5XOH | pdb_00005xoh

Crystal structure of bergaptol o-methyltransferase complex

PDB DOI: https://doi.org/10.2210/pdb5XOH/pdb

Classification: TRANSFERASE
Organism(s): Kitagawia praeruptora
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2017-05-28 Released: 2018-05-23
Deposition Author(s): Zhou, Y., Zeng, Z.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.249 (Depositor), 0.250 (DCC)
R-Value Work:
0.197 (Depositor), 0.200 (DCC)
R-Value Observed:
0.200 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal structure of bergaptol o-methyltransferase complex

Zhou, Y., Zeng, Z.

To be published.

Macromolecule Content

Total Structure Weight: 39.9 kDa
Atom Count: 2,765
Modeled Residue Count: 348
Deposited Residue Count: 359
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bergaptol O-methyltransferase	A	359	Kitagawia praeruptora	Mutation(s): 0 Gene Names: BMT EC: 2.1.1.69
UniProt
Find proteins for A0A166U5H3 (Kitagawia praeruptora) Explore A0A166U5H3 Go to UniProtKB: A0A166U5H3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A166U5H3
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 B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	S-ADENOSYL-L-HOMOCYSTEINE C₁₄ H₂₀ N₆ O₅ S ZJUKTBDSGOFHSH-WFMPWKQPSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
8B6 Query on 8B6 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]	4-oxidanylfuro[3,2-g]chromen-7-one C₁₁ H₆ O₄ GIJHDGJRTUSBJR-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.249 (Depositor), 0.250 (DCC)
R-Value Work: 0.197 (Depositor), 0.200 (DCC)
R-Value Observed: 0.200 (Depositor)

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.436	α = 90
b = 59.436	β = 90
c = 172.5	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2018-05-23

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2018-05-23
Type: Initial release
Version 1.1: 2024-03-27
Changes: Data collection, Database references

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.