3SLB | pdb_00003slb

Crystal structure of BA2930 in complex with AcCoA and cytosine

PDB DOI: https://doi.org/10.2210/pdb3SLB/pdb

Classification: TRANSFERASE
Organism(s): Bacillus anthracis
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2011-06-24 Released: 2011-07-06
Deposition Author(s): Klimecka, M.M., Chruszcz, M., Porebski, P.J., Cymborowski, M., Anderson, W., Minor, W., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.230 (Depositor), 0.240 (DCC)
R-Value Work:
0.174 (Depositor), 0.190 (DCC)
R-Value Observed:
0.177 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.5 of the entry. See complete history.

Literature

Crystal structure of BA2930 in complex with AcCoA and cytosine

Klimecka, M.M., Chruszcz, M., Porebski, P.J., Cymborowski, M., Anderson, W., Minor, W.

To be published.

Macromolecule Content

Total Structure Weight: 125.66 kDa
Atom Count: 9,230
Modeled Residue Count: 1,062
Deposited Residue Count: 1,072
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 N3-acetyltransferase	A, B [auth D], C, D [auth B]	268	Bacillus anthracis	Mutation(s): 1 Gene Names: aacC7, BA_2930, GBAA2930, GBAA_2930 EC: 2.3.1.81 (PDB Primary Data), 2.3.1 (UniProt)
UniProt
Find proteins for A0A3P1UCA6 (Bacillus anthracis) Explore A0A3P1UCA6 Go to UniProtKB: A0A3P1UCA6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A3P1UCA6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ACO Query on ACO Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth D] SDF format, chain M [auth C] SDF format, chain P [auth B] MOL2 format, chain E [auth A] MOL2 format, chain H [auth D] MOL2 format, chain M [auth C] MOL2 format, chain P [auth B] mmCIF format, chain E [auth A] mmCIF format, chain H [auth D] mmCIF format, chain M [auth C] mmCIF format, chain P [auth B]	E [auth A], H [auth D], M [auth C], P [auth B]	*ACETYL COENZYME A** C₂₃ H₃₈ N₇ O₁₇ P₃ S ZSLZBFCDCINBPY-ZSJPKINUSA-N		Interactions Focus chain E [auth A] Focus chain H [auth D] Focus chain M [auth C] Focus chain P [auth B] Interactions & Density Focus chain E [auth A] Focus chain H [auth D] Focus chain M [auth C] Focus chain P [auth B]
CPS Query on CPS Download Ideal Coordinates CCD File SDF format, chain O [auth C] MOL2 format, chain O [auth C] mmCIF format, chain O [auth C]	O [auth C]	3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE C₃₂ H₅₈ N₂ O₇ S UMCMPZBLKLEWAF-BCTGSCMUSA-N		Interactions Focus chain O [auth C] Interactions & Density Focus chain O [auth C]
EPE Query on EPE Download Ideal Coordinates CCD File SDF format, chain K [auth D] MOL2 format, chain K [auth D] mmCIF format, chain K [auth D]	K [auth D]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C₈ H₁₈ N₂ O₄ S JKMHFZQWWAIEOD-UHFFFAOYSA-N		Interactions Focus chain K [auth D] Interactions & Density Focus chain K [auth D]
CYT Query on CYT Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain I [auth D] SDF format, chain N [auth C] SDF format, chain Q [auth B] MOL2 format, chain F [auth A] MOL2 format, chain I [auth D] MOL2 format, chain N [auth C] MOL2 format, chain Q [auth B] mmCIF format, chain F [auth A] mmCIF format, chain I [auth D] mmCIF format, chain N [auth C] mmCIF format, chain Q [auth B]	F [auth A], I [auth D], N [auth C], Q [auth B]	6-AMINOPYRIMIDIN-2(1H)-ONE C₄ H₅ N₃ O OPTASPLRGRRNAP-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain I [auth D] Focus chain N [auth C] Focus chain Q [auth B] Interactions & Density Focus chain F [auth A] Focus chain I [auth D] Focus chain N [auth C] Focus chain Q [auth B]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain J [auth D] SDF format, chain L [auth D] SDF format, chain R [auth B] MOL2 format, chain G [auth A] MOL2 format, chain J [auth D] MOL2 format, chain L [auth D] MOL2 format, chain R [auth B] mmCIF format, chain G [auth A] mmCIF format, chain J [auth D] mmCIF format, chain L [auth D] mmCIF format, chain R [auth B]	G [auth A], J [auth D], L [auth D], R [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain J [auth D] Focus chain L [auth D] Focus chain R [auth B] Interactions & Density Focus chain G [auth A] Focus chain J [auth D] Focus chain L [auth D] Focus chain R [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B [auth D], C, D [auth B]	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.230 (Depositor), 0.240 (DCC)
R-Value Work: 0.174 (Depositor), 0.190 (DCC)
R-Value Observed: 0.177 (Depositor)

Diffraction Data: https://doi.org/10.18430/M33SLB

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.473	α = 90
b = 110.63	β = 112.24
c = 73.78	γ = 90

Software Package:

Software Name	Purpose
MD2	data collection
HKL-3000	phasing
MOLREP	phasing
REFMAC	refinement
Coot	model building
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2011-07-06

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2011-07-06
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2022-04-13
Changes: Database references, Derived calculations, Structure summary
Version 1.3: 2023-09-13
Changes: Data collection, Refinement description
Version 1.4: 2023-12-06
Changes: Data collection
Version 1.5: 2024-11-06
Changes: Structure summary