5FT5 | pdb_00005ft5

Crystal structure of the cysteine desulfurase CsdA (persulfurated) from Escherichia coli at 2.384 Angstroem resolution

PDB DOI: https://doi.org/10.2210/pdb5FT5/pdb

Classification: TRANSFERASE
Organism(s): Escherichia coli K-12
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2016-01-11 Released: 2016-11-23
Deposition Author(s): Fernandez, F.J., Arda, A., Lopez-Estepa, M., Aranda, J., Penya-Soler, E., Garces, F., Quintana, J.F., Round, A., Campos-Oliva, R., Bruix, M., Coll, M., Tunon, I., Jimenez-Barbero, J., Vega, M.C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.38 Å
R-Value Free:
0.225 (Depositor), 0.227 (DCC)
R-Value Work:
0.167 (Depositor), 0.174 (DCC)
R-Value Observed:
0.170 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Mechanism of Sulfur Transfer Across Protein-Protein Interfaces: The Cysteine Desulfurase Model System

Fernandez, F.J., Arda, A., Lopez-Estepa, M., Aranda, J., Penya-Soler, E., Garces, F., Quintana, J.F., Round, A., Campos-Oliva, R., Bruix, M., Coll, M., Tunon, I., Jimenez-Barbero, J., Vega, M.C.

(2016) ACS Catal 6: 3975

DOI: https://doi.org/10.1021/ACSCATAL.6B00360

Macromolecule Content

Total Structure Weight: 88.43 kDa
Atom Count: 6,525
Modeled Residue Count: 802
Deposited Residue Count: 802
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
L-CYSTEINE DESULFURASE CSDA	A, B	401	Escherichia coli K-12	Mutation(s): 0 EC: 2.8.1.7 (PDB Primary Data), 4.4.1 (PDB Primary Data), 4.4.1.16 (PDB Primary Data), 3.13.1 (UniProt)
UniProt
Find proteins for Q46925 (Escherichia coli (strain K12)) Explore Q46925 Go to UniProtKB: Q46925
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q46925
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PLP Query on PLP Download:Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain Q [auth B] MOL2 format, chain K [auth A] MOL2 format, chain Q [auth B] mmCIF format, chain K [auth A] mmCIF format, chain Q [auth B]	K [auth A], Q [auth B]	PYRIDOXAL-5'-PHOSPHATE C₈ H₁₀ N O₆ P NGVDGCNFYWLIFO-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Focus chain Q [auth B] Interactions & Density Focus chain K [auth A] Focus chain Q [auth B]
TLA Query on TLA Download:Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain P [auth B] MOL2 format, chain J [auth A] MOL2 format, chain P [auth B] mmCIF format, chain J [auth A] mmCIF format, chain P [auth B]	J [auth A], P [auth B]	L(+)-TARTARIC ACID C₄ H₆ O₆ FEWJPZIEWOKRBE-JCYAYHJZSA-N		Interactions Focus chain J [auth A] Focus chain P [auth B] Interactions & Density Focus chain J [auth A] Focus chain P [auth B]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain I [auth A] MOL2 format, chain I [auth A] mmCIF format, chain I [auth A]	I [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Interactions & Density Focus chain I [auth A]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] 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 L [auth B] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain O [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] 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 L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] 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 L [auth B] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B]	C [auth A] D [auth A] E [auth A] F [auth A] G [auth A] C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], L [auth B], M [auth B], N [auth B], O [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSS Query on CSS	A, B	L-PEPTIDE LINKING	C₃ H₇ N O₂ S₂		CYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.38 Å
R-Value Free: 0.225 (Depositor), 0.227 (DCC)
R-Value Work: 0.167 (Depositor), 0.174 (DCC)
R-Value Observed: 0.170 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.347	α = 90
b = 99.533	β = 90
c = 141.757	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
AMoRE	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2016-11-23

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2016-11-23
Type: Initial release
Version 1.1: 2019-01-02
Changes: Data collection, Database references, Structure summary
Version 1.2: 2024-01-10
Changes: Data collection, Database references, Derived calculations, Other, Refinement description