7BW9 | pdb_00007bw9

Crystal structure of Serine acetyltransferase isoform 3 in complex with cysteine from Entamoeba histolytica

PDB DOI: https://doi.org/10.2210/pdb7BW9/pdb

Classification: TRANSFERASE
Organism(s): Entamoeba histolytica
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2020-04-14 Released: 2021-04-14
Deposition Author(s): Dharavath, S., Kumar, S., Gourinath, S.
Funding Organization(s): Science and Engineering Research Board (SERB)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.13 Å
R-Value Free:
0.223 (Depositor), 0.220 (DCC)
R-Value Work:
0.174 (Depositor), 0.180 (DCC)
R-Value Observed:
0.175 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of Serine acetyltransferase isoform 3 in complex with cysteine from Entamoeba histolytica

Dharavath, S., Kumar, S.

To be published.

Macromolecule Content

Total Structure Weight: 113.58 kDa
Atom Count: 6,983
Modeled Residue Count: 833
Deposited Residue Count: 1,008
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine acetyltransferase 1, putative	A, B, C	336	Entamoeba histolytica	Mutation(s): 0 Gene Names: KM1_023830 EC: 2.3.1.30
UniProt
Find proteins for Q401L4 (Entamoeba histolytica) Explore Q401L4 Go to UniProtKB: Q401L4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q401L4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CYS (Subject of Investigation/LOI) Query on CYS Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth B] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth B]	D [auth A], E [auth A], F [auth B]	CYSTEINE C₃ H₇ N O₂ S XUJNEKJLAYXESH-REOHCLBHSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.13 Å
R-Value Free: 0.223 (Depositor), 0.220 (DCC)
R-Value Work: 0.174 (Depositor), 0.180 (DCC)
R-Value Observed: 0.175 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 120.323	α = 90
b = 76.307	β = 95.52
c = 96.726	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2021-04-14

Deposition Author(s):

Funding Organization	Location	Grant Number
Science and Engineering Research Board (SERB)	India	--

Revision History (Full details and data files)

Version 1.0: 2021-04-14
Type: Initial release
Version 1.1: 2023-11-29
Changes: Data collection, Database references, Refinement description

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.