6A3X

Crystal structure of a synthase 1 from Santalum album in complex with ligand s

PDB DOI: https://doi.org/10.2210/pdb6A3X/pdb

Classification: TRANSFERASE
Organism(s): Santalum album
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2018-06-18 Released: 2019-06-19
Deposition Author(s): Han, X., Ko, T.P., Liu, W.D., Chen, C.C., Guo, R.T.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.75 ?
R-Value Free: 0.185
R-Value Work: 0.160
R-Value Observed: 0.161

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Literature

Crystal structure of a synthase 1 from Santalum album in complex with ligand s

Han, X., Ko, T.P., Liu, W.D., Chen, C.C., Guo, R.T.

To be published.

Macromolecule Content

Total Structure Weight: 65.53 kDa
Atom Count: 4,625
Modelled Residue Count: 515
Deposited Residue Count: 566
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sesquisabinene B synthase 1	A	566	Santalum album	Mutation(s): 0
UniProt
Find proteins for A0A0A0RDR2 (Santalum album) Explore A0A0A0RDR2 Go to UniProtKB: A0A0A0RDR2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A0A0RDR2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SNE (Subject of Investigation/LOI) Query on SNE 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]	Sabinene C₁₀ H₁₆ NDVASEGYNIMXJL-UWVGGRQHSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
SO4 Query on SO4 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]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.75 ?
R-Value Free: 0.185
R-Value Work: 0.160
R-Value Observed: 0.161
Space Group: C 2 2 2₁

Unit Cell:

Length ( ? )	Angle ( ? )
a = 85.76	α = 90
b = 139.484	β = 90
c = 111.178	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data scaling
PDB_EXTRACT	data extraction
HKL-2000	data reduction
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2019-06-19

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2019-06-19
Type: Initial release
Version 2.0: 2020-09-02
Type: Coordinate replacement
Reason: Model completeness
Changes: Advisory, Atomic model, Data collection, Derived calculations, Other, Refinement description, Structure summary
Version 2.1: 2023-11-22
Changes: Data collection, Database references, Refinement description

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6A3X

Crystal structure of a synthase 1 from Santalum album in complex with ligand s

Crystal structure of a synthase 1 from Santalum album in complex with ligand s

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)