6R4Q

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.180 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


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.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Nickel-binding periplasmic protein
A, B
502Escherichia coli K-12Mutation(s): 0 
Gene Names: nikAb3476JW3441
UniProt
Find proteins for P33590 (Escherichia coli (strain K12))
Explore P33590 
Go to UniProtKB:  P33590
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP33590
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 8 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
EDT
Query on EDT

Download Ideal Coordinates CCD File 
D [auth A]{[-(BIS-CARBOXYMETHYL-AMINO)-ETHYL]-CARBOXYMETHYL-AMINO}-ACETIC ACID
C10 H16 N2 O8
KCXVZYZYPLLWCC-UHFFFAOYSA-N
6RP
Query on 6RP

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X [auth B]bis(pyrzol-1-yl)acetate scorpionate
C8 H8 N4 O2
NJDSSVBTTVUKHM-UHFFFAOYSA-N
RU
Query on RU

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W [auth B]RUTHENIUM ION
Ru
BPEVHDGLPIIAGH-UHFFFAOYSA-N
GOL
Query on GOL

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AA [auth B]
BA [auth B]
CA [auth B]
DA [auth B]
EA [auth B]
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
Query on ACT

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GA [auth B]
HA [auth B]
M [auth A]
N [auth A]
O [auth A]
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
Query on FE

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C [auth A]FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
CL
Query on CL

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E [auth A],
Y [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
CMO
Query on CMO

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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 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.180 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.629α = 90
b = 94.101β = 90
c = 124.418γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
French National Research AgencyFranceCrystalball

Revision History  (Full details and data files)

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