5GPE | pdb_00005gpe

Crystal structure of the transcription regulator PbrR691 from Ralstonia metallidurans CH34 in complex with Lead(II)

PDB DOI: https://doi.org/10.2210/pdb5GPE/pdb

Classification: TRANSCRIPTION
Organism(s): Cupriavidus metallidurans CH34
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2016-08-01 Released: 2016-12-28
Deposition Author(s): Huang, S.Q., Chen, W.Z., Wang, D., Hu, Q.Y., Liu, X.C., Gan, J.H., Chen, H.
Funding Organization(s): National Science Foundation (NSF, China)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.01 Å
R-Value Free:
0.214 (Depositor), 0.221 (DCC)
R-Value Work:
0.177 (Depositor), 0.185 (DCC)
R-Value Observed:
0.178 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Structural Basis for the Selective Pb(II) Recognition of Metalloregulatory Protein PbrR691

Huang, S.Q., Liu, X.C., Wang, D., Chen, W.Z., Hu, Q.Y., Wei, T.B., Zhou, W.Q., Gan, J.H., Chen, H.

(2016) Inorg Chem 55: 12516-12519

PubMed: 27989185 Search on PubMed
DOI: https://doi.org/10.1021/acs.inorgchem.6b02397
Primary Citation Related Structures:
5GPE

PubMed Abstract:
The transcription regulator PbrR691, one of the MerR family proteins, shows extremely high sensitivity and selectivity toward Pb(II) in Ralstonia metallidurans CH34. Here, we present the crystal structure of PbrR691 in complex with Pb(II) at 2.0 Å resolution. The Pb(II) coordinates with three conserved cysteines and adopts a unique trigonal-pyramidal (hemidirected) geometry. To our knowledge, the PbrR691-Pb(II) structure provides the first three-dimensional visualization of a functional hemidirected lead(II) thiolate coordinate geometry in a protein.

Organizational Affiliation

School of Life Sciences, Fudan University , Shanghai 200433, P. R. China.

Macromolecule Content

Total Structure Weight: 121.32 kDa
Atom Count: 8,637
Modeled Residue Count: 1,009
Deposited Residue Count: 1,032
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcriptional regulator, MerR-family	A, B, C, D, E A, B, C, D, E, F, G, H	129	Cupriavidus metallidurans CH34	Mutation(s): 0 Gene Names: pbrR2, Rmet_2302
UniProt
Find proteins for Q1LKZ5 (Cupriavidus metallidurans (strain ATCC 43123 / DSM 2839 / NBRC 102507 / CH34)) Explore Q1LKZ5 Go to UniProtKB: Q1LKZ5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q1LKZ5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PB Query on PB Download:Ideal Coordinates CCD File SDF format, chain P [auth H] SDF format, chain O [auth G] SDF format, chain N [auth F] SDF format, chain M [auth E] SDF format, chain L [auth D] SDF format, chain K [auth C] SDF format, chain J [auth B] SDF format, chain I [auth A] MOL2 format, chain P [auth H] MOL2 format, chain O [auth G] MOL2 format, chain N [auth F] MOL2 format, chain M [auth E] MOL2 format, chain L [auth D] MOL2 format, chain K [auth C] MOL2 format, chain J [auth B] MOL2 format, chain I [auth A] mmCIF format, chain P [auth H] mmCIF format, chain O [auth G] mmCIF format, chain N [auth F] mmCIF format, chain M [auth E] mmCIF format, chain L [auth D] mmCIF format, chain K [auth C] mmCIF format, chain J [auth B] mmCIF format, chain I [auth A]	I [auth A] J [auth B] K [auth C] L [auth D] M [auth E] I [auth A], J [auth B], K [auth C], L [auth D], M [auth E], N [auth F], O [auth G], P [auth H]	LEAD (II) ION Pb RVPVRDXYQKGNMQ-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain J [auth B] Focus chain K [auth C] Focus chain L [auth D] Focus chain M [auth E] Focus chain N [auth F] Focus chain O [auth G] Focus chain P [auth H] Interactions & Density Focus chain I [auth A] Focus chain J [auth B] Focus chain K [auth C] Focus chain L [auth D] Focus chain M [auth E] Focus chain N [auth F] Focus chain O [auth G] Focus chain P [auth H]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.01 Å
R-Value Free: 0.214 (Depositor), 0.221 (DCC)
R-Value Work: 0.177 (Depositor), 0.185 (DCC)
R-Value Observed: 0.178 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.938	α = 109.33
b = 67.903	β = 89.82
c = 89.723	γ = 90.32

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2016-12-28

Deposition Author(s):

Funding Organization	Location	Grant Number
National Science Foundation (NSF, China)	China	--

Revision History (Full details and data files)

Version 1.0: 2016-12-28
Type: Initial release
Version 1.1: 2017-08-16
Changes: Structure summary
Version 1.2: 2021-09-15
Changes: Author supporting evidence, Database references
Version 1.3: 2023-11-08
Changes: Data collection, Refinement description