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Basic information

Entry
Database: PDB / ID: 6kxt
TitleBON1-C2B
ComponentsProtein BONZAI 1
KeywordsLIPID BINDING PROTEIN / Copines / BON1 / C2 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
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
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 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 / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein BONZAI 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,0684
Polymers15,6811
Non-polymers3873
Water3,603200
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-8 kcal/mol
Surface area8680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.844, 69.594, 77.396
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-470-

HOH

21A-536-

HOH

31A-543-

HOH

41A-581-

HOH

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Components

#1: Protein Protein BONZAI 1 / COPINE 1


Mass: 15680.918 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
#2: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 200 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.05 Å3/Da / Density % sol: 40.12 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: Two moles of ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9789 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 10, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 1.25→40.73 Å / Num. obs: 32577 / % possible obs: 90.1 % / Redundancy: 12.2 % / CC1/2: 1 / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.021 / Rrim(I) all: 0.076 / Net I/σ(I): 16.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.25-1.277.71.88680.4031148.8
6.85-40.711.70.0226410.0060.02199.3

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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: 1.25→40.73 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.974 / SU B: 1.284 / SU ML: 0.05 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.053 / ESU R Free: 0.055
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1947 1876 5.8 %RANDOM
Rwork0.1682 ---
obs0.1699 30701 90.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 75.67 Å2 / Biso mean: 20.071 Å2 / Biso min: 11.57 Å2
Baniso -1Baniso -2Baniso -3
1-1.32 Å20 Å20 Å2
2---1.6 Å20 Å2
3---0.28 Å2
Refinement stepCycle: final / Resolution: 1.25→40.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1101 0 22 200 1323
Biso mean--37.87 33.34 -
Num. residues----144
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0131256
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171221
X-RAY DIFFRACTIONr_angle_refined_deg1.8551.631725
X-RAY DIFFRACTIONr_angle_other_deg1.3831.5832899
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9445180
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.72325.83348
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.68415249
X-RAY DIFFRACTIONr_dihedral_angle_4_deg6.238152
X-RAY DIFFRACTIONr_chiral_restr0.0890.2174
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021377
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02217
LS refinement shellResolution: 1.25→1.282 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.372 385 -
Rwork0.324 930 -
obs--50.1 %

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