3GF0 | pdb_00003gf0

Bifunctional dCTP deaminase-dUTPase mutant enzyme variant E145Q from Methanocaldococcus jannaschii in complex with pyrophosphate and magnesium

PDB DOI: https://doi.org/10.2210/pdb3GF0/pdb
Entry: 3GF0 supersedes: 2HXE

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

Deposited: 2009-02-26 Released: 2009-03-10
Deposition Author(s): Siggaard, J.H.B., Johansson, E., Vognsen, T., Helt, S.S., Harris, P., Willemoes, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.62 Å
R-Value Free:
0.229 (Depositor), 0.222 (DCC)
R-Value Work:
0.191 (Depositor), 0.185 (DCC)
R-Value Observed:
0.192 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 3GF0

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

Literature

Pre-steady State Kinetic and Structural Evidence for a Concerted Biofunctionality in dCTP deaminase-dUTPase from Methanocaldococcus jannaschii

Siggaard, J.H.B., Johansson, E., Vognsen, T., Helt, S.S., Harris, P., Larsen, S., Willemoes, M.

To be published.

Macromolecule Content

Total Structure Weight: 23.73 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 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
POP Query on POP Download:Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	PYROPHOSPHATE 2- H₂ O₇ P₂ XPPKVPWEQAFLFU-UHFFFAOYSA-L		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain D [auth A] SDF format, chain C [auth A] SDF format, chain B [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] MOL2 format, chain B [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A] mmCIF format, chain B [auth A]	B [auth A], C [auth A], D [auth A], E [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.62 Å
R-Value Free: 0.229 (Depositor), 0.222 (DCC)
R-Value Work: 0.191 (Depositor), 0.185 (DCC)
R-Value Observed: 0.192 (Depositor)

Space Group: I 4 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 171.569	α = 90
b = 171.569	β = 90
c = 171.569	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2009-03-10

Deposition Author(s):

Siggaard, J.H.B.

This entry supersedes: 2HXE

Revision History (Full details and data files)

Version 1.0: 2009-03-10
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-11-01
Changes: Refinement description
Version 1.3: 2021-11-10
Changes: Database references, Derived calculations
Version 1.4: 2023-11-01
Changes: Data collection, 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.