4DI5 | pdb_00004di5

Co-crystal structure of WT 5-epi-Aristolochene synthase from Nicotiana tobaccum with geraniline

PDB DOI: https://doi.org/10.2210/pdb4DI5/pdb

Classification: Lyase/Lyase inhibitor
Organism(s): Nicotiana tabacum
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2012-01-30 Released: 2012-02-29
Deposition Author(s): Noel, J.P., Starks, C., Crenshaw, C.M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.246 (Depositor), 0.244 (DCC)
R-Value Work:
0.203 (Depositor), 0.200 (DCC)
R-Value Observed:
0.204 (Depositor)

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Ligand Structure Quality Assessment

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

Literature

Co-crystal structure of WT 5-epi-Aristolochene synthase from Nicotiana tobaccum with geraniline

Noel, J.P., Starks, C., Crenshaw, C.M.

To be published.

Macromolecule Content

Total Structure Weight: 62.25 kDa
Atom Count: 4,699
Modeled Residue Count: 535
Deposited Residue Count: 535
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
5-epi-aristolochene synthase	A	535	Nicotiana tabacum	Mutation(s): 0 Gene Names: 5-EAS, EAS3, EAS4 EC: 4.2.3.61 (PDB Primary Data), 4.2.3.226 (UniProt), 4.2.3.227 (UniProt)
UniProt
Find proteins for Q40577 (Nicotiana tabacum) Explore Q40577 Go to UniProtKB: Q40577
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q40577
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
1GA Query on 1GA Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	Geraniline C₁₆ H₂₁ N QEYKICLOTYFCMW-QEKYNVLXSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
DPO Query on DPO Download:Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	DIPHOSPHATE O₇ P₂ XPPKVPWEQAFLFU-UHFFFAOYSA-J		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] mmCIF format, chain B [auth A] mmCIF format, chain C [auth A]	B [auth A], C [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain B [auth A] Focus chain C [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth A] MOL2 format, chain E [auth A] MOL2 format, chain G [auth A] mmCIF format, chain E [auth A] mmCIF format, chain G [auth A]	E [auth A], G [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain G [auth A] Interactions & Density Focus chain E [auth A] Focus chain G [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.246 (Depositor), 0.244 (DCC)
R-Value Work: 0.203 (Depositor), 0.200 (DCC)
R-Value Observed: 0.204 (Depositor)

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 126.448	α = 90
b = 126.448	β = 90
c = 122.78	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
SCALA	data scaling
CNS	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2012-02-29

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2012-02-29
Type: Initial release
Version 1.1: 2024-02-28
Changes: Data collection, Database references, Derived calculations

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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.