4M83 | pdb_00004m83

Ensemble refinement of protein crystal structure (2IYF) of macrolide glycosyltransferases OleD complexed with UDP and Erythromycin A

PDB DOI: https://doi.org/10.2210/pdb4M83/pdb

Classification: Transferase/Antibiotic
Organism(s): Streptomyces antibioticus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2013-08-12 Released: 2013-09-11
Deposition Author(s): Wang, F., Helmich, K.E., Xu, W., Singh, S., Olmos Jr., J.L., Martinez iii, E., Bingman, C.A., Thorson, J.S., Phillips Jr., G.N., Enzyme Discovery for Natural Product Biosynthesis (NatPro)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.201 (Depositor), 0.226 (DCC)
R-Value Work:
0.160 (Depositor), 0.193 (DCC)
R-Value Observed:
0.161 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Re-refinement Note

This entry reflects an alternative modeling of the original data in: 2IYF

Literature

Crystal structure of macrolide glycosyltransferases OleD

Olmos, J.L., Jr., Wang, F., Martinez iii, E., Helmich, K.E., Singh, S., Xu, W., Bingman, C.A., Thorson, J.S., Phillips Jr., G.N.

To be published.

Macromolecule Content

Total Structure Weight: 93.03 kDa
Atom Count: 6,648
Modeled Residue Count: 787
Deposited Residue Count: 830
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Oleandomycin glycosyltransferase	A, B	415	Streptomyces antibioticus	Mutation(s): 0 Gene Names: oleD EC: 2.4.1
UniProt
Find proteins for Q53685 (Streptomyces antibioticus) Explore Q53685 Go to UniProtKB: Q53685
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q53685
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ERY Query on ERY 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]	ERYTHROMYCIN A C₃₇ H₆₇ N O₁₃ ULGZDMOVFRHVEP-RWJQBGPGSA-N		Interactions Focus chain C [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth B]
UDP Query on UDP 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]	URIDINE-5'-DIPHOSPHATE C₉ H₁₄ N₂ O₁₂ P₂ XCCTYIAWTASOJW-XVFCMESISA-N		Interactions Focus chain D [auth A] Focus chain F [auth B] Interactions & Density Focus chain D [auth A] Focus chain F [auth B]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain G [auth B] MOL2 format, chain G [auth B] mmCIF format, chain G [auth B]	G [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain G [auth B] Interactions & Density Focus chain G [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.201 (Depositor), 0.226 (DCC)
R-Value Work: 0.160 (Depositor), 0.193 (DCC)
R-Value Observed: 0.161 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.718	α = 90
b = 65.778	β = 100.42
c = 91.94	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASES	phasing
PHENIX	refinement

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2013-09-11

Deposition Author(s):

Enzyme Discovery for Natural Product Biosynthesis (NatPro)

Revision History (Full details and data files)

Version 1.0: 2013-09-11
Type: Initial release
Version 1.1: 2018-01-24
Changes: Structure summary
Version 1.2: 2024-02-28
Changes: Data collection, Database references, Derived calculations