1VK5

X-ray Structure of Gene Product from Arabidopsis Thaliana At3g22680

PDB DOI: https://doi.org/10.2210/pdb1VK5/pdb

Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
Organism(s): Arabidopsis thaliana
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2004-05-06 Released: 2004-05-18
Deposition Author(s): Wesenberg, G.E., Smith, D.W., Phillips Jr., G.N., Johnson, K.A., Bingman, C.A., Allard, S.T.M., Center for Eukaryotic Structural Genomics (CESG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free:
0.183 (Depositor), 0.190 (DCC)
R-Value Work:
0.160 (Depositor), 0.160 (DCC)
R-Value Observed:
0.161 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Re-refinement Note

A newer entry is available that reflects an alternative modeling of the original data: 2Q3T

Literature

Structure at 1.6 A resolution of the protein from gene locus At3g22680 from Arabidopsis thaliana.

Allard, S.T., Bingman, C.A., Johnson, K.A., Wesenberg, G.E., Bitto, E., Jeon, W.B., Phillips, G.N.

(2005) Acta Crystallogr Sect F Struct Biol Cryst Commun 61: 647-650

PubMed: 16511118 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1107/S1744309105019743
Primary Citation of Related Structures:
1VK5

PubMed Abstract:
The gene product of At3g22680 from Arabidopsis thaliana codes for a protein of unknown function. The crystal structure of the At3g22680 gene product was determined by multiple-wavelength anomalous diffraction and refined to an R factor of 16.0% (Rfree = 18.4%) at 1.60 A resolution. The refined structure shows one monomer in the asymmetric unit, with one molecule of the non-denaturing detergent CHAPS {3-[(3-cholamidopropyl)dimethylammonio]-1-propane sulfonate} tightly bound. Protein At3g22680 shows no structural homology to any other known proteins and represents a new fold in protein conformation space.

Organizational Affiliation

Center for Eukaryotic Structural Genomics, Department of Biochemistry, University of Wisconsin-Madison, USA.

Macromolecule Content

Total Structure Weight: 19.15 kDa
Atom Count: 1,273
Modelled Residue Count: 121
Deposited Residue Count: 157
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
expressed protein	A	157	Arabidopsis thaliana	Mutation(s): 0 Gene Names: At3g22680
UniProt
Find proteins for Q9LUJ3 (Arabidopsis thaliana) Explore Q9LUJ3 Go to UniProtKB: Q9LUJ3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9LUJ3
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CPS Query on CPS Download Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE C₃₂ H₅₈ N₂ O₇ S UMCMPZBLKLEWAF-BCTGSCMUSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] SDF format, chain D [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] mmCIF format, chain B [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A]	B [auth A], C [auth A], D [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A]	F [auth A], G [auth A], H [auth A], I [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.183 (Depositor), 0.190 (DCC)
R-Value Work: 0.160 (Depositor), 0.160 (DCC)
R-Value Observed: 0.161 (Depositor)

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.45	α = 90
b = 83.45	β = 90
c = 60.575	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing
RESOLVE	phasing
ARP/wARP	model building
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2004-05-18

Deposition Author(s):

Center for Eukaryotic Structural Genomics (CESG)

Revision History (Full details and data files)

Version 1.0: 2004-05-18
Type: Initial release
Version 1.1: 2008-02-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Derived calculations, Version format compliance
Version 1.3: 2017-10-04
Changes: Refinement description
Version 1.4: 2023-12-27
Changes: Data collection, Database references, Derived calculations