5I10 | pdb_00005i10

Crystal structure of spinosyn rhamnosyl 4'-O-methyltransferase spnh mutant T242Q from Saccharopolyspora Spinosa

PDB DOI: https://doi.org/10.2210/pdb5I10/pdb

Classification: TRANSFERASE
Organism(s): Saccharopolyspora spinosa
Expression System: Escherichia coli BL21
Mutation(s): Yes

Deposited: 2016-02-05 Released: 2017-02-08
Deposition Author(s): Lin, Y.-C., Huang, S.-P., Huang, B.-L., Chen, Y.-H., Chen, Y.-J., Chiu, H.-T.
Funding Organization(s): National Science Council

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.264 (Depositor), 0.263 (DCC)
R-Value Work:
0.227 (Depositor), 0.228 (DCC)
R-Value Observed:
0.230 (Depositor)

Starting Model: experimental
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This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of spinosyn rhamnosyl 4'-O-methyltransferase spnh mutant T242Q from Saccharopolyspora Spinosa

Lin, Y.-C., Huang, S.-P., Huang, B.-L., Chen, Y.-H., Chen, Y.-J., Chiu, H.-T.

To be published.

Macromolecule Content

Total Structure Weight: 28.13 kDa
Atom Count: 1,622
Modeled Residue Count: 192
Deposited Residue Count: 250
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable O-methyltransferase	A	250	Saccharopolyspora spinosa	Mutation(s): 1 Gene Names: spnH
UniProt
Find proteins for Q9ALM9 (Saccharopolyspora spinosa) Explore Q9ALM9 Go to UniProtKB: Q9ALM9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9ALM9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MG Query on MG 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]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.264 (Depositor), 0.263 (DCC)
R-Value Work: 0.227 (Depositor), 0.228 (DCC)
R-Value Observed: 0.230 (Depositor)

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.776	α = 90
b = 54.776	β = 90
c = 306.532	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
DENZO	data reduction
SCALEPACK	data scaling
PHENIX	phasing

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2017-02-08

Deposition Author(s):

Funding Organization	Location	Grant Number
National Science Council	Taiwan	NSC102-2113-M006-003-MY2

Revision History (Full details and data files)

Version 1.0: 2017-02-08
Type: Initial release
Version 1.1: 2023-11-08
Changes: Data collection, Database references, Refinement description

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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.