4EBK

Crystal structure of aminoglycoside 4'-O-adenylyltransferase ANT(4')-IIb, tobramycin-bound

PDB DOI: https://doi.org/10.2210/pdb4EBK/pdb

Classification: TRANSFERASE
Organism(s): Pseudomonas aeruginosa
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2012-03-23 Released: 2012-04-04
Deposition Author(s): Stogios, P.J., Dong, A., Minasov, G., Evdokimova, E., Egorova, O., Yim, V., Kudritska, M., Courvalin, P., Savchenko, A., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free: 0.221
R-Value Work: 0.172
R-Value Observed: 0.174

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Crystal structure of aminoglycoside 4'-O-adenylyltransferase ANT(4')-IIb, tobramycin-bound

Stogios, P.J., Dong, A., Minasov, G., Evdokimova, E., Egorova, O., Yim, V., Kudritska, M., Courvalin, P., Savchenko, A., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Macromolecule Content

Total Structure Weight: 64.83 kDa
Atom Count: 4,728
Modelled Residue Count: 513
Deposited Residue Count: 544
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aminoglycoside nucleotidyltransferase	A, B	272	Pseudomonas aeruginosa	Mutation(s): 0 Gene Names: ant(4')-IIb
UniProt
Find proteins for D0E7M2 (Pseudomonas aeruginosa) Explore D0E7M2 Go to UniProtKB: D0E7M2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	D0E7M2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TOY Query on TOY Download Ideal Coordinates CCD File SDF format, chain W [auth B] SDF format, chain C [auth A] MOL2 format, chain W [auth B] MOL2 format, chain C [auth A] mmCIF format, chain W [auth B] mmCIF format, chain C [auth A]	C [auth A], W [auth B]	TOBRAMYCIN C₁₈ H₃₇ N₅ O₉ NLVFBUXFDBBNBW-PBSUHMDJSA-N		Interactions Focus chain C [auth A] Focus chain W [auth B] Interactions & Density Focus chain C [auth A] Focus chain W [auth B]
IOD Query on IOD Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain I [auth A] SDF format, chain Y [auth B] SDF format, chain AA [auth B] SDF format, chain BA [auth B] SDF format, chain CA [auth B] SDF format, chain DA [auth B] SDF format, chain H [auth A] SDF format, chain J [auth A] SDF format, chain Z [auth B] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain I [auth A] MOL2 format, chain Y [auth B] MOL2 format, chain AA [auth B] MOL2 format, chain BA [auth B] MOL2 format, chain CA [auth B] MOL2 format, chain DA [auth B] MOL2 format, chain H [auth A] MOL2 format, chain J [auth A] MOL2 format, chain Z [auth B] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain I [auth A] mmCIF format, chain Y [auth B] mmCIF format, chain AA [auth B] mmCIF format, chain BA [auth B] mmCIF format, chain CA [auth B] mmCIF format, chain DA [auth B] mmCIF format, chain H [auth A] mmCIF format, chain J [auth A] mmCIF format, chain Z [auth B]	AA [auth B] BA [auth B] CA [auth B] DA [auth B] E [auth A] AA [auth B], BA [auth B], CA [auth B], DA [auth B], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], Y [auth B], Z [auth B]	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M		Interactions Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain Y [auth B] Focus chain Z [auth B]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain X [auth B] MOL2 format, chain D [auth A] MOL2 format, chain X [auth B] mmCIF format, chain D [auth A] mmCIF format, chain X [auth B]	D [auth A], X [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain X [auth B] Interactions & Density Focus chain D [auth A] Focus chain X [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain EA [auth B] SDF format, chain GA [auth B] SDF format, chain IA [auth B] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain Q [auth A] SDF format, chain R [auth A] SDF format, chain T [auth A] SDF format, chain U [auth A] SDF format, chain FA [auth B] SDF format, chain HA [auth B] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain S [auth A] SDF format, chain V [auth B] MOL2 format, chain EA [auth B] MOL2 format, chain GA [auth B] MOL2 format, chain IA [auth B] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth A] MOL2 format, chain T [auth A] MOL2 format, chain U [auth A] MOL2 format, chain FA [auth B] MOL2 format, chain HA [auth B] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain S [auth A] MOL2 format, chain V [auth B] mmCIF format, chain EA [auth B] mmCIF format, chain GA [auth B] mmCIF format, chain IA [auth B] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain R [auth A] mmCIF format, chain T [auth A] mmCIF format, chain U [auth A] mmCIF format, chain FA [auth B] mmCIF format, chain HA [auth B] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A] mmCIF format, chain P [auth A] mmCIF format, chain S [auth A] mmCIF format, chain V [auth B]	EA [auth B] FA [auth B] GA [auth B] HA [auth B] IA [auth B] EA [auth B], FA [auth B], GA [auth B], HA [auth B], IA [auth B], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A], Q [auth A], R [auth A], S [auth A], T [auth A], U [auth A], V [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain EA [auth B] Focus chain FA [auth B] Focus chain GA [auth B] Focus chain HA [auth B] Focus chain IA [auth B] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth B] Interactions & Density Focus chain EA [auth B] Focus chain FA [auth B] Focus chain GA [auth B] Focus chain HA [auth B] Focus chain IA [auth B] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth B]

Modified Residues 2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
IYR Query on IYR	A, B	L-PEPTIDE LINKING	C₉ H₁₀ I N O₃		TYR
MSE Query on MSE	A, B	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free: 0.221
R-Value Work: 0.172
R-Value Observed: 0.174
Space Group: P 2₁ 2₁ 2₁
Diffraction Data: https://doi.org/10.18430/m34ebk

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.906	α = 90
b = 84.451	β = 90
c = 98.762	γ = 90

Software Package:

Software Name	Purpose
StructureStudio	data collection
PHENIX	model building
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHENIX	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2012-04-04

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2012-04-04
Type: Initial release
Version 1.1: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.2: 2023-12-06
Changes: Data collection
Version 1.3: 2024-11-06
Changes: Structure summary