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- PDB-6kxu: BON1 -

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Basic information

Entry
Database: PDB / ID: 6kxu
TitleBON1
Components(Protein BONZAI ...) x 5
KeywordsLIPID BINDING PROTEIN / Copines / BON1 / C2 domain / vWA domain / Phospholipid / Membrane.
Function / homology
Function and homology information


response to humidity / plasmodesma / calcium-dependent phospholipid binding / response to temperature stimulus / plastid / positive regulation of cell size / cellular response to calcium ion / defense response / metal ion binding / plasma membrane
Similarity search - Function
Copine, C2B domain / Copine / Copine, C-terminal / Copine / C2 domain / Protein kinase C conserved region 2 (CalB) / C2 domain / C2 domain profile. / von Willebrand factor (vWF) type A domain / VWFA domain profile. ...Copine, C2B domain / Copine / Copine, C-terminal / Copine / C2 domain / Protein kinase C conserved region 2 (CalB) / C2 domain / C2 domain profile. / von Willebrand factor (vWF) type A domain / VWFA domain profile. / von Willebrand factor, type A / von Willebrand factor A-like domain superfamily / C2 domain superfamily
Similarity search - Domain/homology
: / Protein BONZAI 1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.83 Å
AuthorsWang, Q.C. / Jiang, M.Q. / Isupov, M.N. / Sun, L.F. / Wu, Y.K.
CitationJournal: 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
DepositionSep 12, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 16, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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


Theoretical massNumber of molelcules
Total (without water)484,16235
Polymers482,5818
Non-polymers1,58127
Water41423
1
A: Protein BONZAI 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,3936
Polymers61,0601
Non-polymers3335
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area26290 Å2
MethodPISA
2
B: Protein BONZAI 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,5373
Polymers58,4201
Non-polymers1172
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area24120 Å2
MethodPISA
3
C: Protein BONZAI 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,3997
Polymers61,0601
Non-polymers3396
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area140 Å2
ΔGint-9 kcal/mol
Surface area26760 Å2
MethodPISA
4
D: Protein BONZAI 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,2685
Polymers61,0601
Non-polymers2074
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-8 kcal/mol
Surface area26670 Å2
MethodPISA
5
E: Protein BONZAI 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,6522
Polymers60,5971
Non-polymers551
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area25980 Å2
MethodPISA
6
F: Protein BONZAI 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,2945
Polymers61,0601
Non-polymers2344
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area27290 Å2
MethodPISA
7
G: Protein BONZAI 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,3663
Polymers58,2491
Non-polymers1172
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area24410 Å2
MethodPISA
8
H: Protein BONZAI 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,2534
Polymers61,0741
Non-polymers1793
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area26940 Å2
MethodPISA
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 number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16A
26G
17A
27H
18B
28C
19B
29D
110B
210E
111B
211F
112B
212G
113B
213H
114C
214D
115C
215E
116C
216F
117C
217G
118C
218H
119D
219E
120D
220F
121D
221G
122D
222H
123E
223F
124E
224G
125E
225H
126F
226G
127F
227H
128G
228H

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYARGARGAA16 - 54226 - 552
21GLYGLYARGARGBB16 - 5421 - 527
12GLYGLYASNASNAA-9 - 5431 - 553
22GLYGLYASNASNCC-9 - 5431 - 553
13GLYGLYASNASNAA-9 - 5431 - 553
23GLYGLYASNASNDD-9 - 5431 - 553
14ALAALAASNASNAA-4 - 5436 - 553
24ALAALAASNASNEE-4 - 5431 - 548
15GLYGLYASNASNAA-9 - 5431 - 553
25GLYGLYASNASNFF-9 - 5431 - 553
16LEULEUILEILEAA17 - 54127 - 551
26LEULEUILEILEGG17 - 5411 - 525
17GLYGLYASNASNAA-9 - 5431 - 553
27GLYGLYASNASNHH-9 - 5431 - 553
18GLYGLYARGARGBB16 - 5421 - 527
28GLYGLYARGARGCC16 - 54226 - 552
19GLYGLYARGARGBB16 - 5421 - 527
29GLYGLYARGARGDD16 - 54226 - 552
110GLYGLYARGARGBB16 - 5421 - 527
210GLYGLYARGARGEE16 - 54221 - 547
111GLYGLYARGARGBB16 - 5421 - 527
211GLYGLYARGARGFF16 - 54226 - 552
112LEULEUARGARGBB17 - 5422 - 527
212LEULEUARGARGGG17 - 5421 - 526
113GLYGLYARGARGBB16 - 5421 - 527
213GLYGLYARGARGHH13 - 54223 - 552
114GLYGLYASNASNCC-9 - 5431 - 553
214GLYGLYASNASNDD-9 - 5431 - 553
115ALAALAASNASNCC-4 - 5436 - 553
215ALAALAASNASNEE-4 - 5431 - 548
116GLYGLYASNASNCC-9 - 5431 - 553
216GLYGLYASNASNFF-9 - 5431 - 553
117LEULEUILEILECC17 - 54127 - 551
217LEULEUILEILEGG17 - 5411 - 525
118GLYGLYASNASNCC-9 - 5431 - 553
218GLYGLYASNASNHH-9 - 5431 - 553
119ALAALAASNASNDD-4 - 5436 - 553
219ALAALAASNASNEE-4 - 5431 - 548
120GLYGLYASNASNDD-9 - 5431 - 553
220GLYGLYASNASNFF-9 - 5431 - 553
121LEULEUILEILEDD17 - 54127 - 551
221LEULEUILEILEGG17 - 5411 - 525
122GLYGLYASNASNDD-9 - 5431 - 553
222GLYGLYASNASNHH-9 - 5431 - 553
123ALAALAASNASNEE-4 - 5431 - 548
223ALAALAASNASNFF-4 - 5436 - 553
124LEULEUILEILEEE17 - 54122 - 546
224LEULEUILEILEGG17 - 5411 - 525
125ALAALAASNASNEE-4 - 5431 - 548
225ALAALAASNASNHH-4 - 5436 - 553
126LEULEUILEILEFF17 - 54127 - 551
226LEULEUILEILEGG17 - 5411 - 525
127GLYGLYASNASNFF-9 - 5431 - 553
227GLYGLYASNASNHH-9 - 5431 - 553
128LEULEUILEILEGG17 - 5411 - 525
228LEULEUILEILEHH17 - 54127 - 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

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Components

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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 / Production host: Escherichia coli (E. coli) / 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 (E. coli) / References: UniProt: Q941L3
#3: Protein Protein BONZAI 1 / COPINE 1


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 Protein BONZAI 1 / COPINE 1


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 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 (E. coli) / References: UniProt: Q941L3

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Non-polymers , 5 types, 50 molecules

#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#8: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#9: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#10: Water ChemComp-HOH / water


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

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Details

Has ligand of interestY

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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: 3.41 Å3/Da / Density % sol: 63.89 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: PEG 8000, Manganese chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9789 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 10, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.733
11-h,-k,l20.267
ReflectionResolution: 2.83→82.31 Å / Num. obs: 148607 / % possible obs: 98.5 % / Redundancy: 7.1 % / CC1/2: 0.997 / Rmerge(I) obs: 0.186 / Rpim(I) all: 0.075 / Rrim(I) all: 0.2 / Net I/σ(I): 7.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.84-2.886.63.5984564469000.2821.4923.9040.692.8
15.53-82.316.40.04862049650.9950.0210.05330.697.8

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.83→82.31 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc 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
RfactorNum. reflection% reflectionSelection details
Rfree0.2495 7471 5 %RANDOM
Rwork0.2038 ---
obs0.206 141110 98.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 289.3 Å2 / Biso mean: 70 Å2 / Biso min: 12.67 Å2
Baniso -1Baniso -2Baniso -3
1--25.04 Å20 Å211.04 Å2
2--86.85 Å20 Å2
3----61.81 Å2
Refinement stepCycle: final / Resolution: 2.83→82.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms33386 0 74 23 33483
Biso mean--83.19 62.69 -
Num. residues----4290
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01234106
X-RAY DIFFRACTIONr_angle_refined_deg1.4481.62546041
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.24454267
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.36123.091644
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.727155988
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.5615168
X-RAY DIFFRACTIONr_chiral_restr0.1160.24504
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0225493
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A152650.09
12B152650.09
21A168530.08
22C168530.08
31A166890.08
32D166890.08
41A161120.09
42E161120.09
51A166660.09
52F166660.09
61A153170.08
62G153170.08
71A163650.09
72H163650.09
81B152120.09
82C152120.09
91B151130.1
92D151130.1
101B153110.09
102E153110.09
111B151080.1
112F151080.1
121B152290.08
122G152290.08
131B153550.09
132H153550.09
141C168150.09
142D168150.09
151C161060.1
152E161060.1
161C168260.09
162F168260.09
171C153230.08
172G153230.08
181C164700.09
182H164700.09
191D159950.1
192E159950.1
201D169220.08
202F169220.08
211D152160.09
212G152160.09
221D163270.1
222H163270.1
231E160350.1
232F160350.1
241E154090.08
242G154090.08
251E163140.08
252H163140.08
261F152400.09
262G152400.09
271F163660.1
272H163660.1
281G154640.08
282H154640.08
LS refinement shellResolution: 2.833→2.907 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.451 509 -
Rwork0.417 9611 -
all-10120 -
obs--91.08 %

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