4Q29

Ensemble Refinement of plu4264 protein from Photorhabdus luminescens

PDB DOI: https://doi.org/10.2210/pdb4Q29/pdb

Classification: Structural Genomics, Unknown Function
Organism(s): Photorhabdus laumondii subsp. laumondii TTO1
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2014-04-07 Released: 2014-05-07
Deposition Author(s): Wang, F., Michalska, K., Li, H., Jedrzejczak, R., Babnigg, G., Bingman, C.A., Yennamalli, R., Weerth, S., Miller, M.D., Thomas, M.G., Joachimiak, A., Phillips Jr., G.N., Enzyme Discovery for Natural Product Biosynthesis (NatPro), Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.35 Å
R-Value Free: 0.155
R-Value Work: 0.126
R-Value Observed: 0.127

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Structure of a cupin protein Plu4264 from Photorhabdus luminescens subsp. laumondii TTO1 at 1.35 angstrom resolution.

Weerth, R.S., Michalska, K., Bingman, C.A., Yennamalli, R.M., Li, H., Jedrzejczak, R., Wang, F., Babnigg, G., Joachimiak, A., Thomas, M.G., Phillips, G.N.

(2015) Proteins 83: 383-388

PubMed: 25354690 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1002/prot.24705
Primary Citation of Related Structures:
4MV2, 4Q29

PubMed Abstract:
Proteins belonging to the cupin superfamily have a wide range of catalytic and noncatalytic functions. Cupin proteins commonly have the capacity to bind a metal ion with the metal frequently determining the function of the protein. We have been investigating the function of homologous cupin proteins that are conserved in more than 40 species of bacteria. To gain insights into the potential function of these proteins we have solved the structure of Plu4264 from Photorhabdus luminescens TTO1 at a resolution of 1.35 Å and identified manganese as the likely natural metal ligand of the protein.

Organizational Affiliation

Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin.

Macromolecule Content

Total Structure Weight: 31.28 kDa
Atom Count: 2,535
Modelled Residue Count: 241
Deposited Residue Count: 256
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
plu4264 protein	A, B	128	Photorhabdus laumondii subsp. laumondii TTO1	Mutation(s): 0 Gene Names: plu4264
UniProt
Find proteins for Q7MZL9 (Photorhabdus laumondii subsp. laumondii (strain DSM 15139 / CIP 105565 / TT01)) Explore Q7MZL9 Go to UniProtKB: Q7MZL9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q7MZL9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NI Query on NI Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain E [auth B] MOL2 format, chain C [auth A] MOL2 format, chain E [auth B] mmCIF format, chain C [auth A] mmCIF format, chain E [auth B]	C [auth A], E [auth B]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth B]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.35 Å
R-Value Free: 0.155
R-Value Work: 0.126
R-Value Observed: 0.127
Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.738	α = 90
b = 147.687	β = 90
c = 83.843	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
SHELX	phasing
MLPHARE	phasing
DM	phasing
ARP/wARP	model building
Coot	model building

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2014-05-07

Deposition Author(s):

Enzyme Discovery for Natural Product Biosynthesis (NatPro)

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2014-05-07
Type: Initial release
Version 1.1: 2014-11-12
Changes: Database references
Version 1.2: 2015-02-11
Changes: Database references
Version 1.3: 2024-11-20
Changes: Data collection, Database references, Derived calculations, Structure summary