9MHO | pdb_00009mho

The structure of Zcp with nickel bound

• PDB DOI: https://doi.org/10.2210/pdb9MHO/pdb

• Classification: METAL BINDING PROTEIN
• Organism(s): Neisseria gonorrhoeae FA 1090
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-12-12 Released: 2025-12-17 
• Deposition Author(s): Bera, A.K., Liyayi, I.K., Criss, A.K., Noinaj, N.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.257 (Depositor), 0.258 (DCC) 
• R-Value Work: 
  0.219 (Depositor), 0.223 (DCC) 
• R-Value Observed: 
  0.222 (Depositor) 

Starting Model: experimental

Literature

The periplasmic zinc binding protein Zcp aids Neisseria gonorrhoeae assimilation to zinc limitation

Liyayi, I.K., Bera, A.K., Mahamarakkalage, R., Ferdausi, F., Noinaj, N., Chazin, W., Cornelissen, C.N., Criss, A.K.

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.

Biological Assembly Evidence: SAXS

Macromolecule Content 

• Total Structure Weight: 63.17 kDa 
• Atom Count: 3,699 
• Modeled Residue Count: 463 
• Deposited Residue Count: 548 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphoribosylglycinamide formyltransferase	A, B	274	Neisseria gonorrhoeae FA 1090	Mutation(s): 0  Gene Names: NGO_1049
UniProt
Find proteins for Q5F7W6 (Neisseria gonorrhoeae (strain ATCC 700825 / FA 1090)) Explore Q5F7W6  Go to UniProtKB:  Q5F7W6

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NI (Subject of Investigation/LOI)	C [auth A], D [auth B]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.257 (Depositor), 0.258 (DCC) 
• R-Value Work:  0.219 (Depositor), 0.223 (DCC) 
• R-Value Observed: 0.222 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.809	α = 90
b = 94.214	β = 90
c = 128.177	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-12-17 
Deposition Author(s): Bera, A.K., Liyayi, I.K., Criss, A.K., Noinaj, N.

---

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	NIH R01AI127793
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	NIH R01AI097312
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	NIH R21 AI161302
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	NIHT32AI007046
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	NIH F31AI167563

Revision History  

• Version 1.0: 2025-12-17
  Type: Initial release