6W80

Crystal structure of Glutamate-1-semialdehyde 2,1-aminomutase from Stenotrophomonas maltophilia K279a in complex with PLP

PDB DOI: https://doi.org/10.2210/pdb6W80/pdb

Classification: ISOMERASE
Organism(s): Stenotrophomonas maltophilia K279a
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2020-03-20 Released: 2020-04-08
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.40 Å
R-Value Free: 0.181
R-Value Work: 0.134
R-Value Observed: 0.136

Starting Model: experimental
View more details

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 Glutamate-1-semialdehyde 2,1-aminomutase from Stenotrophomonas maltophilia K279a in complex with PLP

Abendroth, J., Horanyi, P.S., Lorimer, D.D., Edwards, T.E.

To be published.

Macromolecule Content

Total Structure Weight: 46.39 kDa
Atom Count: 3,837
Modelled Residue Count: 430
Deposited Residue Count: 437
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutamate-1-semialdehyde 2,1-aminomutase	A	437	Stenotrophomonas maltophilia K279a	Mutation(s): 0 Gene Names: hemL, Smlt3873 EC: 5.4.3.8
UniProt
Find proteins for B2FT35 (Stenotrophomonas maltophilia (strain K279a)) Explore B2FT35 Go to UniProtKB: B2FT35
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	B2FT35
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PLP (Subject of Investigation/LOI) Query on PLP Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	PYRIDOXAL-5'-PHOSPHATE C₈ H₁₀ N O₆ P NGVDGCNFYWLIFO-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: 1.40 Å
R-Value Free: 0.181
R-Value Work: 0.134
R-Value Observed: 0.136
Space Group: P 6₅ 2 2
Diffraction Data: https://doi.org/10.18430/m36w80

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.28	α = 90
b = 60.28	β = 90
c = 367.22	γ = 120

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
MoRDa	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2020-04-08

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History (Full details and data files)

Version 1.0: 2020-04-08
Type: Initial release
Version 1.1: 2023-10-18
Changes: Data collection, Database references, Refinement description

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.