8KFR

Crystal structure of ZmMOC1/nicked Holliday junction/Ca2+ complex

• PDB DOI: https://doi.org/10.2210/pdb8KFR/pdb

• Classification: HYDROLASE
• Organism(s): Zea mays
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-08-16 Released: 2024-06-26 
• Deposition Author(s): Zhang, D., Luo, Z., Lin, Z.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.240 
• R-Value Work: 0.201 
• R-Value Observed: 0.203 

Literature

MOC1 cleaves Holliday junctions through a cooperative nick and counter-nick mechanism mediated by metal ions

Zhang, D., Xu, S., Luo, Z., Lin, Z.

(2024) Nat Commun 15: 5140

• DOI: https://doi.org/10.1038/s41467-024-49490-9

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

Macromolecule Content

• Total Structure Weight: 55.79 kDa 
• Atom Count: 3,992 
• Modelled Residue Count: 392 
• Deposited Residue Count: 392 
• Unique protein chains: 1
• Unique nucleic acid chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Holliday junction resolvase MOC1, chloroplastic	A, B	163	Zea mays	Mutation(s): 0  Gene Names: 100192759
UniProt
Find proteins for B4FCI7 (Zea mays) Explore B4FCI7  Go to UniProtKB:  B4FCI7

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (33-MER)	C	33	Zea mays

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (25-MER)	D	25	Zea mays

Entity ID: 4
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*CP*AP*CP*GP*AP*TP*TP*G)-3')	E	8	Zea mays

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	G [auth A], I [auth B], J [auth B], K [auth C]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CA	F [auth A], H [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.240 
• R-Value Work: 0.201 
• R-Value Observed: 0.203 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.98	α = 90
b = 77.6	β = 98.05
c = 63.28	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
autoPROC	data scaling
PHASER	phasing
PHENIX	model building

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-06-26 
Deposition Author(s): Zhang, D., Luo, Z., Lin, Z.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	31971222

Revision History  

• Version 1.0: 2024-06-26
  Type: Initial release