6KXT | pdb_00006kxt

BON1-C2B

PDB DOI: https://doi.org/10.2210/pdb6KXT/pdb

Classification: LIPID BINDING PROTEIN
Organism(s): Arabidopsis thaliana
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2019-09-12 Released: 2020-09-16
Deposition Author(s): Wang, Q.C., Jiang, M.Q., Isupov, M.N., Sun, L.F., Wu, Y.K.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.25 Å
R-Value Free:
0.195 (Depositor), 0.199 (DCC)
R-Value Work:
0.168 (Depositor), 0.177 (DCC)
R-Value Observed:
0.170 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 6KXT

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: 16.07 kDa
Atom Count: 1,418
Modeled Residue Count: 144
Deposited Residue Count: 144
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein BONZAI 1	A	144	Arabidopsis thaliana	Mutation(s): 0 Gene Names: BON1, CPN1, At5g61900, K22G18.2
UniProt
Find proteins for Q941L3 (Arabidopsis thaliana) Explore Q941L3 Go to UniProtKB: Q941L3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q941L3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MES Query on MES Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C₆ H₁₃ N O₄ S SXGZJKUKBWWHRA-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A]	C [auth A], D [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.25 Å
R-Value Free: 0.195 (Depositor), 0.199 (DCC)
R-Value Work: 0.168 (Depositor), 0.177 (DCC)
R-Value Observed: 0.170 (Depositor)

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.844	α = 90
b = 69.594	β = 90
c = 77.396	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
PHENIX	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2020-09-16

Deposition Author(s):

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.