2HXD | pdb_00002hxd

Bifunctional dCTP deaminase-dUTPase mutant enzyme variant E145A from Methanocaldococcus jannaschii in complex with alpha,beta-imido dUTP and magnesium

PDB DOI: https://doi.org/10.2210/pdb2HXD/pdb

Classification: HYDROLASE
Organism(s): Methanocaldococcus jannaschii
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2006-08-03 Released: 2007-08-14
Deposition Author(s): Bynck, J.H., Johansson, E.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.221 (Depositor), 0.230 (DCC)
R-Value Work:
0.178 (Depositor), 0.187 (DCC)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 2HXD

Ligand Structure Quality Assessment

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

Literature

Structural evidence for a concerted Bifunctionality in dCTP deaminase-dUTPase from Methanocaldococcus jannaschii

Bynck, J.H., Willemoes, M., Larsen, S., Johansson, E.

To be published.

Macromolecule Content

Total Structure Weight: 23.9 kDa
Atom Count: 1,756
Modeled Residue Count: 199
Deposited Residue Count: 204
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
dCTP deaminase, dUMP-forming	A	204	Methanocaldococcus jannaschii	Mutation(s): 1 Gene Names: dcd EC: 3.5.4.30
UniProt
Find proteins for Q57872 (Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)) Explore Q57872 Go to UniProtKB: Q57872
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q57872
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
DUP Query on DUP Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE C₉ H₁₆ N₃ O₁₃ P₃ XZLLMTSKYYYJLH-SHYZEUOFSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
MG Query on MG 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]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.221 (Depositor), 0.230 (DCC)
R-Value Work: 0.178 (Depositor), 0.187 (DCC)

Space Group: I 4 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 171.513	α = 90
b = 171.513	β = 90
c = 171.513	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
DNA	data collection
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2007-08-14

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2007-08-14
Type: Initial release
Version 1.1: 2011-07-13
Changes: Derived calculations, Version format compliance
Version 1.2: 2017-10-18
Changes: Refinement description
Version 1.3: 2021-11-10
Changes: Database references, Derived calculations
Version 1.4: 2023-10-25
Changes: Data collection, Refinement description

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

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.