4ZBP

Crystal structure of the AMPCPR-bound AtNUDT7

PDB DOI: https://doi.org/10.2210/pdb4ZBP/pdb

Classification: HYDROLASE
Organism(s): Arabidopsis thaliana
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2015-04-15 Released: 2015-09-09
Deposition Author(s): Tang, Q., Liu, C., Zhong, C., Ding, J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free:
0.290 (Depositor), 0.300 (DCC)
R-Value Work:
0.238 (Depositor), 0.250 (DCC)
R-Value Observed:
0.240 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Crystal Structures of Arabidopsis thaliana Nudix Hydrolase NUDT7 Reveal a Previously Unobserved Conformation.

Tang, Q., Liu, C., Zhong, C., Ding, J.

(2015) Mol Plant 8: 1557-1559

PubMed: 26253775 Search on PubMed
DOI: https://doi.org/10.1016/j.molp.2015.07.010
Primary Citation of Related Structures:
4ZB3, 4ZBP

Organizational Affiliation

National Center for Protein Sciences Shanghai, State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai 200031, China.

Macromolecule Content

Total Structure Weight: 106.52 kDa
Atom Count: 6,428
Modelled Residue Count: 790
Deposited Residue Count: 930
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nudix hydrolase 7	A, B, C	310	Arabidopsis thaliana	Mutation(s): 0 Gene Names: NUDT7, GFG1, NUDX7, At4g12720, T20K18.70 EC: 3.6.1 (PDB Primary Data), 3.6.1.13 (PDB Primary Data), 3.6.1.22 (PDB Primary Data)
UniProt
Find proteins for Q9SU14 (Arabidopsis thaliana) Explore Q9SU14 Go to UniProtKB: Q9SU14
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9SU14
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ADV Query on ADV Download Ideal Coordinates CCD File SDF format, chain G [auth C] MOL2 format, chain G [auth C] mmCIF format, chain G [auth C]	G [auth C]	ALPHA-BETA METHYLENE ADP-RIBOSE C₁₆ H₂₅ N₅ O₁₃ P₂ ZPZRETFSCSWNDT-DBXCYWGHSA-N		Interactions Focus chain G [auth C] Interactions & Density Focus chain G [auth C]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth B] SDF format, chain F [auth B] SDF format, chain H [auth C] MOL2 format, chain D [auth A] MOL2 format, chain E [auth B] MOL2 format, chain F [auth B] MOL2 format, chain H [auth C] mmCIF format, chain D [auth A] mmCIF format, chain E [auth B] mmCIF format, chain F [auth B] mmCIF format, chain H [auth C]	D [auth A], E [auth B], F [auth B], H [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain D [auth A] Focus chain E [auth B] Focus chain F [auth B] Focus chain H [auth C] Interactions & Density Focus chain D [auth A] Focus chain E [auth B] Focus chain F [auth B] Focus chain H [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.290 (Depositor), 0.300 (DCC)
R-Value Work: 0.238 (Depositor), 0.250 (DCC)
R-Value Observed: 0.240 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.202	α = 90
b = 258.72	β = 90
c = 157.548	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data scaling
PDB_EXTRACT	data extraction
HKL-2000	data reduction
PHENIX	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2015-09-09

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2015-09-09
Type: Initial release
Version 1.1: 2015-10-28
Changes: Database references
Version 1.2: 2023-11-08
Changes: Data collection, Database references, Derived calculations, Refinement description