3QW1 | pdb_00003qw1

Crystal structure of the Zn-RIDC1 complex stabilized by BMH crosslinks

PDB DOI: https://doi.org/10.2210/pdb3QW1/pdb

Classification: OXIDOREDUCTASE
Organism(s): Escherichia coli
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2011-02-26 Released: 2011-06-22
Deposition Author(s): Salgado, E.N., Tezcan, F.A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free:
0.318 (Depositor), 0.308 (DCC)
R-Value Work:
0.288 (Depositor), 0.277 (DCC)
R-Value Observed:
0.290 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Templated construction of a zn-selective protein dimerization motif.

Salgado, E.N., Brodin, J.D., To, M.M., Tezcan, F.A.

(2011) Inorg Chem 50: 6323-6329

PubMed: 21648390 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1021/ic200746m
Primary Citation Related Structures:
3QVY, 3QVZ, 3QW0, 3QW1

PubMed Abstract:
Here, we report that the approach of metal-templated ligand synthesis can be applied to construct a dimeric protein assembly ((BMOE)RIDC1(2)), which is stabilized by noncovalent interactions and flexible covalent cross-linkers around the Zn templates. Despite its flexibility, (BMOE)RIDC1(2) selectively binds Zn(II) over other divalent metals and undergoes dimerization upon metal binding. Such simultaneous fulfillment of plasticity and selectivity is a hallmark of cellular signaling events that involve ligand/metal-induced protein dimerization.

Organizational Affiliation

Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, MC 0356, La Jolla, California 92093, USA.

Macromolecule Content

Total Structure Weight: 50.23 kDa
Atom Count: 3,510
Modeled Residue Count: 424
Deposited Residue Count: 424
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome cb562	A, B, C, D	106	Escherichia coli	Mutation(s): 0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEM Query on HEM Download:Ideal Coordinates CCD File SDF format, chain O [auth D] SDF format, chain L [auth C] SDF format, chain I [auth B] SDF format, chain F [auth A] MOL2 format, chain O [auth D] MOL2 format, chain L [auth C] MOL2 format, chain I [auth B] MOL2 format, chain F [auth A] mmCIF format, chain O [auth D] mmCIF format, chain L [auth C] mmCIF format, chain I [auth B] mmCIF format, chain F [auth A]	F [auth A], I [auth B], L [auth C], O [auth D]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain F [auth A] Focus chain I [auth B] Focus chain L [auth C] Focus chain O [auth D] Interactions & Density Focus chain F [auth A] Focus chain I [auth B] Focus chain L [auth C] Focus chain O [auth D]
LCY Query on LCY Download:Ideal Coordinates CCD File SDF format, chain P [auth D] SDF format, chain M [auth C] SDF format, chain J [auth B] SDF format, chain G [auth A] MOL2 format, chain P [auth D] MOL2 format, chain M [auth C] MOL2 format, chain J [auth B] MOL2 format, chain G [auth A] mmCIF format, chain P [auth D] mmCIF format, chain M [auth C] mmCIF format, chain J [auth B] mmCIF format, chain G [auth A]	G [auth A], J [auth B], M [auth C], P [auth D]	1-methylpyrrolidine-2,5-dione C₅ H₇ N O₂ KYEACNNYFNZCST-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain J [auth B] Focus chain M [auth C] Focus chain P [auth D] Interactions & Density Focus chain G [auth A] Focus chain J [auth B] Focus chain M [auth C] Focus chain P [auth D]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain Q [auth D] SDF format, chain N [auth D] SDF format, chain K [auth C] SDF format, chain H [auth B] SDF format, chain E [auth A] MOL2 format, chain Q [auth D] MOL2 format, chain N [auth D] MOL2 format, chain K [auth C] MOL2 format, chain H [auth B] MOL2 format, chain E [auth A] mmCIF format, chain Q [auth D] mmCIF format, chain N [auth D] mmCIF format, chain K [auth C] mmCIF format, chain H [auth B] mmCIF format, chain E [auth A]	E [auth A], H [auth B], K [auth C], N [auth D], Q [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Focus chain K [auth C] Focus chain N [auth D] Focus chain Q [auth D] Interactions & Density Focus chain E [auth A] Focus chain H [auth B] Focus chain K [auth C] Focus chain N [auth D] Focus chain Q [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.318 (Depositor), 0.308 (DCC)
R-Value Work: 0.288 (Depositor), 0.277 (DCC)
R-Value Observed: 0.290 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.298	α = 90
b = 61.843	β = 102.22
c = 70.087	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALA	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
Blu-Ice	data collection

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2011-06-22

Deposition Author(s):

Salgado, E.N.

Tezcan, F.A.

Revision History (Full details and data files)

Version 1.0: 2011-06-22
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2024-11-06
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary