5D09 | pdb_00005d09

Neisseria meningitidis 3 deoxy-D-arabino-heptulosonate 7-phosphate synthase Phe211Ala variant

PDB DOI: https://doi.org/10.2210/pdb5D09/pdb

Classification: TRANSFERASE
Organism(s): Neisseria meningitidis MC58
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2015-08-02 Released: 2016-08-10
Deposition Author(s): Heyes, L.C., Parker, E.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.35 Å
R-Value Free:
0.259 (Depositor), 0.258 (DCC)
R-Value Work:
0.210 (Depositor), 0.216 (DCC)
R-Value Observed:
0.213 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 5D09

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Neisseria meningitidis 3 deoxy-D-arabino-heptulosonate 7-phosphate synthase Phe211Ala variant at 2.35 Angstroms resolution

Heyes, L.C., Parker, E.J.

To be published.

Macromolecule Content

Total Structure Weight: 155.34 kDa
Atom Count: 10,453
Modeled Residue Count: 1,330
Deposited Residue Count: 1,404
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phospho-2-dehydro-3-deoxyheptonate aldolase	A, B, C, D	351	Neisseria meningitidis MC58	Mutation(s): 1 Gene Names: aroG, NMB0307 EC: 2.5.1.54
UniProt
Find proteins for Q9K169 (Neisseria meningitidis serogroup B (strain ATCC BAA-335 / MC58)) Explore Q9K169 Go to UniProtKB: Q9K169
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9K169
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PEP Query on PEP Download:Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	PHOSPHOENOLPYRUVATE C₃ H₅ O₆ P DTBNBXWJWCWCIK-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain L [auth C] SDF format, chain I [auth B] MOL2 format, chain L [auth C] MOL2 format, chain I [auth B] mmCIF format, chain L [auth C] mmCIF format, chain I [auth B]	I [auth B], L [auth C]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain I [auth B] Focus chain L [auth C] Interactions & Density Focus chain I [auth B] Focus chain L [auth C]
TMO Query on TMO Download:Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	trimethylamine oxide C₃ H₉ N O UYPYRKYUKCHHIB-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain M [auth C] MOL2 format, chain J [auth B] MOL2 format, chain M [auth C] mmCIF format, chain J [auth B] mmCIF format, chain M [auth C]	J [auth B], M [auth C]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain J [auth B] Focus chain M [auth C] Interactions & Density Focus chain J [auth B] Focus chain M [auth C]
MN Query on MN Download:Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain K [auth C] SDF format, chain N [auth D] SDF format, chain E [auth A] MOL2 format, chain H [auth B] MOL2 format, chain K [auth C] MOL2 format, chain N [auth D] MOL2 format, chain E [auth A] mmCIF format, chain H [auth B] mmCIF format, chain K [auth C] mmCIF format, chain N [auth D] mmCIF format, chain E [auth A]	E [auth A], H [auth B], K [auth C], N [auth D]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Focus chain K [auth C] Focus chain N [auth D] Interactions & Density Focus chain E [auth A] Focus chain H [auth B] Focus chain K [auth C] Focus chain N [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.35 Å
R-Value Free: 0.259 (Depositor), 0.258 (DCC)
R-Value Work: 0.210 (Depositor), 0.216 (DCC)
R-Value Observed: 0.213 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.675	α = 90
b = 135.727	β = 90
c = 149.356	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2016-08-10

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2016-08-10
Type: Initial release
Version 1.1: 2024-03-06
Changes: Data collection, Database references, Derived calculations

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.