6L08 | pdb_00006l08

Crystal structure of Arabidopsis cytidine deaminase

PDB DOI: https://doi.org/10.2210/pdb6L08/pdb

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

Deposited: 2019-09-26 Released: 2020-08-05
Deposition Author(s): Jia, W., Xiao, W., Lin, L.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free:
0.285 (Depositor), 0.292 (DCC)
R-Value Work:
0.249 (Depositor), 0.260 (DCC)
R-Value Observed:
0.251 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of Arabidopsis thaliana cytidine deaminase.

Wang, J., Guo, Q., Liu, L., Wang, X.

(2020) Biochem Biophys Res Commun 529: 659-665

DOI: https://doi.org/10.1016/j.bbrc.2020.06.084

Macromolecule Content

Total Structure Weight: 67.16 kDa
Atom Count: 4,183
Modeled Residue Count: 569
Deposited Residue Count: 616
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytidine deaminase 1	A, B	308	Arabidopsis thaliana	Mutation(s): 0 Gene Names: CDA1, CDD, DESZ, At2g19570, F3P11 EC: 3.5.4.5
UniProt
Find proteins for O65896 (Arabidopsis thaliana) Explore O65896 Go to UniProtKB: O65896
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O65896
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 (Subject of Investigation/LOI) Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain C [auth B] MOL2 format, chain C [auth B] mmCIF format, chain C [auth B]	C [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth B] Interactions & Density Focus chain C [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free: 0.285 (Depositor), 0.292 (DCC)
R-Value Work: 0.249 (Depositor), 0.260 (DCC)
R-Value Observed: 0.251 (Depositor)

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 112.644	α = 90
b = 112.644	β = 90
c = 111.585	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling
PDB_EXTRACT	data extraction
HKL-2000	data collection
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2020-08-05

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2020-08-05
Type: Initial release
Version 1.1: 2023-11-22
Changes: Data collection, Database references, Refinement description

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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.