6KXK | pdb_00006kxk

BON1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 
    0.266 (Depositor), 0.266 (DCC) 
  • R-Value Work: 
    0.227 (Depositor), 0.227 (DCC) 
  • R-Value Observed: 
    0.229 (Depositor) 

wwPDB Validation 3D Report Full Report

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This is version 1.1 of the entry. See complete history

Literature

Crystal Structure of an Arabidopsis Copine providing insights into this protein family

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

To be published.

Macromolecule Content 

  • Total Structure Weight: 493.52 kDa 
  • Atom Count: 35,097 
  • Modeled Residue Count: 4,345 
  • Deposited Residue Count: 4,370 
  • Unique protein chains: 5

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Protein BONZAI 1
A, C, D, F
553Arabidopsis thalianaMutation(s): 0 
Gene Names: BON1CPN1At5g61900K22G18.2
UniProt
Find proteins for Q941L3 (Arabidopsis thaliana)
Explore Q941L3 
Go to UniProtKB:  Q941L3
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ941L3
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Protein BONZAI 1528Arabidopsis thalianaMutation(s): 0 
Gene Names: BON1CPN1At5g61900K22G18.2
UniProt
Find proteins for Q941L3 (Arabidopsis thaliana)
Explore Q941L3 
Go to UniProtKB:  Q941L3
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ941L3
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Protein BONZAI 1550Arabidopsis thalianaMutation(s): 0 
Gene Names: BON1CPN1At5g61900K22G18.2
UniProt
Find proteins for Q941L3 (Arabidopsis thaliana)
Explore Q941L3 
Go to UniProtKB:  Q941L3
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ941L3
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Protein BONZAI 1527Arabidopsis thalianaMutation(s): 0 
Gene Names: BON1CPN1At5g61900K22G18.2
UniProt
Find proteins for Q941L3 (Arabidopsis thaliana)
Explore Q941L3 
Go to UniProtKB:  Q941L3
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ941L3
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Protein BONZAI 1553Arabidopsis thalianaMutation(s): 0 
Gene Names: BON1CPN1At5g61900K22G18.2
UniProt
Find proteins for Q941L3 (Arabidopsis thaliana)
Explore Q941L3 
Go to UniProtKB:  Q941L3
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ941L3
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PG4

Query on PG4



Download:Ideal Coordinates CCD File
DC [auth D],
QA [auth B]
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
PGE

Query on PGE



Download:Ideal Coordinates CCD File
FA [auth A],
OB [auth C],
SA [auth B],
UD [auth F],
V [auth A]
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
PEG

Query on PEG



Download:Ideal Coordinates CCD File
AB [auth C]
BC [auth D]
CB [auth C]
DB [auth C]
EC [auth D]
AB [auth C],
BC [auth D],
CB [auth C],
DB [auth C],
EC [auth D],
GA [auth A],
HC [auth D],
I [auth A],
J [auth A],
KC [auth D],
O [auth A],
OD [auth F],
RA [auth B],
RB [auth D],
RC [auth E],
S [auth A],
XC [auth E]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL

Query on GOL



Download:Ideal Coordinates CCD File
AC [auth D]
BA [auth A]
CA [auth A]
CD [auth E]
DA [auth A]
AC [auth D],
BA [auth A],
CA [auth A],
CD [auth E],
DA [auth A],
EB [auth C],
FE [auth G],
GE [auth H],
JB [auth C],
KD [auth F],
LE [auth H],
NA [auth B],
PB [auth C],
QD [auth F],
R [auth A],
SB [auth D],
SD [auth F],
UB [auth D],
UC [auth E],
VC [auth E],
W [auth A],
WC [auth E],
YC [auth E],
YD [auth F],
Z [auth A],
ZA [auth C],
ZB [auth D]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO

Query on EDO



Download:Ideal Coordinates CCD File
AA [auth A]
AD [auth E]
BB [auth C]
BD [auth E]
BE [auth G]
AA [auth A],
AD [auth E],
BB [auth C],
BD [auth E],
BE [auth G],
CC [auth D],
CE [auth G],
DD [auth F],
DE [auth G],
EA [auth A],
ED [auth F],
EE [auth G],
FB [auth C],
FC [auth D],
FD [auth F],
GB [auth C],
GC [auth D],
GD [auth F],
HA [auth B],
HB [auth C],
HD [auth F],
HE [auth H],
IA [auth B],
IB [auth C],
IC [auth D],
ID [auth F],
IE [auth H],
JA [auth B],
JC [auth D],
JD [auth F],
JE [auth H],
K [auth A],
KA [auth B],
KB [auth C],
KE [auth H],
L [auth A],
LA [auth B],
LB [auth C],
LC [auth D],
LD [auth F],
M [auth A],
MA [auth B],
MB [auth C],
MC [auth D],
MD [auth F],
ME [auth H],
N [auth A],
NB [auth C],
NC [auth D],
ND [auth F],
NE [auth H],
OA [auth B],
OC [auth D],
P [auth A],
PA [auth B],
PD [auth F],
Q [auth A],
RD [auth F],
SC [auth E],
T [auth A],
TA [auth B],
TB [auth D],
TC [auth E],
TD [auth F],
U [auth A],
UA [auth B],
VA [auth B],
VB [auth D],
VD [auth F],
WA [auth B],
WB [auth D],
WD [auth F],
X [auth A],
XA [auth B],
XB [auth D],
XD [auth F],
Y [auth A],
YA [auth C],
YB [auth D],
ZC [auth E],
ZD [auth F]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CA
(Subject of Investigation/LOI)

Query on CA



Download:Ideal Coordinates CCD File
AE [auth F],
QC [auth D]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
PC [auth D],
QB [auth C]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free:  0.266 (Depositor), 0.266 (DCC) 
  • R-Value Work:  0.227 (Depositor), 0.227 (DCC) 
  • R-Value Observed: 0.229 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 122.284α = 90
b = 118.716β = 90.2
c = 222.253γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-09-16
    Type: Initial release
  • Version 1.1: 2024-03-27
    Changes: Data collection, Database references, Refinement description