6EGP | pdb_00006egp

Crystal Structure of a Trigonal Pyramidal Pb(II)S3 Complex in a Three-stranded Coiled coil Peptide

• PDB DOI: https://doi.org/10.2210/pdb6EGP/pdb

• Classification: DE NOVO PROTEIN
• Organism(s): synthetic construct
• Mutation(s): No 


• Deposited: 2018-08-20 Released: 2020-02-26 
• Deposition Author(s): Ruckthong, L., Stuckey, J.A., Pecoraro, V.L.
• Funding Organization(s): National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.77 Å
• R-Value Free: 
  0.208 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.184 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.185 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of a Trigonal Pyramidal Pb(II)S3 Complex in a Three-stranded Coiled coil Peptide

Ruckthong, L., Stuckey, J.A., Pecoraro, V.L.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: mass spectrometry

Macromolecule Content 

• Total Structure Weight: 4.35 kDa 
• Atom Count: 355 
• Modeled Residue Count: 36 
• Deposited Residue Count: 36 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pb(II)(GRAND CoilSerL12AL16C)3-	A	36	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PB	C [auth A]	LEAD (II) ION Pb RVPVRDXYQKGNMQ-UHFFFAOYSA-N
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.77 Å
• R-Value Free:  0.208 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.184 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.185 (Depositor) 

Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.726	α = 90
b = 37.726	β = 90
c = 140.042	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
HKL-2000	data scaling
MOLREP	phasing
BUSTER-TNT	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-02-26 
Deposition Author(s): Ruckthong, L., Stuckey, J.A., Pecoraro, V.L.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)	United States	R01ES012236

Revision History  

• Version 1.0: 2020-02-26
  Type: Initial release
  
• Version 1.1: 2023-10-11
  Changes: Data collection, Database references, Derived calculations, Refinement description