3CEP | pdb_00003cep

Structure of a tryptophan synthase quinonoid intermediate

PDB DOI: https://doi.org/10.2210/pdb3CEP/pdb

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

Deposited: 2008-02-29 Released: 2008-04-01
Deposition Author(s): Barends, T.R.M., Domratcheva, T., Kulik, V., Blumenstein, L., Dunn, M.F., Schlichting, I.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.238 (Depositor), 0.200 (DCC)
R-Value Work:
0.198 (Depositor), 0.202 (DCC)
R-Value Observed:
0.200 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Structure and mechanistic implications of a tryptophan synthase quinonoid intermediate.

Barends, T.R., Domratcheva, T., Kulik, V., Blumenstein, L., Niks, D., Dunn, M.F., Schlichting, I.

(2008) Chembiochem 9: 1024-1028

PubMed: 18351684 Search on PubMed
DOI: https://doi.org/10.1002/cbic.200700703
Primary Citation Related Structures:
3CEP

Organizational Affiliation

Abteilung Biomolekulare Mechanismen, Max Planck Institut für Medizinische Forschung, Jahnstrasse 29, 69120 Heidelberg, Germany.

Macromolecule Content

Total Structure Weight: 72.65 kDa
Atom Count: 5,266
Modeled Residue Count: 659
Deposited Residue Count: 664
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 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	396	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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0A2K1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PLP Query on PLP Download:Ideal Coordinates CCD File SDF format, chain H [auth B] MOL2 format, chain H [auth B] mmCIF format, chain H [auth B]	H [auth B]	PYRIDOXAL-5'-PHOSPHATE C₈ H₁₀ N O₆ P NGVDGCNFYWLIFO-UHFFFAOYSA-N		Interactions Focus chain H [auth B] Interactions & Density Focus chain H [auth B]
G3P Query on G3P 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]	SN-GLYCEROL-3-PHOSPHATE C₃ H₉ O₆ P AWUCVROLDVIAJX-GSVOUGTGSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
CS Query on CS Download:Ideal Coordinates CCD File SDF format, chain E [auth B] SDF format, chain F [auth B] SDF format, chain G [auth B] MOL2 format, chain E [auth B] MOL2 format, chain F [auth B] MOL2 format, chain G [auth B] mmCIF format, chain E [auth B] mmCIF format, chain F [auth B] mmCIF format, chain G [auth B]	E [auth B], F [auth B], G [auth B]	CESIUM ION Cs NCMHKCKGHRPLCM-UHFFFAOYSA-N		Interactions Focus chain E [auth B] Focus chain F [auth B] Focus chain G [auth B] Interactions & Density Focus chain E [auth B] Focus chain F [auth B] Focus chain G [auth B]
IDM Query on IDM Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain J [auth B] MOL2 format, chain D [auth A] MOL2 format, chain J [auth B] mmCIF format, chain D [auth A] mmCIF format, chain J [auth B]	D [auth A], J [auth B]	INDOLINE C₈ H₉ N LPAGFVYQRIESJQ-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain J [auth B] Interactions & Density Focus chain D [auth A] Focus chain J [auth B]
MH6 Query on MH6 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]	3-hydroxy-2-iminopropanoic acid C₃ H₅ N O₃ MUHXUPVPXJXCGV-DUXPYHPUSA-N		Interactions Focus chain I [auth B] Interactions & Density Focus chain I [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.238 (Depositor), 0.200 (DCC)
R-Value Work: 0.198 (Depositor), 0.202 (DCC)
R-Value Observed: 0.200 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 184.024	α = 90
b = 58.908	β = 95.19
c = 67.086	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
ADSC	data collection
XDS	data reduction
XSCALE	data scaling
CNS	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2008-04-01

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2008-04-01
Type: Initial release
Version 1.1: 2011-07-13
Changes: Non-polymer description, Version format compliance
Version 1.2: 2014-12-17
Changes: Experimental preparation
Version 1.3: 2023-11-01
Changes: Data collection, Database references, Derived calculations, Refinement description