5FT4 | pdb_00005ft4

Crystal structure of the cysteine desulfurase CsdA from Escherichia coli at 1.996 Angstroem resolution

PDB DOI: https://doi.org/10.2210/pdb5FT4/pdb

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

Deposited: 2016-01-11 Released: 2016-12-21
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: 2.00 Å
R-Value Free:
0.191 (Depositor), 0.197 (DCC)
R-Value Work:
0.138 (Depositor), 0.151 (DCC)
R-Value Observed:
0.141 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

The Mechanism of Sulfur Transfer Across Protein- Protein Interfaces: The Csd Model

Fernandez, F.J., Arda, A., Lopez-Estepa, M., Aranda, J., Penya-Soler, E., Garces, 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: 88.36 kDa
Atom Count: 6,860
Modeled Residue Count: 798
Deposited Residue Count: 802
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PLP Query on PLP Download:Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain C [auth A] MOL2 format, chain G [auth B] MOL2 format, chain C [auth A] mmCIF format, chain G [auth B] mmCIF format, chain C [auth A]	C [auth A], G [auth B]	PYRIDOXAL-5'-PHOSPHATE C₈ H₁₀ N O₆ P NGVDGCNFYWLIFO-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain G [auth B] Interactions & Density Focus chain C [auth A] Focus chain G [auth B]
CIT Query on CIT Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain L [auth B] SDF format, chain N [auth B] SDF format, chain M [auth B] MOL2 format, chain F [auth A] MOL2 format, chain L [auth B] MOL2 format, chain N [auth B] MOL2 format, chain M [auth B] mmCIF format, chain F [auth A] mmCIF format, chain L [auth B] mmCIF format, chain N [auth B] mmCIF format, chain M [auth B]	F [auth A], L [auth B], M [auth B], N [auth B]	CITRIC ACID C₆ H₈ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Interactions & Density Focus chain F [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain H [auth B] SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain I [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain I [auth B] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain H [auth B] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B] mmCIF format, chain I [auth B]	D [auth A] E [auth A] H [auth B] I [auth B] J [auth B] D [auth A], E [auth A], H [auth B], I [auth B], J [auth B], K [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.191 (Depositor), 0.197 (DCC)
R-Value Work: 0.138 (Depositor), 0.151 (DCC)
R-Value Observed: 0.141 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.095	α = 90
b = 102.561	β = 114.45
c = 71.258	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
SCALA	data scaling
PHENIX	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2016-12-21

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2016-12-21
Type: Initial release
Version 1.1: 2017-07-12
Changes: Refinement description
Version 1.2: 2019-01-02
Changes: Data collection, Database references, Structure summary
Version 1.3: 2025-04-09
Changes: Data collection, Database references, Derived calculations, Other, Structure summary