5CVJ | pdb_00005cvj

Monolignol 4-O-methyltransferase 5 - coniferyl alcohol

PDB DOI: https://doi.org/10.2210/pdb5CVJ/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:
0.180 (Depositor), 0.190 (DCC)
R-Value Work:
0.151 (Depositor), 0.160 (DCC)
R-Value Observed:
0.152 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Structure of coniferyl alcohol bound monolignol 4-O-methyltransferase at 1.68 Angstroms resolution

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

To be published.

Macromolecule Content

Total Structure Weight: 163.54 kDa
Atom Count: 12,039
Modeled Residue Count: 1,432
Deposited Residue Count: 1,472
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
(Iso)eugenol O-methyltransferase	A [auth D], B [auth A], C [auth B], D [auth C]	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% Identity50% Identity70% Identity90% Identity95% Identity100% 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 E [auth D] SDF format, chain J [auth A] SDF format, chain O [auth B] SDF format, chain Y [auth C] MOL2 format, chain E [auth D] MOL2 format, chain J [auth A] MOL2 format, chain O [auth B] MOL2 format, chain Y [auth C] mmCIF format, chain E [auth D] mmCIF format, chain J [auth A] mmCIF format, chain O [auth B] mmCIF format, chain Y [auth C]	E [auth D], J [auth A], O [auth B], Y [auth C]	S-ADENOSYL-L-HOMOCYSTEINE C₁₄ H₂₀ N₆ O₅ S ZJUKTBDSGOFHSH-WFMPWKQPSA-N		Interactions Focus chain E [auth D] Focus chain J [auth A] Focus chain O [auth B] Focus chain Y [auth C] Interactions & Density Focus chain E [auth D] Focus chain J [auth A] Focus chain O [auth B] Focus chain Y [auth C]
N7I Query on N7I Download Ideal Coordinates CCD File SDF format, chain F [auth D] SDF format, chain K [auth A] SDF format, chain P [auth B] SDF format, chain Z [auth C] MOL2 format, chain F [auth D] MOL2 format, chain K [auth A] MOL2 format, chain P [auth B] MOL2 format, chain Z [auth C] mmCIF format, chain F [auth D] mmCIF format, chain K [auth A] mmCIF format, chain P [auth B] mmCIF format, chain Z [auth C]	F [auth D], K [auth A], P [auth B], Z [auth C]	4-[(1E)-3-hydroxyprop-1-en-1-yl]-2-methoxyphenol C₁₀ H₁₂ O₃ JMFRWRFFLBVWSI-NSCUHMNNSA-N		Interactions Focus chain F [auth D] Focus chain K [auth A] Focus chain P [auth B] Focus chain Z [auth C] Interactions & Density Focus chain F [auth D] Focus chain K [auth A] Focus chain P [auth B] Focus chain Z [auth C]
NO3 Query on NO3 Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain BA [auth C] SDF format, chain CA [auth C] SDF format, chain DA [auth C] SDF format, chain G [auth D] SDF format, chain H [auth D] SDF format, chain I [auth D] SDF format, chain L [auth A] SDF format, chain N [auth A] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain T [auth B] SDF format, chain U [auth B] SDF format, chain V [auth B] SDF format, chain W [auth B] SDF format, chain X [auth B] SDF format, chain M [auth A] MOL2 format, chain AA [auth C] MOL2 format, chain BA [auth C] MOL2 format, chain CA [auth C] MOL2 format, chain DA [auth C] MOL2 format, chain G [auth D] MOL2 format, chain H [auth D] MOL2 format, chain I [auth D] MOL2 format, chain L [auth A] MOL2 format, chain N [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B] MOL2 format, chain V [auth B] MOL2 format, chain W [auth B] MOL2 format, chain X [auth B] MOL2 format, chain M [auth A] mmCIF format, chain AA [auth C] mmCIF format, chain BA [auth C] mmCIF format, chain CA [auth C] mmCIF format, chain DA [auth C] mmCIF format, chain G [auth D] mmCIF format, chain H [auth D] mmCIF format, chain I [auth D] mmCIF format, chain L [auth A] mmCIF format, chain N [auth A] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B] mmCIF format, chain S [auth B] mmCIF format, chain T [auth B] mmCIF format, chain U [auth B] mmCIF format, chain V [auth B] mmCIF format, chain W [auth B] mmCIF format, chain X [auth B] mmCIF format, chain M [auth A]	AA [auth C] BA [auth C] CA [auth C] DA [auth C] G [auth D] AA [auth C], BA [auth C], CA [auth C], DA [auth C], G [auth D], H [auth D], I [auth D], L [auth A], M [auth A], N [auth A], Q [auth B], R [auth B], S [auth B], T [auth B], U [auth B], V [auth B], W [auth B], X [auth B]	NITRATE ION N O₃ NHNBFGGVMKEFGY-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Focus chain BA [auth C] Focus chain CA [auth C] Focus chain DA [auth C] Focus chain G [auth D] Focus chain H [auth D] Focus chain I [auth D] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Interactions & Density Focus chain AA [auth C] Focus chain BA [auth C] Focus chain CA [auth C] Focus chain DA [auth C] Focus chain G [auth D] Focus chain H [auth D] Focus chain I [auth D] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.180 (Depositor), 0.190 (DCC)
R-Value Work: 0.151 (Depositor), 0.160 (DCC)
R-Value Observed: 0.152 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.07	α = 90
b = 150.36	β = 93.19
c = 67.93	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

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: 2019-12-04
Changes: Author supporting evidence, Derived calculations
Version 1.2: 2024-03-06
Changes: Data collection, Database references