7SU6 | pdb_00007su6

DIHYDRONEOPTERIN ALDOLASE (DHNA) Lys98Ala FROM YERSINIA PESTIS CO-CRYSTALLIZED with 7,8-dihydroneopterin

• PDB DOI: https://doi.org/10.2210/pdb7SU6/pdb

• Classification: BIOSYNTHETIC PROTEIN
• Organism(s): Yersinia pestis
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2021-11-16 Released: 2022-12-28 
• Deposition Author(s): Bourne, C.R.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 
  0.292 (Depositor), 0.290 (DCC) 
• R-Value Work: 
  0.241 (Depositor), 0.240 (DCC) 
• R-Value Observed: 
  0.244 (Depositor) 

Starting Model: experimental

Literature

DIHYDRONEOPTERIN ALDOLASE (DHNA) Lys98Ala FROM YERSINIA PESTIS CO-CRYSTALLIZED with 7,8-dihydroneopterin

Bourne, C.R., Tan, A.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D4  (Explore in 3D)
Global Stoichiometry: Homo 8-mer - A8 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 65.62 kDa 
• Atom Count: 3,930 
• Modeled Residue Count: 454 
• Deposited Residue Count: 572 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
7,8-dihydroneopterin aldolase	A, B, C, D	143	Yersinia pestis	Mutation(s): 1  Gene Names: y3531 EC: 4.1.2.25
UniProt
Find proteins for A0A5P8YJX5 (Yersinia pestis) Explore A0A5P8YJX5  Go to UniProtKB:  A0A5P8YJX5

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NPR (Subject of Investigation/LOI)	E [auth A], G [auth B], I [auth C], J [auth D]	2-AMINO-7,8-DIHYDRO-6-(1,2,3-TRIHYDROXYPROPYL)-4(1H)-PTERIDINONE C9 H13 N5 O4 YQIFAMYNGGOTFB-NJGYIYPDSA-N
MPD	F [auth A], H [auth B]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free:  0.292 (Depositor), 0.290 (DCC) 
• R-Value Work:  0.241 (Depositor), 0.240 (DCC) 
• R-Value Observed: 0.244 (Depositor) 

Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.426	α = 90
b = 79.248	β = 90
c = 96.549	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-12-28 
Deposition Author(s): Bourne, C.R.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)		P20GM103447

Revision History  

• Version 1.0: 2022-12-28
  Type: Initial release
  
• Version 1.1: 2023-10-25
  Changes: Data collection, Refinement description