4QC9 | pdb_00004qc9

Crystal structure of Vaccinia virus uracil-DNA glycosylase mutant 3GD4

PDB DOI: https://doi.org/10.2210/pdb4QC9/pdb

Classification: HYDROLASE
Organism(s): Vaccinia virus Ankara
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2014-05-09 Released: 2015-05-13
Deposition Author(s): Sartmatova, D., Nash, T., Schormann, N., Nuth, M., Ricciardi, R., Banerjee, S., Chattopadhyay, D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.26 Å
R-Value Free:
0.229 (Depositor), 0.234 (DCC)
R-Value Work:
0.185 (Depositor), 0.194 (DCC)
R-Value Observed:
0.187 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Crystal structure of Vaccinia virus uracil-DNA glycosylase mutant 3GD4

Sartmatova, D., Nash, T., Schormann, N., Nuth, M., Ricciardi, R., Banerjee, S., Chattopadhyay, D.

To be published.

Macromolecule Content

Total Structure Weight: 101.86 kDa
Atom Count: 7,285
Modeled Residue Count: 875
Deposited Residue Count: 884
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uracil-DNA glycosylase	A, B [auth C], C [auth D], D [auth B]	221	Vaccinia virus Ankara	Mutation(s): 4 Gene Names: ACAM3000_MVA_101, D4, MVA101R, UNG EC: 3.2.2.27
UniProt
Find proteins for P04303 (Vaccinia virus (strain Western Reserve)) Explore P04303 Go to UniProtKB: P04303
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P04303
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain O [auth B] SDF format, chain N [auth B] SDF format, chain M [auth D] SDF format, chain J [auth C] SDF format, chain E [auth A] MOL2 format, chain O [auth B] MOL2 format, chain N [auth B] MOL2 format, chain M [auth D] MOL2 format, chain J [auth C] MOL2 format, chain E [auth A] mmCIF format, chain O [auth B] mmCIF format, chain N [auth B] mmCIF format, chain M [auth D] mmCIF format, chain J [auth C] mmCIF format, chain E [auth A]	E [auth A], J [auth C], M [auth D], N [auth B], O [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth A] Focus chain J [auth C] Focus chain M [auth D] Focus chain N [auth B] Focus chain O [auth B] Interactions & Density Focus chain E [auth A] Focus chain J [auth C] Focus chain M [auth D] Focus chain N [auth B] Focus chain O [auth B]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain Q [auth B] SDF format, chain P [auth B] SDF format, chain L [auth D] SDF format, chain K [auth C] SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain F [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain P [auth B] MOL2 format, chain L [auth D] MOL2 format, chain K [auth C] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] mmCIF format, chain Q [auth B] mmCIF format, chain P [auth B] mmCIF format, chain L [auth D] mmCIF format, chain K [auth C] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A]	F [auth A] G [auth A] H [auth A] I [auth A] K [auth C] F [auth A], G [auth A], H [auth A], I [auth A], K [auth C], L [auth D], P [auth B], Q [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain K [auth C] Focus chain L [auth D] Focus chain P [auth B] Focus chain Q [auth B] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain K [auth C] Focus chain L [auth D] Focus chain P [auth B] Focus chain Q [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.26 Å
R-Value Free: 0.229 (Depositor), 0.234 (DCC)
R-Value Work: 0.185 (Depositor), 0.194 (DCC)
R-Value Observed: 0.187 (Depositor)

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.378	α = 90
b = 93.378	β = 90
c = 285.182	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
RAPD	data collection
XDS	data reduction
SCALA	data scaling
PHASER	phasing
REFMAC	refinement

Structure Validation

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Entry History

Deposition Data

Released Date: 2015-05-13

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2015-05-13
Type: Initial release
Version 1.1: 2016-06-29
Changes: Source and taxonomy
Version 1.2: 2019-07-17
Changes: Data collection, Refinement description
Version 1.3: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description