5ISY | pdb_00005isy

Crystal structure of Nudix family protein with NAD

• PDB DOI: https://doi.org/10.2210/pdb5ISY/pdb

• Classification: RNA BINDING PROTEIN
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2016-03-15 Released: 2016-09-14 
• Deposition Author(s): Zhang, D., Guan, Z., Zou, T., Yin, P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 
  0.244 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.182 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.185 (Depositor) 

Starting Model: experimental

Literature

Structural basis of prokaryotic NAD-RNA decapping by NudC

Zhang, D., Liu, Y., Wang, Q., Guan, Z., Wang, J., Liu, J., Zou, T., Yin, P.

(2016) Cell Res 26: 1062-1066

• PubMed: 27561816 
• DOI: https://doi.org/10.1038/cr.2016.98
• Primary Citation of Related Structures:  
  5ISY

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Organizational Affiliation: 
• National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, China.
Center for Structural Biology, School of Life Science, Tsinghua University, Beijing 100084, China.
College of Life Sciences and Technology, Huazhong Agricultural University, Wuhan 430070, China.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 61.32 kDa 
• Atom Count: 4,338 
• Modeled Residue Count: 502 
• Deposited Residue Count: 518 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH pyrophosphatase	A, B [auth C]	259	Escherichia coli K-12	Mutation(s): 1  Gene Names: nudC, yjaD, b3996, JW5548 EC: 3.6.1.22 (PDB Primary Data), 3.6.1 (UniProt)
UniProt
Find proteins for P32664 (Escherichia coli (strain K12)) Explore P32664  Go to UniProtKB:  P32664

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD	D [auth A], F [auth C]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N
ZN	C [auth A], E [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free:  0.244 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.182 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.185 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.411	α = 90
b = 98.702	β = 90
c = 113.739	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data collection
HKL-3000	data processing
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-09-14 
Deposition Author(s): Zhang, D., Guan, Z., Zou, T., Yin, P.

Revision History  

• Version 1.0: 2016-09-14
  Type: Initial release
  
• Version 1.1: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description