5CVU | pdb_00005cvu

sinpyl alcohol bound monolignol 4-O-methyltransferase 5

PDB DOI: https://doi.org/10.2210/pdb5CVU/pdb

Classification: TRANSFERASE
Organism(s): Clarkia breweri
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2015-07-27 Released: 2015-09-16
Deposition Author(s): Cai, Y., Liu, C.-J.
Funding Organization(s): Department of Energy (DOE, United States)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.168 (Depositor), 0.182 (DCC)
R-Value Work:
0.168 (Depositor)
R-Value Observed:
0.168 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Structure of sinapyl alcohol bound monolignol 4-O-methyltransferase at 1.60 Angstroms resolution

Cai, Y., Liu, C.-J.

To be published.

Macromolecule Content

Total Structure Weight: 163.11 kDa
Atom Count: 11,634
Modeled Residue Count: 1,429
Deposited Residue Count: 1,472
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
(Iso)eugenol O-methyltransferase	A, B, C, D	368	Clarkia breweri	Mutation(s): 5 Gene Names: IEMT1 EC: 2.1.1.146
UniProt
Find proteins for O04385 (Clarkia breweri) Explore O04385 Go to UniProtKB: O04385
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O04385
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SAH Query on SAH Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain K [auth B] SDF format, chain S [auth D] SDF format, chain N [auth C] MOL2 format, chain F [auth A] MOL2 format, chain K [auth B] MOL2 format, chain S [auth D] MOL2 format, chain N [auth C] mmCIF format, chain F [auth A] mmCIF format, chain K [auth B] mmCIF format, chain S [auth D] mmCIF format, chain N [auth C]	F [auth A], K [auth B], N [auth C], S [auth D]	S-ADENOSYL-L-HOMOCYSTEINE C₁₄ H₂₀ N₆ O₅ S ZJUKTBDSGOFHSH-WFMPWKQPSA-N		Interactions Focus chain F [auth A] Focus chain K [auth B] Focus chain N [auth C] Focus chain S [auth D] Interactions & Density Focus chain F [auth A] Focus chain K [auth B] Focus chain N [auth C] Focus chain S [auth D]
55B Query on 55B Download:Ideal Coordinates CCD File SDF format, chain R [auth D] SDF format, chain M [auth C] SDF format, chain J [auth B] SDF format, chain E [auth A] MOL2 format, chain R [auth D] MOL2 format, chain M [auth C] MOL2 format, chain J [auth B] MOL2 format, chain E [auth A] mmCIF format, chain R [auth D] mmCIF format, chain M [auth C] mmCIF format, chain J [auth B] mmCIF format, chain E [auth A]	E [auth A], J [auth B], M [auth C], R [auth D]	4-[(1E)-3-hydroxyprop-1-en-1-yl]-2,6-dimethoxyphenol C₁₁ H₁₄ O₄ LZFOPEXOUVTGJS-ONEGZZNKSA-N		Interactions Focus chain E [auth A] Focus chain J [auth B] Focus chain M [auth C] Focus chain R [auth D] Interactions & Density Focus chain E [auth A] Focus chain J [auth B] Focus chain M [auth C] Focus chain R [auth D]
NO3 Query on NO3 Download:Ideal Coordinates CCD File SDF format, chain U [auth D] SDF format, chain T [auth D] SDF format, chain Q [auth C] SDF format, chain P [auth C] SDF format, chain O [auth C] SDF format, chain L [auth B] SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] MOL2 format, chain U [auth D] MOL2 format, chain T [auth D] MOL2 format, chain Q [auth C] MOL2 format, chain P [auth C] MOL2 format, chain O [auth C] MOL2 format, chain L [auth B] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] mmCIF format, chain U [auth D] mmCIF format, chain T [auth D] mmCIF format, chain Q [auth C] mmCIF format, chain P [auth C] mmCIF format, chain O [auth C] mmCIF format, chain L [auth B] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A]	G [auth A] H [auth A] I [auth A] L [auth B] O [auth C] G [auth A], H [auth A], I [auth A], L [auth B], O [auth C], P [auth C], Q [auth C], T [auth D], U [auth D]	NITRATE ION N O₃ NHNBFGGVMKEFGY-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain L [auth B] Focus chain O [auth C] Focus chain P [auth C] Focus chain Q [auth C] Focus chain T [auth D] Focus chain U [auth D] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain L [auth B] Focus chain O [auth C] Focus chain P [auth C] Focus chain Q [auth C] Focus chain T [auth D] Focus chain U [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.168 (Depositor), 0.182 (DCC)
R-Value Work: 0.168 (Depositor)
R-Value Observed: 0.168 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.54	α = 90
b = 151.63	β = 92.55
c = 68.39	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2015-09-16

Deposition Author(s):

Cai, Y.

Liu, C.-J.

Funding Organization	Location	Grant Number
Department of Energy (DOE, United States)	United States	DEAC0298CH10886

Revision History (Full details and data files)

Version 1.0: 2015-09-16
Type: Initial release
Version 1.1: 2017-09-20
Changes: Author supporting evidence, Derived calculations
Version 1.2: 2019-12-04
Changes: Author supporting evidence
Version 1.3: 2024-10-16
Changes: Data collection, Database references, Structure summary