	14	D
1	15	C
2	15	E
1	16	C
2	16	F
1	17	C
2	17	G
1	18	C
2	18	H
1	19	D
2	19	E
1	20	D
2	20	F
1	21	D
2	21	G
1	22	D
2	22	H
1	23	E
2	23	F
1	24	E
2	24	G
1	25	E
2	25	H
1	26	F
2	26	G
1	27	F
2	27	H
1	28	G
2	28	H

NCS domain segments:

Component-ID: _ / Refine code: _

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	ALA	ALA	ASN	ASN	A	A	-4 - 543	6 - 553
2	4	ALA	ALA	ASN	ASN	E	E	-4 - 543	1 - 548
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	ILE	ILE	A	A	17 - 541	27 - 551
2	6	LEU	LEU	ILE	ILE	G	G	17 - 541	1 - 525
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	21 - 547
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	ALA	ALA	ASN	ASN	C	C	-4 - 543	6 - 553
2	15	ALA	ALA	ASN	ASN	E	E	-4 - 543	1 - 548
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	ILE	ILE	C	C	17 - 541	27 - 551
2	17	LEU	LEU	ILE	ILE	G	G	17 - 541	1 - 525
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	ALA	ALA	ASN	ASN	D	D	-4 - 543	6 - 553
2	19	ALA	ALA	ASN	ASN	E	E	-4 - 543	1 - 548
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	ILE	ILE	D	D	17 - 541	27 - 551
2	21	LEU	LEU	ILE	ILE	G	G	17 - 541	1 - 525
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	ALA	ALA	ASN	ASN	E	E	-4 - 543	1 - 548
2	23	ALA	ALA	ASN	ASN	F	F	-4 - 543	6 - 553
1	24	LEU	LEU	ILE	ILE	E	E	17 - 541	22 - 546
2	24	LEU	LEU	ILE	ILE	G	G	17 - 541	1 - 525
1	25	ALA	ALA	ASN	ASN	E	E	-4 - 543	1 - 548
2	25	ALA	ALA	ASN	ASN	H	H	-4 - 543	6 - 553
1	26	LEU	LEU	ILE	ILE	F	F	17 - 541	27 - 551
2	26	LEU	LEU	ILE	ILE	G	G	17 - 541	1 - 525
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	ILE	ILE	G	G	17 - 541	1 - 525
2	28	LEU	LEU	ILE	ILE	H	H	17 - 541	27 - 551

NCS ensembles :

ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28

Components

Protein BONZAI ... , 5 types, 8 molecules A C D F B E G H

#1: Protein

A C D F
Protein BONZAI 1 / COPINE 1

Details:

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 / Production host: Escherichia coli (E. coli) / References: UniProt: Q941L3

#2: Protein

B Protein BONZAI 1 / COPINE 1

Details:

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 (E. coli) / References: UniProt: Q941L3

#3: Protein

E Protein BONZAI 1 / COPINE 1

Details:

Mass: 60596.625 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 (E. coli) / References: UniProt: Q941L3

#4: Protein

G Protein BONZAI 1 / COPINE 1

Details:

Mass: 58249.121 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 (E. coli) / References: UniProt: Q941L3

#5: Protein

H Protein BONZAI 1 / COPINE 1

Details:

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 (E. coli) / References: UniProt: Q941L3

Non-polymers , 5 types, 50 molecules

#6: Chemical

A-601 A-602 A-603 B-601 C-601 C-602 C-603 C-604 D-601 F-601 F-602 G-601 H-601 H-602
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL

Details:

Mass: 62.068 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C₂H₆O₂

#7: Chemical

A-604 ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL

Details:

Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃

#8: Chemical

A-605 B-602 C-606 D-603 D-604 E-601 F-603 F-604 G-602 H-603
ChemComp-MN / MANGANESE (II) ION

Details:

Mass: 54.938 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION

#9: Chemical

C-605 D-602 ChemComp-CL / CHLORIDE ION

Details:

Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl

#10: Water

ChemComp-HOH / water

Details:

Mass: 18.015 Da / Num. of mol.: 23 / Source method: isolated from a natural source / Formula: H₂O

Details

• Has ligand of interest: Y

Experimental details

Experiment

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

Sample preparation

• Crystal: Density Matthews: 3.41 ų/Da / Density % sol: 63.89 %
• Crystal grow: Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: PEG 8000, Manganese chloride

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: Sep 10, 2018
• Radiation: Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
• Radiation wavelength: Wavelength: 0.9789 Å / Relative weight: 1

Reflection twin

Crystal-ID	ID	Operator	Domain-ID	Fraction
1	1	H, K, L	1	0.733
1	1	-h,-k,l	2	0.267

• Reflection: Resolution: 2.83→82.31 Å / Num. obs: 148607 / % possible obs: 98.5 % / Redundancy: 7.1 % / CC_1/2: 0.997 / R_merge(I) obs: 0.186 / R_pim(I) all: 0.075 / R_rim(I) all: 0.2 / Net I/σ(I): 7.5

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	Rmerge(I) obs	Num. measured all	Num. unique obs	CC1/2	Rpim(I) all	Rrim(I) all	Net I/σ(I) obs	% possible all
2.84-2.88	6.6	3.598	45644	6900	0.282	1.492	3.904	0.6	92.8
15.53-82.31	6.4	0.048	6204	965	0.995	0.021	0.053	30.6	97.8

Processing

Software

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

Refinement

Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.83→82.31 Å / Cor.coef. F_o:F_c: 0.949 / Cor.coef. F_o:F_c free: 0.925 / SU B: 10.631 / SU ML: 0.216 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.27 / ESU R Free: 0.075 / Details: U VALUES : REFINED INDIVIDUALLY

	Rfactor	Num. reflection	% reflection	Selection details
Rfree	0.2495	7471	5 %	RANDOM
Rwork	0.2038	-	-	-
obs	0.206	141110	98.17 %	-

• Solvent computation: Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å

Displacement parameters

B_iso max: 289.3 Ų / B_iso mean: 70 Ų / B_iso min: 12.67 Ų

	Baniso -1	Baniso -2	Baniso -3
1-	-25.04 Å2	0 Å2	11.04 Å2
2-	-	86.85 Å2	0 Å2
3-	-	-	-61.81 Å2

Refinement step

Cycle: final / Resolution: 2.83→82.31 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	33386	0	74	23	33483
Biso mean	-	-	83.19	62.69	-
Num. residues	-	-	-	-	4290

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.012	34106
X-RAY DIFFRACTION	r_angle_refined_deg	1.448	1.625	46041
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.244	5	4267
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	39.361	23.09	1644
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	20.727	15	5988
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	23.56	15	168
X-RAY DIFFRACTION	r_chiral_restr	0.116	0.2	4504
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	25493

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	15265	0.09
1	2	B	15265	0.09
2	1	A	16853	0.08
2	2	C	16853	0.08
3	1	A	16689	0.08
3	2	D	16689	0.08
4	1	A	16112	0.09
4	2	E	16112	0.09
5	1	A	16666	0.09
5	2	F	16666	0.09
6	1	A	15317	0.08
6	2	G	15317	0.08
7	1	A	16365	0.09
7	2	H	16365	0.09
8	1	B	15212	0.09
8	2	C	15212	0.09
9	1	B	15113	0.1
9	2	D	15113	0.1
10	1	B	15311	0.09
10	2	E	15311	0.09
11	1	B	15108	0.1
11	2	F	15108	0.1
12	1	B	15229	0.08
12	2	G	15229	0.08
13	1	B	15355	0.09
13	2	H	15355	0.09
14	1	C	16815	0.09
14	2	D	16815	0.09
15	1	C	16106	0.1
15	2	E	16106	0.1
16	1	C	16826	0.09
16	2	F	16826	0.09
17	1	C	15323	0.08
17	2	G	15323	0.08
18	1	C	16470	0.09
18	2	H	16470	0.09
19	1	D	15995	0.1
19	2	E	15995	0.1
20	1	D	16922	0.08
20	2	F	16922	0.08
21	1	D	15216	0.09
21	2	G	15216	0.09
22	1	D	16327	0.1
22	2	H	16327	0.1
23	1	E	16035	0.1
23	2	F	16035	0.1
24	1	E	15409	0.08
24	2	G	15409	0.08
25	1	E	16314	0.08
25	2	H	16314	0.08
26	1	F	15240	0.09
26	2	G	15240	0.09
27	1	F	16366	0.1
27	2	H	16366	0.1
28	1	G	15464	0.08
28	2	H	15464	0.08

LS refinement shell

Resolution: 2.833→2.907 Å / R_factor R_free error: 0 / Total num. of bins used: 20

	Rfactor	Num. reflection	% reflection
Rfree	0.451	509	-
Rwork	0.417	9611	-
all	-	10120	-
obs	-	-	91.08 %