3R5X

Crystal Structure of D-alanine--D-Alanine Ligase from Bacillus anthracis complexed with ATP

PDB DOI: https://doi.org/10.2210/pdb3R5X/pdb

Classification: LIGASE
Organism(s): Bacillus anthracis
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2011-03-20 Released: 2011-04-06
Deposition Author(s): Kim, Y., Mulligan, R., Hasseman, J., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.221
R-Value Work: 0.177
R-Value Observed: 0.180

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 D-alanine--D-Alanine Ligase from Bacillus anthracis complexed with ATP

Kim, Y., Hasseman, J., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Macromolecule Content

Total Structure Weight: 141.73 kDa
Atom Count: 10,379
Modelled Residue Count: 1,183
Deposited Residue Count: 1,228
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
D-alanine--D-alanine ligase	A, B, C, D	307	Bacillus anthracis	Mutation(s): 0 Gene Names: BAS2435, BA_2610, ddl, ddlB, GBAA_2610 EC: 6.3.2.4
UniProt
Find proteins for Q81Q29 (Bacillus anthracis) Explore Q81Q29 Go to UniProtKB: Q81Q29
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q81Q29
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ATP Query on ATP Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain H [auth B] SDF format, chain K [auth C] SDF format, chain O [auth D] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B] MOL2 format, chain K [auth C] MOL2 format, chain O [auth D] mmCIF format, chain F [auth A] mmCIF format, chain H [auth B] mmCIF format, chain K [auth C] mmCIF format, chain O [auth D]	F [auth A], H [auth B], K [auth C], O [auth D]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain F [auth A] Focus chain H [auth B] Focus chain K [auth C] Focus chain O [auth D] Interactions & Density Focus chain F [auth A] Focus chain H [auth B] Focus chain K [auth C] Focus chain O [auth D]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain Q [auth D] MOL2 format, chain Q [auth D] mmCIF format, chain Q [auth D]	Q [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain Q [auth D] Interactions & Density Focus chain Q [auth D]
ACY Query on ACY Download Ideal Coordinates CCD File SDF format, chain R [auth D] MOL2 format, chain R [auth D] mmCIF format, chain R [auth D]	R [auth D]	ACETIC ACID C₂ H₄ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-N		Interactions Focus chain R [auth D] Interactions & Density Focus chain R [auth D]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth B] SDF format, chain I [auth B] SDF format, chain J [auth C] SDF format, chain L [auth C] SDF format, chain N [auth D] SDF format, chain P [auth D] MOL2 format, chain E [auth A] MOL2 format, chain G [auth B] MOL2 format, chain I [auth B] MOL2 format, chain J [auth C] MOL2 format, chain L [auth C] MOL2 format, chain N [auth D] MOL2 format, chain P [auth D] mmCIF format, chain E [auth A] mmCIF format, chain G [auth B] mmCIF format, chain I [auth B] mmCIF format, chain J [auth C] mmCIF format, chain L [auth C] mmCIF format, chain N [auth D] mmCIF format, chain P [auth D]	E [auth A] G [auth B] I [auth B] J [auth C] L [auth C] E [auth A], G [auth B], I [auth B], J [auth C], L [auth C], N [auth D], P [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth B] Focus chain J [auth C] Focus chain L [auth C] Focus chain N [auth D] Focus chain P [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth B] Focus chain J [auth C] Focus chain L [auth C] Focus chain N [auth D] Focus chain P [auth D]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain M [auth C] MOL2 format, chain M [auth C] mmCIF format, chain M [auth C]	M [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain M [auth C] Interactions & Density Focus chain M [auth C]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B, C, D	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: 0.221
R-Value Work: 0.177
R-Value Observed: 0.180
Space Group: P 1
Diffraction Data: https://doi.org/10.18430/m33r5x

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.336	α = 73.36
b = 68.992	β = 84.96
c = 92.387	γ = 75.46

Software Package:

Software Name	Purpose
SBC-Collect	data collection
HKL-3000	data collection
HKL-3000	phasing
SHELXS	phasing
MLPHARE	phasing
BUCCANEER	model building
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
BUCCANEER	phasing