6R4Q | pdb_00006r4q

Crystal structure of the periplasmic nickel-binding protein NikA from Escherichia coli in complex with Ru(bpza)CO H2O Cl

• PDB DOI: https://doi.org/10.2210/pdb6R4Q/pdb

• Classification: METAL BINDING PROTEIN
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2019-03-22 Released: 2020-04-08 
• Deposition Author(s): Cavazza, C., Menage, S.
• Funding Organization(s): French National Research Agency

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.232 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.178 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.180 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of the periplasmic nickel-binding protein NikA from Escherichia coli in complex with Ru(bpza)CO H2O Cl

Cavazza, C., Menage, S.

To be published.

Biological Assembly 1  

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

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

Biological Assembly Evidence: light scattering

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 115.68 kDa 
• Atom Count: 8,848 
• Modeled Residue Count: 996 
• Deposited Residue Count: 1,004 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nickel-binding periplasmic protein	A, B	502	Escherichia coli K-12	Mutation(s): 0  Gene Names: nikA, b3476, JW3441
UniProt
Find proteins for P33590 (Escherichia coli (strain K12)) Explore P33590  Go to UniProtKB:  P33590

Small Molecules

Ligands 8 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDT	D [auth A]	{[-(BIS-CARBOXYMETHYL-AMINO)-ETHYL]-CARBOXYMETHYL-AMINO}-ACETIC ACID C10 H16 N2 O8 KCXVZYZYPLLWCC-UHFFFAOYSA-N
6RP	X [auth B]	bis(pyrzol-1-yl)acetate scorpionate C8 H8 N4 O2 NJDSSVBTTVUKHM-UHFFFAOYSA-N
RU	W [auth B]	RUTHENIUM ION Ru BPEVHDGLPIIAGH-UHFFFAOYSA-N
GOL	AA [auth B], BA [auth B], CA [auth B], DA [auth B], EA [auth B], F [auth A], FA [auth B], G [auth A], H [auth A], I [auth A], IA [auth B], J [auth A], JA [auth B], K [auth A], L [auth A], P [auth A], Q [auth A], S [auth A], U [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACT	GA [auth B], HA [auth B], M [auth A], N [auth A], O [auth A], R [auth A], T [auth A], V [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
FE	C [auth A]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N
CL	E [auth A], Y [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
CMO	Z [auth B]	CARBON MONOXIDE C O UGFAIRIUMAVXCW-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.232 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.178 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.180 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.629	α = 90
b = 94.101	β = 90
c = 124.418	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
REFMAC	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-04-08 
Deposition Author(s): Cavazza, C., Menage, S.

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Funding Organization	Location	Grant Number
French National Research Agency	France	Crystalball

Revision History  

• Version 1.0: 2020-04-08
  Type: Initial release
  
• Version 1.1: 2024-01-24
  Changes: Data collection, Database references, Derived calculations, Refinement description