5XOQ | pdb_00005xoq

Crystal structure of O-Acetylserine Sulfhydrylase with bound Transcription Factor peptide inhibitor from Planctomyces limnophilus

• PDB DOI: https://doi.org/10.2210/pdb5XOQ/pdb

• Classification: TRANSFERASE/TRANSFERASE INHIBITOR
• Organism(s): Planctopirus limnophila DSM 3776, Planctopirus limnophila
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2017-05-30 Released: 2018-05-30 
• Deposition Author(s): Singh, R.P., Saini, N.
• Funding Organization(s): CSIR

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.87 Å
• R-Value Free: 
  0.200 (Depositor), 0.198 (DCC) 
• R-Value Work: 
  0.162 (Depositor), 0.161 (DCC) 
• R-Value Observed: 
  0.164 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of O-Acetylserine Sulfhydrylase with bound Transcription Factor peptide inhibitor from Planctomyces limnophilus

Singh, R.P., Saini, N.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 67.68 kDa 
• Atom Count: 5,112 
• Modeled Residue Count: 636 
• Deposited Residue Count: 636 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cysteine synthase	A, B	310	Planctopirus limnophila DSM 3776	Mutation(s): 0  Gene Names: Plim_3256 EC: 2.5.1.47
UniProt
Find proteins for D5STP0 (Planctopirus limnophila (strain ATCC 43296 / DSM 3776 / IFAM 1008 / Mu 290)) Explore D5STP0  Go to UniProtKB:  D5STP0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
GLY-PHE-SER-GLY-GLY-ASP-GLY-ILE	C, D	8	Planctopirus limnophila	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG	E [auth A], F [auth B]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
LLP	A, B	L-PEPTIDE LINKING	C14 H22 N3 O7 P		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.87 Å
• R-Value Free:  0.200 (Depositor), 0.198 (DCC) 
• R-Value Work:  0.162 (Depositor), 0.161 (DCC) 
• R-Value Observed: 0.164 (Depositor) 

Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.041	α = 90
b = 99.686	β = 90
c = 125.884	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2018-05-30 
Deposition Author(s): Singh, R.P., Saini, N.

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Funding Organization	Location	Grant Number
CSIR	India	--

Revision History  

• Version 1.0: 2018-05-30
  Type: Initial release
  
• Version 1.1: 2018-09-19
  Changes: Data collection, Database references
• Version 1.2: 2023-11-22
  Changes: Data collection, Database references, Refinement description