2Q4W

Ensemble refinement of the protein crystal structure of cytokinin oxidase/dehydrogenase (CKX) from Arabidopsis thaliana At5g21482

PDB DOI: https://doi.org/10.2210/pdb2Q4W/pdb

Classification: OXIDOREDUCTASE
Organism(s): Arabidopsis thaliana
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2007-05-31 Released: 2007-06-19
Deposition Author(s): Levin, E.J., Kondrashov, D.A., Wesenberg, G.E., Phillips Jr., G.N., Center for Eukaryotic Structural Genomics (CESG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.201 (Depositor), 0.210 (DCC)
R-Value Work:
0.143 (Depositor), 0.150 (DCC)
R-Value Observed:
0.143 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.6 of the entry. See complete history.

Re-refinement Note

This entry reflects an alternative modeling of the original data in: 2EXR

Literature

Crystal structure of Arabidopsis thaliana cytokinin dehydrogenase.

Bae, E., Bingman, C.A., Bitto, E., Aceti, D.J., Phillips, G.N.

(2008) Proteins 70: 303-306

PubMed: 17886275 Search on PubMed
DOI: https://doi.org/10.1002/prot.21678
Primary Citation of Related Structures:
2EXR, 2Q4W

Organizational Affiliation

Center for Eukaryotic Structural Genomics, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA.

Macromolecule Content

Total Structure Weight: 59.15 kDa
Atom Count: 4,539
Modelled Residue Count: 491
Deposited Residue Count: 524
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytokinin dehydrogenase 7	A	524	Arabidopsis thaliana	Mutation(s): 8 Gene Names: CKX7, CKX5 EC: 1.5.99.12
UniProt
Find proteins for Q9FUJ1 (Arabidopsis thaliana) Explore Q9FUJ1 Go to UniProtKB: Q9FUJ1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9FUJ1
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD Query on FAD 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]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.201 (Depositor), 0.210 (DCC)
R-Value Work: 0.143 (Depositor), 0.150 (DCC)
R-Value Observed: 0.143 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.858	α = 90
b = 114.502	β = 90
c = 190.92	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
PDB_EXTRACT	data extraction
CNS	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2007-06-19

Deposition Author(s):

Center for Eukaryotic Structural Genomics (CESG)

Revision History (Full details and data files)

Version 1.0: 2007-06-19
Type: Initial release
Version 1.1: 2007-09-25
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2011-08-10
Changes: Other
Version 1.4: 2023-08-30
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.5: 2023-11-15
Changes: Data collection
Version 1.6: 2024-11-06
Changes: Structure summary