3LST | pdb_00003lst

Crystal Structure of CalO1, Methyltransferase in Calicheamicin Biosynthesis, SAH bound form

PDB DOI: https://doi.org/10.2210/pdb3LST/pdb

Classification: TRANSFERASE
Organism(s): Micromonospora echinospora
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2010-02-12 Released: 2010-03-02
Deposition Author(s): Chang, A., Singh, S., Bingman, C.A., Thorson, J.S., Phillips Jr., G.N., Center for Eukaryotic Structural Genomics (CESG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free:
0.251 (Depositor), 0.247 (DCC)
R-Value Work:
0.200 (Depositor), 0.204 (DCC)
R-Value Observed:
0.203 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Structural characterization of CalO1: a putative orsellinic acid methyltransferase in the calicheamicin-biosynthetic pathway.

Chang, A., Singh, S., Bingman, C.A., Thorson, J.S., Phillips, G.N.

(2011) Acta Crystallogr D Biol Crystallogr 67: 197-203

PubMed: 21358050 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1107/S090744491100360X
Primary Citation Related Structures:
3LST

PubMed Abstract:
The X-ray structure determination at 2.4 Å resolution of the putative orsellinic acid C3 O-methyltransferase (CalO1) involved in calicheamicin biosynthesis is reported. Comparison of CalO1 with a homology model of the functionally related calicheamicin orsellinic acid C2 O-methyltransferase (CalO6) implicates several residues that are likely to contribute to the regiospecificity of alkylation. Consistent with the proposed requirement of an acyl-carrier-protein-bound substrate, this structural study also reveals structural determinants within CalO1 that are anticipated to accommodate an association with an acyl carrier protein.

Organizational Affiliation

Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA.

Macromolecule Content

Total Structure Weight: 76.77 kDa
Atom Count: 5,303
Modeled Residue Count: 666
Deposited Residue Count: 696
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CalO1 Methyltransferase	A, B	348	Micromonospora echinospora	Mutation(s): 0 Gene Names: calO1
UniProt
Find proteins for Q8KNE5 (Micromonospora echinospora) Explore Q8KNE5 Go to UniProtKB: Q8KNE5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8KNE5
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 E [auth B] SDF format, chain C [auth A] MOL2 format, chain E [auth B] MOL2 format, chain C [auth A] mmCIF format, chain E [auth B] mmCIF format, chain C [auth A]	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]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain D [auth A] MOL2 format, chain F [auth B] MOL2 format, chain D [auth A] mmCIF format, chain F [auth B] mmCIF format, chain D [auth A]	D [auth A], F [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain F [auth B] Interactions & Density Focus chain D [auth A] Focus chain F [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.251 (Depositor), 0.247 (DCC)
R-Value Work: 0.200 (Depositor), 0.204 (DCC)
R-Value Observed: 0.203 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.515	α = 90
b = 93.603	β = 90
c = 240.971	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SHARP	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2010-03-02

Deposition Author(s):

Center for Eukaryotic Structural Genomics (CESG)

Revision History (Full details and data files)

Version 1.0: 2010-03-02
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-11-01
Changes: Refinement description
Version 1.3: 2024-10-16
Changes: Data collection, Database references, Derived calculations, Structure summary