7XEQ | pdb_00007xeq

NifS with D-cysteine

PDB DOI: https://doi.org/10.2210/pdb7XEQ/pdb

Classification: BIOSYNTHETIC PROTEIN
Organism(s): Helicobacter pylori
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2022-03-31 Released: 2023-04-05
Deposition Author(s): Nakamura, R., Fujishiro, T.
Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free:
0.225 (Depositor), 0.226 (DCC)
R-Value Work:
0.181 (Depositor), 0.182 (DCC)
R-Value Observed:
0.183 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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Literature

X-ray crystallographic snapshots of the thioazolidine formation upon the PLP during inhibition of SufS by D-cysteine

Nakamura, R., Takahashi, Y., Fujishiro, T.

To be published.

Macromolecule Content

Total Structure Weight: 44.57 kDa
Atom Count: 2,826
Modeled Residue Count: 355
Deposited Residue Count: 401
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cysteine desulfurase IscS	A	401	Helicobacter pylori	Mutation(s): 2 Gene Names: iscS, HP_0220 EC: 2.8.1.7
UniProt
Find proteins for O25008 (Helicobacter pylori (strain ATCC 700392 / 26695)) Explore O25008 Go to UniProtKB: O25008
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O25008
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
9YX (Subject of Investigation/LOI) Query on 9YX Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	(2~{S},4~{S})-2-[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]-1,3-thiazolidine-4-carboxylic acid C₁₁ H₁₅ N₂ O₇ P S CXFXHBNEDOKOBZ-XCBNKYQSSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
IPA Query on IPA Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	ISOPROPYL ALCOHOL C₃ H₈ O KFZMGEQAYNKOFK-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
CL Query on CL 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]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free: 0.225 (Depositor), 0.226 (DCC)
R-Value Work: 0.181 (Depositor), 0.182 (DCC)
R-Value Observed: 0.183 (Depositor)

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 103.5	α = 90
b = 103.5	β = 90
c = 132.6	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2023-04-05

Deposition Author(s):

Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	17K14510

Revision History (Full details and data files)

Version 1.0: 2023-04-05
Type: Initial release
Version 1.1: 2023-11-29
Changes: Data collection, Refinement description

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