4M7P | pdb_00004m7p

Ensemble refinement of protein crystal structure of macrolide glycosyltransferases OleD

PDB DOI: https://doi.org/10.2210/pdb4M7P/pdb

Classification: TRANSFERASE
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: 1.77 Å
R-Value Free:
0.188 (Depositor), 0.242 (DCC)
R-Value Work:
0.150 (Depositor), 0.200 (DCC)
R-Value Observed:
0.152 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 4M7P

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

Literature

Crystal structure of macrolide glycosyltransferases OleD

Olmos Jr., J.L., 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: 45.95 kDa
Atom Count: 3,173
Modeled Residue Count: 395
Deposited Residue Count: 418
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Oleandomycin glycosyltransferase	A	418	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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NA Query on NA 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]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.77 Å
R-Value Free: 0.188 (Depositor), 0.242 (DCC)
R-Value Work: 0.150 (Depositor), 0.200 (DCC)
R-Value Observed: 0.152 (Depositor)

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 124.134	α = 90
b = 124.134	β = 90
c = 67.636	γ = 120

Software Package:

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

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2013-09-11

Deposition Author(s):

Olmos Jr., J.L.

Martinez iii, E.

Phillips Jr., G.N.

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: 2024-11-20
Changes: Data collection, Database references, Derived calculations, Structure summary

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.