7F2A

Crystal structure of Neisseria meningitidis EarP bound TDP

• PDB DOI: https://doi.org/10.2210/pdb7F2A/pdb

• Classification: TRANSFERASE
• Organism(s): Neisseria meningitidis
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2021-06-10 Released: 2022-06-15 
• Deposition Author(s): Yoo, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.58 Å
• R-Value Free: 0.269 
• R-Value Work: 0.216 
• R-Value Observed: 0.220 

Literature

Crystal structure of Neisseria meningitidis EarP bound TDP

Yoo, Y.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content

• Total Structure Weight: 89.34 kDa 
• Atom Count: 6,198 
• Modelled Residue Count: 752 
• Deposited Residue Count: 764 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Elongation factor P maturation arginine rhamnosyltransferase EarP	A, B [auth F]	382	Neisseria meningitidis	Mutation(s): 0  Gene Names: earP, CNQ34_12095, ERS040961_00525, ERS514851_01386, H7969_05560, JY21_02145, NMA510612_1261
UniProt
Find proteins for X5EQ00 (Neisseria meningitidis) Explore X5EQ00  Go to UniProtKB:  X5EQ00

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TYD (Subject of Investigation/LOI)	C [auth A], G [auth F]	THYMIDINE-5'-DIPHOSPHATE C10 H16 N2 O11 P2 UJLXYODCHAELLY-XLPZGREQSA-N
SO4	D [auth A], E [auth A], F [auth A], H [auth F]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.58 Å
• R-Value Free: 0.269 
• R-Value Work: 0.216 
• R-Value Observed: 0.220 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.855	α = 90
b = 125.287	β = 90
c = 128.278	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2022-06-15 
Deposition Author(s): Yoo, Y.

Revision History  

• Version 1.0: 2022-06-15
  Type: Initial release
  
• Version 1.1: 2024-11-13
  Changes: Data collection, Structure summary