5K08 | pdb_00005k08

RecA mini intein-Zeise's salt complex

• PDB DOI: https://doi.org/10.2210/pdb5K08/pdb

• Classification: HYDROLASE
• Organism(s): Mycobacterium tuberculosis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2016-05-17 Released: 2016-09-21 
• Deposition Author(s): Li, Z., Li, H.M.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Cancer Institute (NIH/NCI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 
  0.210 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.180 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.182 (Depositor) 

Starting Model: experimental

Literature

Structural insights into protein splicing inhibition by platinum therapeutics as potential anti-microbials

Chan, H., Pearson, S., Green, C.M., Li, Z., Zhang, J., Lippard, S., Belfort, G., Shekhtman, A., Li, H.M., Belfort, M.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 16.67 kDa 
• Atom Count: 1,255 
• Modelled Residue Count: 142 
• Deposited Residue Count: 142 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RecA mini intein	A	142	Mycobacterium tuberculosis	Mutation(s): 0
UniProt
Find proteins for P9WHJ3 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WHJ3  Go to UniProtKB:  P9WHJ3

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZPT	B [auth A], C [auth A]	Trichloro(ethene)platinate(II) C2 H4 Cl3 Pt LJEKXYSRMGLQBW-UHFFFAOYSA-K
TCE	E [auth A]	3,3',3''-phosphanetriyltripropanoic acid C9 H15 O6 P PZBFGYYEXUXCOF-UHFFFAOYSA-N
SO4	D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free:  0.210 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.180 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.182 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.687	α = 90
b = 63.93	β = 90
c = 37.307	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SCALEPACK	data scaling
PDB_EXTRACT	data extraction
DENZO	data reduction
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2016-09-21 
Deposition Author(s): Li, Z., Li, H.M.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM39422
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM44844
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	CA039442

Revision History  

• Version 1.0: 2016-09-21
  Type: Initial release
  
• Version 1.1: 2017-09-20
  Changes: Author supporting evidence, Derived calculations
• Version 1.2: 2019-12-04
  Changes: Author supporting evidence
• Version 1.3: 2023-09-27
  Changes: Data collection, Database references, Refinement description