4I9D

X-ray structure of NikA in complex with Fe-N,N'-Bis(2-pyridylmethyl)-N-carboxymethyl-N'-methyl

PDB DOI: https://doi.org/10.2210/pdb4I9D/pdb

Classification: METAL TRANSPORT
Organism(s): Escherichia coli BL21(DE3)
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2012-12-05 Released: 2013-04-17
Deposition Author(s): Cherrier, M.V., Amara, P., Iannello, M., Cavazza, C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.195
R-Value Work: 0.152
R-Value Observed: 0.154

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

An artificial oxygenase built from scratch: substrate binding site identified using a docking approach.

Esmieu, C., Cherrier, M.V., Amara, P., Girgenti, E., Marchi-Delapierre, C., Oddon, F., Iannello, M., Jorge-Robin, A., Cavazza, C., Menage, S.

(2013) Angew Chem Int Ed Engl 52: 3922-3925

PubMed: 23440925 Search on PubMed
DOI: https://doi.org/10.1002/anie.201209021
Primary Citation of Related Structures:
4I9D

Organizational Affiliation

Laboratoire Chimie et Biologie des Métaux, Université Joseph Fourier-Grenoble 1, CEA, DSV/iRTSV, LCBM, CNRS, UMR5249, 38041 Grenoble, France.

Macromolecule Content

Total Structure Weight: 117.06 kDa
Atom Count: 9,819
Modelled Residue Count: 995
Deposited Residue Count: 1,004
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nickel-binding periplasmic protein	A, B	502	Escherichia coli BL21(DE3)	Mutation(s): 0 Gene Names: b3476, JW3441, nikA EC: 3.6.3.24
UniProt
Find proteins for P33590 (Escherichia coli (strain K12)) Explore P33590 Go to UniProtKB: P33590
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P33590
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
L4D Query on L4D Download Ideal Coordinates CCD File SDF format, chain GA [auth A] SDF format, chain WA [auth B] MOL2 format, chain GA [auth A] MOL2 format, chain WA [auth B] mmCIF format, chain GA [auth A] mmCIF format, chain WA [auth B]	GA [auth A], WA [auth B]	{(S)-N-(2-{methyl[(pyridin-2-yl-kappaN)methyl]amino-kappaN}ethyl)-N-[(pyridin-2-yl-kappaN)methyl]glycinato-kappa~2~N,O}iron(2+) C₁₇ H₂₁ Fe N₄ O₂ KEGLXUIHTNIIAB-UHFFFAOYSA-M		Interactions Focus chain GA [auth A] Focus chain WA [auth B] Interactions & Density Focus chain GA [auth A] Focus chain WA [auth B]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A]	F [auth A], G [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain F [auth A] Focus chain G [auth A] Interactions & Density Focus chain F [auth A] Focus chain G [auth A]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain BA [auth A] SDF format, chain E [auth A] SDF format, chain H [auth A] SDF format, chain HA [auth A] SDF format, chain IA [auth A] SDF format, chain J [auth A] SDF format, chain JA [auth A] SDF format, chain K [auth A] SDF format, chain KA [auth B] SDF format, chain L [auth A] SDF format, chain LA [auth B] SDF format, chain N [auth A] SDF format, chain NA [auth B] SDF format, chain P [auth A] SDF format, chain PA [auth B] SDF format, chain TA [auth B] SDF format, chain U [auth A] SDF format, chain UA [auth B] SDF format, chain X [auth A] SDF format, chain XA [auth B] SDF format, chain ZA [auth B] MOL2 format, chain BA [auth A] MOL2 format, chain E [auth A] MOL2 format, chain H [auth A] MOL2 format, chain HA [auth A] MOL2 format, chain IA [auth A] MOL2 format, chain J [auth A] MOL2 format, chain JA [auth A] MOL2 format, chain K [auth A] MOL2 format, chain KA [auth B] MOL2 format, chain L [auth A] MOL2 format, chain LA [auth B] MOL2 format, chain N [auth A] MOL2 format, chain NA [auth B] MOL2 format, chain P [auth A] MOL2 format, chain PA [auth B] MOL2 format, chain TA [auth B] MOL2 format, chain U [auth A] MOL2 format, chain UA [auth B] MOL2 format, chain X [auth A] MOL2 format, chain XA [auth B] MOL2 format, chain ZA [auth B] mmCIF format, chain BA [auth A] mmCIF format, chain E [auth A] mmCIF format, chain H [auth A] mmCIF format, chain HA [auth A] mmCIF format, chain IA [auth A] mmCIF format, chain J [auth A] mmCIF format, chain JA [auth A] mmCIF format, chain K [auth A] mmCIF format, chain KA [auth B] mmCIF format, chain L [auth A] mmCIF format, chain LA [auth B] mmCIF format, chain N [auth A] mmCIF format, chain NA [auth B] mmCIF format, chain P [auth A] mmCIF format, chain PA [auth B] mmCIF format, chain TA [auth B] mmCIF format, chain U [auth A] mmCIF format, chain UA [auth B] mmCIF format, chain X [auth A] mmCIF format, chain XA [auth B] mmCIF format, chain ZA [auth B]	BA [auth A] E [auth A] H [auth A] HA [auth A] IA [auth A] BA [auth A], E [auth A], H [auth A], HA [auth A], IA [auth A], J [auth A], JA [auth A], K [auth A], KA [auth B], L [auth A], LA [auth B], N [auth A], NA [auth B], P [auth A], PA [auth B], TA [auth B], U [auth A], UA [auth B], X [auth A], XA [auth B], ZA [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain BA [auth A] Focus chain E [auth A] Focus chain H [auth A] Focus chain HA [auth A] Focus chain IA [auth A] Focus chain J [auth A] Focus chain JA [auth A] Focus chain K [auth A] Focus chain KA [auth B] Focus chain L [auth A] Focus chain LA [auth B] Focus chain N [auth A] Focus chain NA [auth B] Focus chain P [auth A] Focus chain PA [auth B] Focus chain TA [auth B] Focus chain U [auth A] Focus chain UA [auth B] Focus chain X [auth A] Focus chain XA [auth B] Focus chain ZA [auth B] Interactions & Density Focus chain BA [auth A] Focus chain E [auth A] Focus chain H [auth A] Focus chain HA [auth A] Focus chain IA [auth A] Focus chain J [auth A] Focus chain JA [auth A] Focus chain K [auth A] Focus chain KA [auth B] Focus chain L [auth A] Focus chain LA [auth B] Focus chain N [auth A] Focus chain NA [auth B] Focus chain P [auth A] Focus chain PA [auth B] Focus chain TA [auth B] Focus chain U [auth A] Focus chain UA [auth B] Focus chain X [auth A] Focus chain XA [auth B] Focus chain ZA [auth B]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain AA [auth A] SDF format, chain C [auth A] SDF format, chain CA [auth A] SDF format, chain D [auth A] SDF format, chain DA [auth A] SDF format, chain EA [auth A] SDF format, chain FA [auth A] SDF format, chain I [auth A] SDF format, chain M [auth A] SDF format, chain MA [auth B] SDF format, chain O [auth A] SDF format, chain OA [auth B] SDF format, chain Q [auth A] SDF format, chain QA [auth B] SDF format, chain R [auth A] SDF format, chain RA [auth B] SDF format, chain S [auth A] SDF format, chain SA [auth B] SDF format, chain T [auth A] SDF format, chain V [auth A] SDF format, chain VA [auth B] SDF format, chain W [auth A] SDF format, chain Y [auth A] SDF format, chain YA [auth B] SDF format, chain Z [auth A] MOL2 format, chain AA [auth A] MOL2 format, chain C [auth A] MOL2 format, chain CA [auth A] MOL2 format, chain D [auth A] MOL2 format, chain DA [auth A] MOL2 format, chain EA [auth A] MOL2 format, chain FA [auth A] MOL2 format, chain I [auth A] MOL2 format, chain M [auth A] MOL2 format, chain MA [auth B] MOL2 format, chain O [auth A] MOL2 format, chain OA [auth B] MOL2 format, chain Q [auth A] MOL2 format, chain QA [auth B] MOL2 format, chain R [auth A] MOL2 format, chain RA [auth B] MOL2 format, chain S [auth A] MOL2 format, chain SA [auth B] MOL2 format, chain T [auth A] MOL2 format, chain V [auth A] MOL2 format, chain VA [auth B] MOL2 format, chain W [auth A] MOL2 format, chain Y [auth A] MOL2 format, chain YA [auth B] MOL2 format, chain Z [auth A] mmCIF format, chain AA [auth A] mmCIF format, chain C [auth A] mmCIF format, chain CA [auth A] mmCIF format, chain D [auth A] mmCIF format, chain DA [auth A] mmCIF format, chain EA [auth A] mmCIF format, chain FA [auth A] mmCIF format, chain I [auth A] mmCIF format, chain M [auth A] mmCIF format, chain MA [auth B] mmCIF format, chain O [auth A] mmCIF format, chain OA [auth B] mmCIF format, chain Q [auth A] mmCIF format, chain QA [auth B] mmCIF format, chain R [auth A] mmCIF format, chain RA [auth B] mmCIF format, chain S [auth A] mmCIF format, chain SA [auth B] mmCIF format, chain T [auth A] mmCIF format, chain V [auth A] mmCIF format, chain VA [auth B] mmCIF format, chain W [auth A] mmCIF format, chain Y [auth A] mmCIF format, chain YA [auth B] mmCIF format, chain Z [auth A]	AA [auth A] C [auth A] CA [auth A] D [auth A] DA [auth A] AA [auth A], C [auth A], CA [auth A], D [auth A], DA [auth A], EA [auth A], FA [auth A], I [auth A], M [auth A], MA [auth B], O [auth A], OA [auth B], Q [auth A], QA [auth B], R [auth A], RA [auth B], S [auth A], SA [auth B], T [auth A], V [auth A], VA [auth B], W [auth A], Y [auth A], YA [auth B], Z [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain AA [auth A] Focus chain C [auth A] Focus chain CA [auth A] Focus chain D [auth A] Focus chain DA [auth A] Focus chain EA [auth A] Focus chain FA [auth A] Focus chain I [auth A] Focus chain M [auth A] Focus chain MA [auth B] Focus chain O [auth A] Focus chain OA [auth B] Focus chain Q [auth A] Focus chain QA [auth B] Focus chain R [auth A] Focus chain RA [auth B] Focus chain S [auth A] Focus chain SA [auth B] Focus chain T [auth A] Focus chain V [auth A] Focus chain VA [auth B] Focus chain W [auth A] Focus chain Y [auth A] Focus chain YA [auth B] Focus chain Z [auth A] Interactions & Density Focus chain AA [auth A] Focus chain C [auth A] Focus chain CA [auth A] Focus chain D [auth A] Focus chain DA [auth A] Focus chain EA [auth A] Focus chain FA [auth A] Focus chain I [auth A] Focus chain M [auth A] Focus chain MA [auth B] Focus chain O [auth A] Focus chain OA [auth B] Focus chain Q [auth A] Focus chain QA [auth B] Focus chain R [auth A] Focus chain RA [auth B] Focus chain S [auth A] Focus chain SA [auth B] Focus chain T [auth A] Focus chain V [auth A] Focus chain VA [auth B] Focus chain W [auth A] Focus chain Y [auth A] Focus chain YA [auth B] Focus chain Z [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.195
R-Value Work: 0.152
R-Value Observed: 0.154
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.67	α = 90
b = 94.73	β = 90
c = 124.87	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
PHASER	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2013-04-17

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2013-04-17
Type: Initial release
Version 1.1: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description