5JFY | pdb_00005jfy

Crystal structure of a plant cytidine deaminase

PDB DOI: https://doi.org/10.2210/pdb5JFY/pdb

Classification: HYDROLASE
Organism(s): Brassica oleracea var. capitata
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2016-04-19 Released: 2017-04-26
Deposition Author(s): Taylor, M.W., Lee, J.E.
Funding Organization(s): Canadian Institutes of Health Research (CIHR)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.214 (Depositor), 0.181 (DCC)
R-Value Work:
0.181 (Depositor), 0.184 (DCC)
R-Value Observed:
0.182 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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

Literature

To be published

Taylor, M.W., Lee, J.E.

To be published.

Macromolecule Content

Total Structure Weight: 60.63 kDa
Atom Count: 3,804
Modeled Residue Count: 476
Deposited Residue Count: 556
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Deoxycytidine deaminase	A, B, C, D	139	Brassica oleracea var. capitata	Mutation(s): 0
UniProt
Find proteins for H2EMX8 (Brassica oleracea var. capitata) Explore H2EMX8 Go to UniProtKB: H2EMX8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	H2EMX8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEZ Query on HEZ Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain U [auth D] MOL2 format, chain H [auth A] MOL2 format, chain U [auth D] mmCIF format, chain H [auth A] mmCIF format, chain U [auth D]	H [auth A], U [auth D]	HEXANE-1,6-DIOL C₆ H₁₄ O₂ XXMIOPMDWAUFGU-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain U [auth D] Interactions & Density Focus chain H [auth A] Focus chain U [auth D]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain O [auth C] SDF format, chain P [auth C] SDF format, chain Q [auth C] MOL2 format, chain O [auth C] MOL2 format, chain P [auth C] MOL2 format, chain Q [auth C] mmCIF format, chain O [auth C] mmCIF format, chain P [auth C] mmCIF format, chain Q [auth C]	O [auth C], P [auth C], Q [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain O [auth C] Focus chain P [auth C] Focus chain Q [auth C] Interactions & Density Focus chain O [auth C] Focus chain P [auth C] Focus chain Q [auth C]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain J [auth B] SDF format, chain N [auth C] SDF format, chain T [auth D] MOL2 format, chain F [auth A] MOL2 format, chain J [auth B] MOL2 format, chain N [auth C] MOL2 format, chain T [auth D] mmCIF format, chain F [auth A] mmCIF format, chain J [auth B] mmCIF format, chain N [auth C] mmCIF format, chain T [auth D]	F [auth A], J [auth B], N [auth C], T [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain J [auth B] Focus chain N [auth C] Focus chain T [auth D] Interactions & Density Focus chain F [auth A] Focus chain J [auth B] Focus chain N [auth C] Focus chain T [auth D]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain R [auth C] MOL2 format, chain G [auth A] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain R [auth C] mmCIF format, chain G [auth A] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B] mmCIF format, chain R [auth C]	G [auth A], K [auth B], L [auth B], R [auth C]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain G [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain R [auth C] Interactions & Density Focus chain G [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain R [auth C]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain S [auth D] SDF format, chain M [auth C] SDF format, chain E [auth A] MOL2 format, chain I [auth B] MOL2 format, chain S [auth D] MOL2 format, chain M [auth C] MOL2 format, chain E [auth A] mmCIF format, chain I [auth B] mmCIF format, chain S [auth D] mmCIF format, chain M [auth C] mmCIF format, chain E [auth A]	E [auth A], I [auth B], M [auth C], S [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain E [auth A] Focus chain I [auth B] Focus chain M [auth C] Focus chain S [auth D] Interactions & Density Focus chain E [auth A] Focus chain I [auth B] Focus chain M [auth C] Focus chain S [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.214 (Depositor), 0.181 (DCC)
R-Value Work: 0.181 (Depositor), 0.184 (DCC)
R-Value Observed: 0.182 (Depositor)

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.808	α = 90
b = 99.808	β = 90
c = 143.061	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHASER	phasing
PDB_EXTRACT	data extraction
Aimless	data scaling
Coot	model building
XDS	data reduction

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2017-04-26

Deposition Author(s):

Taylor, M.W.

Lee, J.E.

Funding Organization	Location	Grant Number
Canadian Institutes of Health Research (CIHR)	Canada	--

Revision History (Full details and data files)

Version 1.0: 2017-04-26
Type: Initial release
Version 1.1: 2017-05-03
Changes: Data collection
Version 1.2: 2017-09-27
Changes: Author supporting evidence
Version 1.3: 2020-01-08
Changes: Author supporting evidence
Version 1.4: 2023-09-27
Changes: Data collection, Database references, Derived calculations, Refinement description