6K16 | pdb_00006k16

Crystal Structure of Sesquisabinene B Synthase 1 from Santalum album

PDB DOI: https://doi.org/10.2210/pdb6K16/pdb

Classification: LYASE
Organism(s): Santalum album
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2019-05-09 Released: 2019-06-12
Deposition Author(s): Singh, S., Thulasiram, H.V., Kulkarni, K.A.
Funding Organization(s): Council of Scientific & Industrial Research

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.228 (Depositor), 0.220 (DCC)
R-Value Work:
0.197 (Depositor)
R-Value Observed:
0.200 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history.

Literature

Dynamic coupling analysis on plant sesquiterpene synthases provides leads for the identification of product specificity determinants

Singh, S., Thulasiram, H.V., Sengupta, D., Kulkarni, K.

(2021) Biochem Biophys Res Commun 536: 107-114

DOI: https://doi.org/10.1016/j.bbrc.2020.12.041

Macromolecule Content

Total Structure Weight: 64.24 kDa
Atom Count: 4,140
Modeled Residue Count: 506
Deposited Residue Count: 555
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sesquisabinene B synthase 1	A	555	Santalum album	Mutation(s): 1
UniProt
Find proteins for A0A0A0RDR2 (Santalum album) Explore A0A0A0RDR2 Go to UniProtKB: A0A0A0RDR2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A0A0RDR2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain B [auth A] mmCIF format, chain C [auth A] mmCIF format, chain B [auth A]	B [auth A], C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.228 (Depositor), 0.220 (DCC)
R-Value Work: 0.197 (Depositor)
R-Value Observed: 0.200 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 141.059	α = 90
b = 85.821	β = 97.56
c = 53.399	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2019-06-12

Deposition Author(s):

Thulasiram, H.V.

Funding Organization	Location	Grant Number
Council of Scientific & Industrial Research	India	BSC0124

Revision History (Full details and data files)

Version 1.0: 2019-06-12
Type: Initial release
Version 1.1: 2021-01-13
Changes: Database references
Version 1.2: 2023-11-22
Changes: Data collection, Database references, Refinement description

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.