5CGQ | pdb_00005cgq

Crystal structure of Tryptophan Synthase from Salmonella typhimurium in complex with F9 ligand in the alpha-site and the product L-Tryptophan in the beta-site.

PDB DOI: https://doi.org/10.2210/pdb5CGQ/pdb

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

Deposited: 2015-07-09 Released: 2016-07-13
Deposition Author(s): Hilario, E., Caulkins, B.G., Young, R.P., Dunn, M.F., Mueller, L.J., Fan, L.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.18 ?
R-Value Free:
0.161 (Depositor), 0.160 (DCC)
R-Value Work:
0.140 (Depositor), 0.140 (DCC)
R-Value Observed:
0.141 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Crystal structure of Tryptophan Synthase from Salmonella typhimurium in complex with F9 ligand and the product L-Tryptophan in the beta-site.

Hilario, E., Caulkins, B.G., Young, R.P., Dunn, M.F., Mueller, L.J., Fan, L.

To be published.

Macromolecule Content

Total Structure Weight: 73.06 kDa
Atom Count: 6,222
Modeled Residue Count: 658
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	Mutation(s): 0 Gene Names: trpA 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

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(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	Mutation(s): 0 Gene Names: trpB 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

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
F9F Query on F9F Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	2-({[4-(TRIFLUOROMETHOXY)PHENYL]SULFONYL}AMINO)ETHYL DIHYDROGEN PHOSPHATE C₉ H₁₁ F₃ N O₇ P S JDDKDMFCTOZVCJ-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
PLP Query on PLP Download Ideal Coordinates CCD File SDF format, chain E [auth B] MOL2 format, chain E [auth B] mmCIF format, chain E [auth B]	E [auth B]	PYRIDOXAL-5'-PHOSPHATE C₈ H₁₀ N O₆ P NGVDGCNFYWLIFO-UHFFFAOYSA-N		Interactions Focus chain E [auth B] Interactions & Density Focus chain E [auth B]
TRP Query on TRP Download Ideal Coordinates CCD File SDF format, chain F [auth B] MOL2 format, chain F [auth B] mmCIF format, chain F [auth B]	F [auth B]	TRYPTOPHAN C₁₁ H₁₂ N₂ O₂ QIVBCDIJIAJPQS-VIFPVBQESA-N		Interactions Focus chain F [auth B] Interactions & Density Focus chain F [auth B]
BCN Query on BCN Download Ideal Coordinates CCD File SDF format, chain G [auth B] MOL2 format, chain G [auth B] mmCIF format, chain G [auth B]	G [auth B]	BICINE C₆ H₁₃ N O₄ FSVCELGFZIQNCK-UHFFFAOYSA-N		Interactions Focus chain G [auth B] Interactions & Density Focus chain G [auth B]
CS Query on CS Download Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain I [auth B] SDF format, chain D [auth A] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] MOL2 format, chain D [auth A] mmCIF format, chain H [auth B] mmCIF format, chain I [auth B] mmCIF format, chain D [auth A]	D [auth A], H [auth B], I [auth B]	CESIUM ION Cs NCMHKCKGHRPLCM-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain H [auth B] Focus chain I [auth B] Interactions & Density Focus chain D [auth A] Focus chain H [auth B] Focus chain I [auth B]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain J [auth B] MOL2 format, chain J [auth B] mmCIF format, chain J [auth B]	J [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain J [auth B] Interactions & Density Focus chain J [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.18 ?
R-Value Free: 0.161 (Depositor), 0.160 (DCC)
R-Value Work: 0.140 (Depositor), 0.140 (DCC)
R-Value Observed: 0.141 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( ? )	Angle ( ? )
a = 182.553	α = 90
b = 59.3	β = 94.82
c = 67.368	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2016-07-13

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01GM097569

Revision History (Full details and data files)

Version 1.0: 2016-07-13
Type: Initial release
Version 1.1: 2017-09-27
Changes: Author supporting evidence, Derived calculations, Refinement description
Version 1.2: 2019-12-25
Changes: Author supporting evidence
Version 1.3: 2023-09-27
Changes: Data collection, Database references, Derived calculations, Refinement description