9NWN | pdb_00009nwn

Structure of minimal CRISPR polymerase bound to ApNHpp

• PDB DOI: https://doi.org/10.2210/pdb9NWN/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Escherichia coli
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2025-03-24 Released: 2025-08-27 
• Deposition Author(s): Doherty, E.E., Bolling, C.B., Wilcox, X.E., Doudna, J.A.
• Funding Organization(s): Howard Hughes Medical Institute (HHMI), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.28 Å
• R-Value Free: 
  0.249 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.224 (Depositor), 0.225 (DCC) 
• R-Value Observed: 
  0.227 (Depositor) 

Starting Model: in silico

Literature

Structure of minimal CRISPR polymerase bound to ApNHpp

Doherty, E.E., Bolling, C.B., Wilcox, X.E., Doudna, J.A.

To be published.

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)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 29.15 kDa 
• Atom Count: 2,032 
• Modeled Residue Count: 240 
• Deposited Residue Count: 250 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MCpol domain-containing protein	A [auth B], B [auth A]	125	Escherichia coli	Mutation(s): 0  Gene Names: DU321_04150
UniProt
Find proteins for A0A426EXS8 (Escherichia coli) Explore A0A426EXS8  Go to UniProtKB:  A0A426EXS8

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZAN (Subject of Investigation/LOI)	C [auth B], E [auth A]	5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]adenosine C10 H17 N6 O12 P3 WUPFAKUEHUVIDK-KQYNXXCUSA-N
MG (Subject of Investigation/LOI)	D [auth B], F [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.28 Å
• R-Value Free:  0.249 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.224 (Depositor), 0.225 (DCC) 
• R-Value Observed: 0.227 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.135	α = 90
b = 56.769	β = 90
c = 93.705	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-08-27 
Deposition Author(s): Doherty, E.E., Bolling, C.B., Wilcox, X.E., Doudna, J.A.

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Funding Organization	Location	Grant Number
Howard Hughes Medical Institute (HHMI)	United States	--
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	F32GM153031

Revision History  

• Version 1.0: 2025-08-27
  Type: Initial release