6LCN | pdb_00006lcn

Crystal structure of Serine Acetyltransferase from Planctomyces limnophilus at 2.15A

PDB DOI: https://doi.org/10.2210/pdb6LCN/pdb

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

Deposited: 2019-11-19 Released: 2020-12-02
Deposition Author(s): Kumar, N., Singh, R.P., Singh, A.K., Kumaran, S.
Funding Organization(s): Department of Health & Human Services (HHS), Council of Scientific & Industrial Research

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free:
0.223 (Depositor), 0.220 (DCC)
R-Value Work:
0.187 (Depositor), 0.190 (DCC)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Understanding Mechanics of competitive-allostery Using Engineered Cysteine Synthase Assembly

Kumar, N., Singh, R.P., Kumaran, S.

To be published.

Macromolecule Content

Total Structure Weight: 222.24 kDa
Atom Count: 14,969
Modeled Residue Count: 1,797
Deposited Residue Count: 1,986
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 O-acetyltransferase	A, B, C, D, E A, B, C, D, E, F	331	Planctopirus limnophila DSM 3776	Mutation(s): 0 Gene Names: Plim_1307 EC: 2.3.1.30
UniProt
Find proteins for D5SUT9 (Planctopirus limnophila (strain ATCC 43296 / DSM 3776 / IFAM 1008 / Mu 290)) Explore D5SUT9 Go to UniProtKB: D5SUT9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	D5SUT9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PEG (Subject of Investigation/LOI) Query on PEG Download Ideal Coordinates CCD File SDF format, chain S [auth F] SDF format, chain O [auth D] SDF format, chain K [auth C] SDF format, chain J [auth B] MOL2 format, chain S [auth F] MOL2 format, chain O [auth D] MOL2 format, chain K [auth C] MOL2 format, chain J [auth B] mmCIF format, chain S [auth F] mmCIF format, chain O [auth D] mmCIF format, chain K [auth C] mmCIF format, chain J [auth B]	J [auth B], K [auth C], O [auth D], S [auth F]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain J [auth B] Focus chain K [auth C] Focus chain O [auth D] Focus chain S [auth F] Interactions & Density Focus chain J [auth B] Focus chain K [auth C] Focus chain O [auth D] Focus chain S [auth F]
GOL (Subject of Investigation/LOI) Query on GOL Download Ideal Coordinates CCD File SDF format, chain R [auth F] SDF format, chain Q [auth E] SDF format, chain N [auth D] SDF format, chain L [auth C] SDF format, chain H [auth A] SDF format, chain G [auth A] MOL2 format, chain R [auth F] MOL2 format, chain Q [auth E] MOL2 format, chain N [auth D] MOL2 format, chain L [auth C] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] mmCIF format, chain R [auth F] mmCIF format, chain Q [auth E] mmCIF format, chain N [auth D] mmCIF format, chain L [auth C] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A]	G [auth A] H [auth A] L [auth C] N [auth D] Q [auth E] G [auth A], H [auth A], L [auth C], N [auth D], Q [auth E], R [auth F]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain L [auth C] Focus chain N [auth D] Focus chain Q [auth E] Focus chain R [auth F] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain L [auth C] Focus chain N [auth D] Focus chain Q [auth E] Focus chain R [auth F]
CL (Subject of Investigation/LOI) Query on CL Download Ideal Coordinates CCD File SDF format, chain P [auth D] SDF format, chain M [auth C] SDF format, chain I [auth A] MOL2 format, chain P [auth D] MOL2 format, chain M [auth C] MOL2 format, chain I [auth A] mmCIF format, chain P [auth D] mmCIF format, chain M [auth C] mmCIF format, chain I [auth A]	I [auth A], M [auth C], P [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain I [auth A] Focus chain M [auth C] Focus chain P [auth D] Interactions & Density Focus chain I [auth A] Focus chain M [auth C] Focus chain P [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free: 0.223 (Depositor), 0.220 (DCC)
R-Value Work: 0.187 (Depositor), 0.190 (DCC)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.719	α = 90
b = 113.165	β = 90
c = 230.133	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2020-12-02

Deposition Author(s):

Funding Organization	Location	Grant Number
Department of Health & Human Services (HHS)	India	No.3/1/3/JRF-2015/HRD-LS/48/30922/131
Council of Scientific & Industrial Research	India	--

Revision History (Full details and data files)

Version 1.0: 2020-12-02
Type: Initial release
Version 1.1: 2022-03-23
Changes: Author supporting evidence, Database references
Version 1.2: 2023-11-22
Changes: Data collection, Derived calculations, Refinement description
Version 1.3: 2024-10-30
Changes: Structure summary

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Crystal structure of Serine Acetyltransferase from Planctomyces limnophilus at 2.15A

Understanding Mechanics of competitive-allostery Using Engineered Cysteine Synthase Assembly

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations