5D04 | pdb_00005d04

Neisseria meningitidis 3 deoxy-D-arabino-heptulosonate 7-phosphate synthase Val223Ala variant regulated

PDB DOI: https://doi.org/10.2210/pdb5D04/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: 1.70 Å
R-Value Free:
0.178 (Depositor), 0.187 (DCC)
R-Value Work:
0.152 (Depositor), 0.165 (DCC)
R-Value Observed:
0.153 (Depositor)

wwPDB Validation 3D Report Full Report

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 Val223Ala variant regulated at 1.70 Angstroms resolution

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

To be published.

Macromolecule Content

Total Structure Weight: 78.69 kDa
Atom Count: 6,003
Modeled Residue Count: 692
Deposited Residue Count: 702
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phospho-2-dehydro-3-deoxyheptonate aldolase	A [auth C], B [auth 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
PHE Query on PHE Download:Ideal Coordinates CCD File SDF format, chain R [auth D] SDF format, chain I [auth C] MOL2 format, chain R [auth D] MOL2 format, chain I [auth C] mmCIF format, chain R [auth D] mmCIF format, chain I [auth C]	I [auth C], R [auth D]	PHENYLALANINE C₉ H₁₁ N O₂ COLNVLDHVKWLRT-QMMMGPOBSA-N		Interactions Focus chain I [auth C] Focus chain R [auth D] Interactions & Density Focus chain I [auth C] Focus chain R [auth D]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain Q [auth D] SDF format, chain P [auth D] SDF format, chain O [auth D] SDF format, chain H [auth C] MOL2 format, chain Q [auth D] MOL2 format, chain P [auth D] MOL2 format, chain O [auth D] MOL2 format, chain H [auth C] mmCIF format, chain Q [auth D] mmCIF format, chain P [auth D] mmCIF format, chain O [auth D] mmCIF format, chain H [auth C]	H [auth C], O [auth D], P [auth D], Q [auth D]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain H [auth C] Focus chain O [auth D] Focus chain P [auth D] Focus chain Q [auth D] Interactions & Density Focus chain H [auth C] Focus chain O [auth D] Focus chain P [auth D] Focus chain Q [auth D]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain T [auth D] SDF format, chain S [auth D] SDF format, chain K [auth C] SDF format, chain J [auth C] MOL2 format, chain T [auth D] MOL2 format, chain S [auth D] MOL2 format, chain K [auth C] MOL2 format, chain J [auth C] mmCIF format, chain T [auth D] mmCIF format, chain S [auth D] mmCIF format, chain K [auth C] mmCIF format, chain J [auth C]	J [auth C], K [auth C], S [auth D], T [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain J [auth C] Focus chain K [auth C] Focus chain S [auth D] Focus chain T [auth D] Interactions & Density Focus chain J [auth C] Focus chain K [auth C] Focus chain S [auth D] Focus chain T [auth D]
MN Query on MN Download:Ideal Coordinates CCD File SDF format, chain L [auth D] SDF format, chain C MOL2 format, chain L [auth D] MOL2 format, chain C mmCIF format, chain L [auth D] mmCIF format, chain C	C, L [auth D]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain C Focus chain L [auth D] Interactions & Density Focus chain C Focus chain L [auth D]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain D [auth C] SDF format, chain G [auth C] SDF format, chain N [auth D] SDF format, chain M [auth D] SDF format, chain F [auth C] SDF format, chain E [auth C] MOL2 format, chain D [auth C] MOL2 format, chain G [auth C] MOL2 format, chain N [auth D] MOL2 format, chain M [auth D] MOL2 format, chain F [auth C] MOL2 format, chain E [auth C] mmCIF format, chain D [auth C] mmCIF format, chain G [auth C] mmCIF format, chain N [auth D] mmCIF format, chain M [auth D] mmCIF format, chain F [auth C] mmCIF format, chain E [auth C]	D [auth C] E [auth C] F [auth C] G [auth C] M [auth D] D [auth C], E [auth C], F [auth C], G [auth C], M [auth D], N [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain D [auth C] Focus chain E [auth C] Focus chain F [auth C] Focus chain G [auth C] Focus chain M [auth D] Focus chain N [auth D] Interactions & Density Focus chain D [auth C] Focus chain E [auth C] Focus chain F [auth C] Focus chain G [auth C] Focus chain M [auth D] Focus chain N [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.178 (Depositor), 0.187 (DCC)
R-Value Work: 0.152 (Depositor), 0.165 (DCC)
R-Value Observed: 0.153 (Depositor)

Space Group: P 2₁ 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.62	α = 90
b = 75.43	β = 90
c = 143.939	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2016-08-10

Deposition Author(s):

Heyes, L.C.

Parker, E.J.

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, Structure summary