6DZ4 | pdb_00006dz4

Crystal structure of Salmonella typhimurium Tryptophan Synthase with sodium ion at the metal coordination site and (E)-N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)-L-serine at the beta-site

PDB DOI: https://doi.org/10.2210/pdb6DZ4/pdb

Classification: LYASE/LYASE Inhibitor
Organism(s): Salmonella enterica subsp. enterica serovar Typhimurium str. LT2
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2018-07-02 Released: 2019-07-10
Deposition Author(s): Hilario, E., Dunn, M.F., Mueller, L.J., Fan, L.
Funding Organization(s): National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.45 Å
R-Value Free:
0.186 (Depositor), 0.190 (DCC)
R-Value Work:
0.147 (Depositor), 0.150 (DCC)
R-Value Observed:
0.149 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 3.1 of the entry. See complete history.

Literature

Crystal structure of Salmonella typhimurium Tryptophan Synthase with sodium ion at the metal coordination site and (E)-N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)-L-serine at the beta site

Hilario, E., Dunn, M.F., Mueller, L.J., Fan, L.

To be published.

Macromolecule Content

Total Structure Weight: 73.22 kDa
Atom Count: 5,920
Modelled Residue Count: 650
Deposited Residue Count: 665
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tryptophan synthase alpha chain	A	268	Salmonella enterica subsp. enterica serovar Typhimurium str. LT2	Mutation(s): 0 Gene Names: trpA, STM1727 EC: 4.2.1.20
UniProt
Find proteins for P00929 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)) Explore P00929 Go to UniProtKB: P00929
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00929
Sequence Annotations Expand
Reference Sequence LOADING

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Tryptophan synthase beta chain	B	397	Salmonella enterica subsp. enterica serovar Typhimurium str. LT2	Mutation(s): 0 Gene Names: trpB, STM1726 EC: 4.2.1.20
UniProt
Find proteins for P0A2K1 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)) Explore P0A2K1 Go to UniProtKB: P0A2K1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0A2K1
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
KOU (Subject of Investigation/LOI) Query on KOU Download Ideal Coordinates CCD File SDF format, chain I [auth B] MOL2 format, chain I [auth B] mmCIF format, chain I [auth B]	I [auth B]	(E)-N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)-L-serine C₁₁ H₁₅ N₂ O₈ P ZTQZHYMXYBDMIL-BIMOUXMDSA-N		Interactions Focus chain I [auth B] Interactions & Density Focus chain I [auth B]
DMS Query on DMS Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain U [auth B] SDF format, chain V [auth B] SDF format, chain W [auth B] SDF format, chain X [auth B] SDF format, chain T [auth B] SDF format, chain Y [auth B] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain U [auth B] MOL2 format, chain V [auth B] MOL2 format, chain W [auth B] MOL2 format, chain X [auth B] MOL2 format, chain T [auth B] MOL2 format, chain Y [auth B] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain R [auth B] mmCIF format, chain S [auth B] mmCIF format, chain U [auth B] mmCIF format, chain V [auth B] mmCIF format, chain W [auth B] mmCIF format, chain X [auth B] mmCIF format, chain T [auth B] mmCIF format, chain Y [auth B]	E [auth A] F [auth A] G [auth A] H [auth A] R [auth B] E [auth A], F [auth A], G [auth A], H [auth A], R [auth B], S [auth B], T [auth B], U [auth B], V [auth B], W [auth B], X [auth B], Y [auth B]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain N [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain N [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain N [auth B]	C [auth A] D [auth A] L [auth B] M [auth B] N [auth B] C [auth A], D [auth A], L [auth B], M [auth B], N [auth B], O [auth B], P [auth B], Q [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B]
NA (Subject of Investigation/LOI) Query on NA Download Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain J [auth B] mmCIF format, chain K [auth B] mmCIF format, chain J [auth B]	J [auth B], K [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain J [auth B] Focus chain K [auth B] Interactions & Density Focus chain J [auth B] Focus chain K [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.45 Å
R-Value Free: 0.186 (Depositor), 0.190 (DCC)
R-Value Work: 0.147 (Depositor), 0.150 (DCC)
R-Value Observed: 0.149 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 182.509	α = 90
b = 59.3	β = 94.69
c = 67.325	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2019-07-10

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)	United States	2R01GM097569-06A1

Revision History (Full details and data files)

Version 1.0: 2019-07-10
Type: Initial release
Version 1.1: 2019-12-18
Changes: Author supporting evidence
Version 2.0: 2020-05-06
Changes: Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary
Version 3.0: 2020-06-10
Type: Coordinate replacement
Reason: Model orientation/position
Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Derived calculations, Refinement description, Structure summary
Version 3.1: 2023-10-11
Changes: Data collection, Database references, Derived calculations, Refinement description