5CVV

coniferyl alcohol bound monolignol 4-O-methyltransferase 9

PDB DOI: https://doi.org/10.2210/pdb5CVV/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: 1.73 Å
R-Value Free: 0.212
R-Value Work: 0.181
R-Value Observed: 0.183

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Structure of coniferyl alcohol bound monolignol 4-O-methyltransferase 9 at 1.73 Angstroms resolution

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

To be published.

Macromolecule Content

Total Structure Weight: 81.22 kDa
Atom Count: 5,713
Modelled Residue Count: 700
Deposited Residue Count: 736
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
(Iso)eugenol O-methyltransferase	A, B	368	Clarkia breweri	Mutation(s): 9 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O04385
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SAH Query on SAH Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain E [auth B] MOL2 format, chain C [auth A] MOL2 format, chain E [auth B]	C [auth A], E [auth B]	S-ADENOSYL-L-HOMOCYSTEINE C₁₄ H₂₀ N₆ O₅ S ZJUKTBDSGOFHSH-WFMPWKQPSA-N		Interactions Focus chain C [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth B]
N7I Query on N7I Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A]	D [auth A]	4-[(1E)-3-hydroxyprop-1-en-1-yl]-2-methoxyphenol C₁₀ H₁₂ O₃ JMFRWRFFLBVWSI-NSCUHMNNSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.73 Å
R-Value Free: 0.212
R-Value Work: 0.181
R-Value Observed: 0.183
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.29	α = 90
b = 67.48	β = 93.18
c = 74.07	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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: 2024-03-06
Changes: Data collection, Database references

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Help and Resources

5CVV

coniferyl alcohol bound monolignol 4-O-methyltransferase 9

Structure of coniferyl alcohol bound monolignol 4-O-methyltransferase 9 at 1.73 Angstroms resolution

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)