2ES4

Crystal structure of the Burkholderia glumae lipase-specific foldase in complex with its cognate lipase

PDB DOI: https://doi.org/10.2210/pdb2ES4/pdb

Classification: HYDROLASE
Organism(s): Burkholderia glumae
Expression System: Escherichia coli
Mutation(s): Yes
Membrane Protein: Yes OPM

Deposited: 2005-10-25 Released: 2006-03-07
Deposition Author(s): Pauwels, K., Wyns, L., Tommassen, J., Savvides, S.N., Van Gelder, P.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free: 0.219
R-Value Work: 0.199

wwPDB Validation 3D Report Full Report

This is version 1.6 of the entry. See complete history.

Literature

Structure of a membrane-based steric chaperone in complex with its lipase substrate.

Pauwels, K., Lustig, A., Wyns, L., Tommassen, J., Savvides, S.N., Van Gelder, P.

(2006) Nat Struct Mol Biol 13: 374-375

PubMed: 16518399 Search on PubMed
DOI: https://doi.org/10.1038/nsmb1065
Primary Citation of Related Structures:
2ES4

PubMed Abstract:
Secretion via the type II secretion pathway in Gram-negative bacteria often relies crucially on steric chaperones in the periplasm. Here, we report the crystal structure of the soluble form of a lipase-specific foldase (Lif) from Burkholderia glumae in complex with its cognate lipase. The structure reveals how Lif uses a novel alpha-helical scaffold to embrace lipase, thereby creating an unusually extensive folding platform.

Organizational Affiliation

Department of Molecular and Cellular Interactions, Flanders Interuniversity Institute for Biotechnology (VIB) and Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium.

Macromolecule Content

Total Structure Weight: 137.8 kDa
Atom Count: 9,463
Modelled Residue Count: 1,178
Deposited Residue Count: 1,302
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lipase	A, C [auth B]	319	Burkholderia glumae	Mutation(s): 0 EC: 3.1.1.3 Membrane Entity: Yes
UniProt
Find proteins for P0DUB8 (Burkholderia plantarii) Explore P0DUB8 Go to UniProtKB: P0DUB8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0DUB8
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Lipase chaperone	B [auth D], D [auth E]	332	Burkholderia glumae	Mutation(s): 1 Gene Names: lifO, lipB Membrane Entity: Yes
UniProt
Find proteins for Q05490 (Burkholderia plantarii) Explore Q05490 Go to UniProtKB: Q05490
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q05490
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
IOD Query on IOD Download Ideal Coordinates CCD File SDF format, chain F [auth D] SDF format, chain H [auth B] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain L [auth E] SDF format, chain M [auth E] SDF format, chain N [auth E] MOL2 format, chain F [auth D] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain L [auth E] MOL2 format, chain M [auth E] MOL2 format, chain N [auth E]	F [auth D] H [auth B] I [auth B] J [auth B] K [auth B] F [auth D], H [auth B], I [auth B], J [auth B], K [auth B], L [auth E], M [auth E], N [auth E]	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M		Interactions Focus chain F [auth D] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth E] Focus chain M [auth E] Focus chain N [auth E] Interactions & Density Focus chain F [auth D] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth E] Focus chain M [auth E] Focus chain N [auth E]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth B] MOL2 format, chain E [auth A] MOL2 format, chain G [auth B]	E [auth A], G [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Interactions & Density Focus chain E [auth A] Focus chain G [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSO Query on CSO	B [auth D], D [auth E]	L-PEPTIDE LINKING	C₃ H₇ N O₃ S		CYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free: 0.219
R-Value Work: 0.199
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 183	α = 90
b = 75.7	β = 117.6
c = 116.6	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
CNS	refinement
PDB_EXTRACT	data extraction

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2006-03-07

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2006-03-07
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2017-10-18
Changes: Refinement description
Version 1.4: 2018-01-24
Changes: Database references
Version 1.5: 2023-08-23
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.6: 2023-11-15
Changes: Data collection