7K0B | pdb_00007k0b

The internal aldimine form of Salmonella typhimurium Tryptophan Synthase mutant beta-Q114A with cesium ion at the metal coordination site. A random beta-P270L mutation was inserted during PCR step

PDB DOI: https://doi.org/10.2210/pdb7K0B/pdb

Classification: LYASE/LYASE INHIBITOR
Organism(s): Salmonella enterica subsp. enterica serovar Typhimurium str. LT2
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2020-09-04 Released: 2021-09-22
Deposition Author(s): Hilario, E., Dunn, M.F., Mueller, L.J.
Funding Organization(s): National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.57 ?
R-Value Free:
0.236 (Depositor), 0.240 (DCC)
R-Value Work:
0.199 (Depositor), 0.200 (DCC)
R-Value Observed:
0.201 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

The internal aldimine form of Salmonella typhimurium Tryptophan Synthase mutant beta-Q114A with cesium ion at the metal coordination site. A random beta-P270L mutation was inserted during PCR step.

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

To be published.

Macromolecule Content

Total Structure Weight: 74.63 kDa
Atom Count: 5,808
Modeled Residue Count: 651
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

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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 str. LT2	Mutation(s): 2 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

Small Molecules

Ligands 9 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PLP (Subject of Investigation/LOI) Query on PLP Download Ideal Coordinates CCD File SDF format, chain Q [auth B] MOL2 format, chain Q [auth B] mmCIF format, chain Q [auth B]	Q [auth B]	PYRIDOXAL-5'-PHOSPHATE C₈ H₁₀ N O₆ P NGVDGCNFYWLIFO-UHFFFAOYSA-N		Interactions Focus chain Q [auth B] Interactions & Density Focus chain Q [auth B]
BCN Query on BCN Download Ideal Coordinates CCD File SDF format, chain W [auth B] MOL2 format, chain W [auth B] mmCIF format, chain W [auth B]	W [auth B]	BICINE C₆ H₁₃ N O₄ FSVCELGFZIQNCK-UHFFFAOYSA-N		Interactions Focus chain W [auth B] Interactions & Density Focus chain W [auth B]
CS Query on CS Download Ideal Coordinates CCD File SDF format, chain JA [auth B] SDF format, chain IA [auth B] MOL2 format, chain JA [auth B] MOL2 format, chain IA [auth B] mmCIF format, chain JA [auth B] mmCIF format, chain IA [auth B]	IA [auth B], JA [auth B]	CESIUM ION Cs NCMHKCKGHRPLCM-UHFFFAOYSA-N		Interactions Focus chain IA [auth B] Focus chain JA [auth B] Interactions & Density Focus chain IA [auth B] Focus chain JA [auth B]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A] mmCIF format, chain H [auth A]	H [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]
SER Query on SER Download Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	SERINE C₃ H₇ N O₃ MTCFGRXMJLQNBG-REOHCLBHSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain U [auth B] MOL2 format, chain U [auth B] mmCIF format, chain U [auth B]	U [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain U [auth B] Interactions & Density Focus chain U [auth B]
DMS Query on DMS Download Ideal Coordinates CCD File SDF format, chain BA [auth B] SDF format, chain GA [auth B] SDF format, chain HA [auth B] SDF format, chain K [auth A] SDF format, chain AA [auth B] SDF format, chain CA [auth B] SDF format, chain DA [auth B] SDF format, chain EA [auth B] SDF format, chain FA [auth B] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain X [auth B] SDF format, chain Y [auth B] SDF format, chain Z [auth B] MOL2 format, chain BA [auth B] MOL2 format, chain GA [auth B] MOL2 format, chain HA [auth B] MOL2 format, chain K [auth A] MOL2 format, chain AA [auth B] MOL2 format, chain CA [auth B] MOL2 format, chain DA [auth B] MOL2 format, chain EA [auth B] MOL2 format, chain FA [auth B] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain X [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain Z [auth B] mmCIF format, chain BA [auth B] mmCIF format, chain GA [auth B] mmCIF format, chain HA [auth B] mmCIF format, chain K [auth A] mmCIF format, chain AA [auth B] mmCIF format, chain CA [auth B] mmCIF format, chain DA [auth B] mmCIF format, chain EA [auth B] mmCIF format, chain FA [auth B] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain X [auth B] mmCIF format, chain Y [auth B] mmCIF format, chain Z [auth B]	AA [auth B] BA [auth B] CA [auth B] DA [auth B] EA [auth B] AA [auth B], BA [auth B], CA [auth B], DA [auth B], EA [auth B], FA [auth B], GA [auth B], HA [auth B], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], X [auth B], Y [auth B], Z [auth B]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain EA [auth B] Focus chain FA [auth B] Focus chain GA [auth B] Focus chain HA [auth B] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain EA [auth B] Focus chain FA [auth B] Focus chain GA [auth B] Focus chain HA [auth B] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain G [auth A] SDF format, chain V [auth B] SDF format, chain C [auth A] SDF format, chain F [auth A] SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain T [auth B] MOL2 format, chain D [auth A] MOL2 format, chain G [auth A] MOL2 format, chain V [auth B] MOL2 format, chain C [auth A] MOL2 format, chain F [auth A] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] mmCIF format, chain D [auth A] mmCIF format, chain G [auth A] mmCIF format, chain V [auth B] mmCIF format, chain C [auth A] mmCIF format, chain F [auth A] mmCIF format, chain R [auth B] mmCIF format, chain S [auth B] mmCIF format, chain T [auth B]	C [auth A] D [auth A] F [auth A] G [auth A] R [auth B] C [auth A], D [auth A], F [auth A], G [auth A], R [auth B], S [auth B], T [auth B], V [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain V [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain V [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain MA [auth B] SDF format, chain NA [auth B] SDF format, chain KA [auth B] SDF format, chain LA [auth B] SDF format, chain O [auth A] SDF format, chain OA [auth B] SDF format, chain P [auth A] MOL2 format, chain MA [auth B] MOL2 format, chain NA [auth B] MOL2 format, chain KA [auth B] MOL2 format, chain LA [auth B] MOL2 format, chain O [auth A] MOL2 format, chain OA [auth B] MOL2 format, chain P [auth A] mmCIF format, chain MA [auth B] mmCIF format, chain NA [auth B] mmCIF format, chain KA [auth B] mmCIF format, chain LA [auth B] mmCIF format, chain O [auth A] mmCIF format, chain OA [auth B] mmCIF format, chain P [auth A]	KA [auth B] LA [auth B] MA [auth B] NA [auth B] O [auth A] KA [auth B], LA [auth B], MA [auth B], NA [auth B], O [auth A], OA [auth B], P [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain KA [auth B] Focus chain LA [auth B] Focus chain MA [auth B] Focus chain NA [auth B] Focus chain O [auth A] Focus chain OA [auth B] Focus chain P [auth A] Interactions & Density Focus chain KA [auth B] Focus chain LA [auth B] Focus chain MA [auth B] Focus chain NA [auth B] Focus chain O [auth A] Focus chain OA [auth B] Focus chain P [auth A]