4PDY | pdb_00004pdy

Crystal structure of aminoglycoside phosphotransferase from Alicyclobacillus acidocaldarius subsp. acidocaldarius DSM 446

PDB DOI: https://doi.org/10.2210/pdb4PDY/pdb

Classification: TRANSFERASE
Organism(s): Alicyclobacillus acidocaldarius subsp. acidocaldarius DSM 446
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2014-04-22 Released: 2014-05-07
Deposition Author(s): Chang, C., Li, H., Bearden, J., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.35 Å
R-Value Free:
0.174 (Depositor), 0.172 (DCC)
R-Value Work:
0.131 (Depositor), 0.131 (DCC)
R-Value Observed:
0.133 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

Crystal structure of aminoglycoside phosphotransferase from Alicyclobacillus acidocaldarius subsp. acidocaldarius DSM 446

Chang, C., Li, H., Bearden, J., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

To be published.

Macromolecule Content

Total Structure Weight: 41.27 kDa
Atom Count: 3,265
Modeled Residue Count: 332
Deposited Residue Count: 351
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aminoglycoside phosphotransferase	A	351	Alicyclobacillus acidocaldarius subsp. acidocaldarius DSM 446	Mutation(s): 0 Gene Names: Aaci_0449
UniProt
Find proteins for C8WS74 (Alicyclobacillus acidocaldarius subsp. acidocaldarius (strain ATCC 27009 / DSM 446 / BCRC 14685 / JCM 5260 / KCTC 1825 / NBRC 15652 / NCIMB 11725 / NRRL B-14509 / 104-IA)) Explore C8WS74 Go to UniProtKB: C8WS74
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	C8WS74
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HIS Query on HIS Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	HISTIDINE C₆ H₁₀ N₃ O₂ HNDVDQJCIGZPNO-YFKPBYRVSA-O		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
SCN Query on SCN Download:Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A] D [auth A] E [auth A] F [auth A] G [auth A] C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A]	THIOCYANATE ION C N S ZMZDMBWJUHKJPS-UHFFFAOYSA-M		Interactions Focus chain C [auth A] Focus chain D [auth A] 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] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] 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]

Modified Residues 1 Unique
ID	Chains	Modified Residue	Modification Type	Formula	2D Diagram
MSE Query on MSE	A	MET	Selenomethionine	C₅ H₁₁ N O₂ Se

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.35 Å
R-Value Free: 0.174 (Depositor), 0.172 (DCC)
R-Value Work: 0.131 (Depositor), 0.131 (DCC)
R-Value Observed: 0.133 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.522	α = 90
b = 51.955	β = 90
c = 145.851	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2014-05-07

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2014-05-07
Type: Initial release
Version 1.1: 2015-02-04
Changes: Derived calculations
Version 1.2: 2017-11-22
Changes: Database references, Derived calculations, Other, Refinement description, Source and taxonomy, Structure summary
Version 1.3: 2023-12-27
Changes: Data collection, Database references, Refinement description
Version 1.4: 2024-11-20
Changes: Structure summary