3TML

Crystal structure of 2-dehydro-3-deoxyphosphooctonate aldolase from Burkholderia cenocepacia

PDB DOI: https://doi.org/10.2210/pdb3TML/pdb

Classification: TRANSFERASE
Organism(s): Burkholderia cenocepacia J2315
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2011-08-31 Released: 2011-09-21
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.225
R-Value Work: 0.187
R-Value Observed: 0.189

wwPDB Validation 3D Report Full Report

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

Literature

Combining functional and structural genomics to sample the essential Burkholderia structome.

Baugh, L., Gallagher, L.A., Patrapuvich, R., Clifton, M.C., Gardberg, A.S., Edwards, T.E., Armour, B., Begley, D.W., Dieterich, S.H., Dranow, D.M., Abendroth, J., Fairman, J.W., Fox, D., Staker, B.L., Phan, I., Gillespie, A., Choi, R., Nakazawa-Hewitt, S., Nguyen, M.T., Napuli, A., Barrett, L., Buchko, G.W., Stacy, R., Myler, P.J., Stewart, L.J., Manoil, C., Van Voorhis, W.C.

(2013) PLoS One 8: e53851-e53851

PubMed: 23382856 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1371/journal.pone.0053851
Primary Citation of Related Structures:
3D63, 3DAH, 3EIZ, 3EJ2, 3EK2, 3EZO, 3F0F, 3FTP, 3GK0, 3GK3, 3GVF, 3GWA, 3GWE, 3IML, 3SZ8, 3T4C, 3TML, 3TMQ, 3TXY, 3U7J, 3UE9, 3UK1, 3UK2, 3UND, 3UPT, 3URR, 3UW1, 3UW2, 3UW3, 3V2I, 3V7N, 3V8H, 3V9O, 3V9P, 3VAV, 4DDO, 4DFE, 4DHE, 4DHK, 4DUT, 4DZ4, 4E4T, 4EFI, 4EG0, 4EGJ, 4EK2, 4EQY, 4EWG, 4EXQ, 4F2G

PubMed Abstract:
The genus Burkholderia includes pathogenic gram-negative bacteria that cause melioidosis, glanders, and pulmonary infections of patients with cancer and cystic fibrosis. Drug resistance has made development of new antimicrobials critical. Many approaches to discovering new antimicrobials, such as structure-based drug design and whole cell phenotypic screens followed by lead refinement, require high-resolution structures of proteins essential to the parasite.

Organizational Affiliation

Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington, United States of America.

Macromolecule Content

Total Structure Weight: 125.85 kDa
Atom Count: 8,373
Modelled Residue Count: 1,054
Deposited Residue Count: 1,152
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
2-dehydro-3-deoxyphosphooctonate aldolase	A, B, C, D	288	Burkholderia cenocepacia J2315	Mutation(s): 0 Gene Names: kdsA, BceJ2315_21430, BCAL2180 EC: 2.5.1.55
UniProt
Find proteins for B4EDA2 (Burkholderia cenocepacia (strain ATCC BAA-245 / DSM 16553 / LMG 16656 / NCTC 13227 / J2315 / CF5610)) Explore B4EDA2 Go to UniProtKB: B4EDA2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	B4EDA2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain I [auth C] SDF format, chain J [auth C] SDF format, chain M [auth D] SDF format, chain N [auth D] SDF format, chain F [auth B] MOL2 format, chain E [auth A] MOL2 format, chain I [auth C] MOL2 format, chain J [auth C] MOL2 format, chain M [auth D] MOL2 format, chain N [auth D] MOL2 format, chain F [auth B]	E [auth A] F [auth B] I [auth C] J [auth C] M [auth D] E [auth A], F [auth B], I [auth C], J [auth C], M [auth D], N [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth A] Focus chain F [auth B] Focus chain I [auth C] Focus chain J [auth C] Focus chain M [auth D] Focus chain N [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth B] Focus chain I [auth C] Focus chain J [auth C] Focus chain M [auth D] Focus chain N [auth D]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain H [auth B] SDF format, chain K [auth C] SDF format, chain L [auth C] MOL2 format, chain G [auth B] MOL2 format, chain H [auth B] MOL2 format, chain K [auth C] MOL2 format, chain L [auth C]	G [auth B], H [auth B], K [auth C], L [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain G [auth B] Focus chain H [auth B] Focus chain K [auth C] Focus chain L [auth C] Interactions & Density Focus chain G [auth B] Focus chain H [auth B] Focus chain K [auth C] Focus chain L [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.225
R-Value Work: 0.187
R-Value Observed: 0.189
Space Group: P 2₁ 2₁ 2₁
Diffraction Data: https://doi.org/10.18430/M33TML

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.38	α = 90
b = 149.01	β = 90
c = 151.07	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
Blu-Ice	data collection
XDS	data reduction

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2011-09-21

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History (Full details and data files)

Version 1.0: 2011-09-21
Type: Initial release
Version 1.1: 2013-10-09
Changes: Database references
Version 1.2: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description

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Deposit Data

Help and Resources

3TML

Crystal structure of 2-dehydro-3-deoxyphosphooctonate aldolase from Burkholderia cenocepacia

Combining functional and structural genomics to sample the essential Burkholderia structome.

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)