6OJO

Dihydroneopterin aldolase (DHNA) from Yersinia pestis co-crystallized with pterine

PDB DOI: https://doi.org/10.2210/pdb6OJO/pdb

Classification: BIOSYNTHETIC PROTEIN
Organism(s): Yersinia pestis
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2019-04-11 Released: 2020-04-15
Deposition Author(s): Bourne, C.R.
Funding Organization(s): National Science Foundation (NSF, United States)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.89 Å
R-Value Free: 0.206
R-Value Work: 0.184
R-Value Observed: 0.185

Starting Model: experimental
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This is version 1.1 of the entry. See complete history.

Literature

Dihydroneopterin aldolase (DHNA) from Yersinia pestis co-crystallized with pterine

Bourne, C.R.

To be published.

Macromolecule Content

Total Structure Weight: 65.25 kDa
Atom Count: 4,241
Modelled Residue Count: 470
Deposited Residue Count: 572
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
7,8-dihydroneopterin aldolase	A, B, C, D	143	Yersinia pestis	Mutation(s): 0 Gene Names: y3531 EC: 4.1.2.25
UniProt
Find proteins for A0A5P8YJX5 (Yersinia pestis) Explore A0A5P8YJX5 Go to UniProtKB: A0A5P8YJX5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A5P8YJX5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PE0 Query on PE0 Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth B] SDF format, chain G [auth C] SDF format, chain H [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth B] MOL2 format, chain G [auth C] MOL2 format, chain H [auth D] mmCIF format, chain E [auth A] mmCIF format, chain F [auth B] mmCIF format, chain G [auth C] mmCIF format, chain H [auth D]	E [auth A], F [auth B], G [auth C], H [auth D]	PTERINE C₆ H₅ N₅ O HNXQXTQTPAJEJL-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.89 Å
R-Value Free: 0.206
R-Value Work: 0.184
R-Value Observed: 0.185
Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.086	α = 90
b = 81.489	β = 90
c = 96.624	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	data scaling
PHENIX	phasing

Structure Validation

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Entry History & Funding Information

Deposition Data

Released Date: 2020-04-15

Deposition Author(s):

Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	1359457

Revision History (Full details and data files)

Version 1.0: 2020-04-15
Type: Initial release
Version 1.1: 2023-10-11
Changes: Data collection, Database references, Refinement description

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.