2XIO

Structure of putative deoxyribonuclease TATDN1 isoform a

PDB DOI: https://doi.org/10.2210/pdb2XIO/pdb

Classification: HYDROLASE
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2010-06-30 Released: 2010-07-14
Deposition Author(s): Muniz, J.R.C., Cocking, R., Puranik, S., Krojer, T., Raynor, J., Vollmar, M., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Weigelt, J., Bountra, C., Yue, W.W., Kavanagh, K.L., Oppermann, U.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.19 Å
R-Value Free:
0.192 (Depositor), 0.194 (DCC)
R-Value Work:
0.172 (Depositor), 0.173 (DCC)
R-Value Observed:
0.173 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Structure of Putative Deoxyribonuclease Tatdn1 Isoform A

Muniz, J.R.C., Cocking, R., Puranik, S., Krojer, T., Raynor, J., Vollmar, M., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Weigelt, J., Bountra, C., Yue, W.W., Kavanagh, K.L., Oppermann, U.

To be published.

Macromolecule Content

Total Structure Weight: 34.28 kDa
Atom Count: 3,035
Modelled Residue Count: 293
Deposited Residue Count: 301
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PUTATIVE DEOXYRIBONUCLEASE TATDN1	A	301	Homo sapiens	Mutation(s): 0 EC: 3.1.21
UniProt & NIH Common Fund Data Resources
Find proteins for Q6P1N9 (Homo sapiens) Explore Q6P1N9 Go to UniProtKB: Q6P1N9
PHAROS: Q6P1N9 GTEx: ENSG00000147687
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q6P1N9
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
NI Query on NI 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]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
NA Query on NA 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]	SODIUM ION Na FKNQFGJONOIPTF-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: 1.19 Å
R-Value Free: 0.192 (Depositor), 0.194 (DCC)
R-Value Work: 0.172 (Depositor), 0.173 (DCC)
R-Value Observed: 0.173 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.48	α = 90
b = 50.94	β = 90
c = 155.24	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2010-07-14

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2010-07-14
Type: Initial release
Version 1.1: 2012-12-05
Changes: Database references, Refinement description, Structure summary, Version format compliance
Version 1.2: 2018-01-24
Changes: Database references
Version 1.3: 2024-11-13
Changes: Data collection, Database references, Derived calculations, Other, Structure summary