5VNX | pdb_00005vnx

Crystal structure of an 8-amino-7-oxononanoate synthase from Burkholderia multivorans with a potential glycine-PLP-Lys242 cyclized intermediate or byproduct

PDB DOI: https://doi.org/10.2210/pdb5VNX/pdb

Classification: TRANSFERASE
Organism(s): Burkholderia multivorans ATCC 17616
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2017-05-01 Released: 2017-05-17
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free:
0.167 (Depositor), 0.170 (DCC)
R-Value Work:
0.146 (Depositor), 0.150 (DCC)
R-Value Observed:
0.146 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 2.0 of the entry. See complete history.

Literature

Crystal structure of a 8-amino-7-oxononanoate synthase from Burkholderia multivorans with a potential glycine-PLP-Lys242 cyclized intermediate or byproduct

Conrady, D.G., Abendroth, J., Lorimer, D.D., Edwards, T.E.

To be published.

Macromolecule Content

Total Structure Weight: 125.78 kDa
Atom Count: 10,651
Modeled Residue Count: 1,177
Deposited Residue Count: 1,179
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
8-amino-7-oxononanoate synthase	A, B, C	393	Burkholderia multivorans ATCC 17616	Mutation(s): 0 Gene Names: bioF, Bmul_0373, BMULJ_02881 EC: 2.3.1.47
UniProt
Find proteins for A9AE46 (Burkholderia multivorans (strain ATCC 17616 / 249)) Explore A9AE46 Go to UniProtKB: A9AE46
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A9AE46
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BEN Query on BEN Download Ideal Coordinates CCD File SDF format, chain N [auth C] SDF format, chain K [auth B] SDF format, chain J [auth B] SDF format, chain E [auth A] SDF format, chain D [auth A] MOL2 format, chain N [auth C] MOL2 format, chain K [auth B] MOL2 format, chain J [auth B] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain N [auth C] mmCIF format, chain K [auth B] mmCIF format, chain J [auth B] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A]	D [auth A], E [auth A], J [auth B], K [auth B], N [auth C]	BENZAMIDINE C₇ H₈ N₂ PXXJHWLDUBFPOL-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain N [auth C] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain N [auth C]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain P [auth C] SDF format, chain O [auth C] SDF format, chain H [auth A] MOL2 format, chain P [auth C] MOL2 format, chain O [auth C] MOL2 format, chain H [auth A] mmCIF format, chain P [auth C] mmCIF format, chain O [auth C] mmCIF format, chain H [auth A]	H [auth A], O [auth C], P [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain H [auth A] Focus chain O [auth C] Focus chain P [auth C] Interactions & Density Focus chain H [auth A] Focus chain O [auth C] Focus chain P [auth C]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain S [auth C] SDF format, chain R [auth C] SDF format, chain Q [auth C] SDF format, chain M [auth B] SDF format, chain L [auth B] SDF format, chain I [auth A] SDF format, chain G [auth A] SDF format, chain F [auth A] MOL2 format, chain S [auth C] MOL2 format, chain R [auth C] MOL2 format, chain Q [auth C] MOL2 format, chain M [auth B] MOL2 format, chain L [auth B] MOL2 format, chain I [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] mmCIF format, chain S [auth C] mmCIF format, chain R [auth C] mmCIF format, chain Q [auth C] mmCIF format, chain M [auth B] mmCIF format, chain L [auth B] mmCIF format, chain I [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A]	F [auth A] G [auth A] I [auth A] L [auth B] M [auth B] F [auth A], G [auth A], I [auth A], L [auth B], M [auth B], Q [auth C], R [auth C], S [auth C]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain Q [auth C] Focus chain R [auth C] Focus chain S [auth C] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain Q [auth C] Focus chain R [auth C] Focus chain S [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free: 0.167 (Depositor), 0.170 (DCC)
R-Value Work: 0.146 (Depositor), 0.150 (DCC)
R-Value Observed: 0.146 (Depositor)

Diffraction Data: https://doi.org/10.18430/M35VNX

Space Group: C 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 177.53	α = 90
b = 262.09	β = 90
c = 65.34	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2017-05-17

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History (Full details and data files)

Version 1.0: 2017-05-17
Type: Initial release
Version 1.1: 2023-10-04
Changes: Data collection, Database references, Other, Refinement description
Version 2.0: 2023-11-15
Changes: Atomic model, Data collection, Derived calculations