8RSX | pdb_00008rsx

TRYPTOPHAN SYNTHASE measured via serial crystallography from a silicon HARE-chip

PDB DOI: https://doi.org/10.2210/pdb8RSX/pdb

Classification: LYASE
Organism(s): Salmonella enterica subsp. enterica serovar Typhimurium
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2024-01-25 Released: 2024-12-04
Deposition Author(s): Sung, S., Bosman, R., Prester, A., von Soosten, L., Dibenedetto, S., Bartels, K., von Stetten, D., Mehrabi, P., Schulz, E.C., Wilmanns, M.
Funding Organization(s): German Research Foundation (DFG), German Federal Ministry for Economic Affairs and Energy

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.220 (Depositor), 0.229 (DCC)
R-Value Work:
0.179 (Depositor), 0.190 (DCC)
R-Value Observed:
0.181 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

A systematic comparison of Kapton-based HARE chips for fixed-target serial crystallography

Bosman, R., Prester, A., Sung, S., von Soosten, L., Dibenedetto, S., Bartels, K., von Stetten, D., Mehrabi, P., Blatter, M., Lu, G., Suer, B., Wilmanns, M., Osbild, M., Schulz, E.C.

(2024) Cell Rep Phys Sci 5: 101987

DOI: https://doi.org/10.1016/j.xcrp.2024.101987

Macromolecule Content

Total Structure Weight: 71.64 kDa
Atom Count: 5,133
Modeled Residue Count: 651
Deposited Residue Count: 662
Unique protein chains: 2

Macromolecules

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| 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, 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00929
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Tryptophan synthase beta chain	B [auth E]	394	Salmonella enterica subsp. enterica serovar Typhimurium	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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0A2K1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CS Query on CS Download:Ideal Coordinates CCD File SDF format, chain C [auth E] MOL2 format, chain C [auth E] mmCIF format, chain C [auth E]	C [auth E]	CESIUM ION Cs NCMHKCKGHRPLCM-UHFFFAOYSA-N		Interactions Focus chain C [auth E] Interactions & Density Focus chain C [auth E]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain D [auth E] MOL2 format, chain D [auth E] mmCIF format, chain D [auth E]	D [auth E]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain D [auth E] Interactions & Density Focus chain D [auth E]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
LLP Query on LLP	B [auth E]	L-PEPTIDE LINKING	C₁₄ H₂₂ N₃ O₇ P		LYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.220 (Depositor), 0.229 (DCC)
R-Value Work: 0.179 (Depositor), 0.190 (DCC)
R-Value Observed: 0.181 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 183.6	α = 90
b = 61.5	β = 94.55
c = 67.6	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
CrystFEL	data reduction
CrystFEL	data scaling
PHASER	phasing

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2024-12-04

Deposition Author(s):

Funding Organization	Location	Grant Number
German Research Foundation (DFG)	Germany	458246365
German Research Foundation (DFG)	Germany	451079909
German Federal Ministry for Economic Affairs and Energy	Germany	01KI2114
German Research Foundation (DFG)	Germany	508072649