3KAO

Crystal structure of tagatose 1,6-diphosphate aldolase from Staphylococcus aureus

PDB DOI: https://doi.org/10.2210/pdb3KAO/pdb

Classification: LYASE
Organism(s): Staphylococcus aureus subsp. aureus Mu50
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2009-10-19 Released: 2009-10-27
Deposition Author(s): Chang, C., Marshall, N., Cobb, G., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.171
R-Value Work: 0.148
R-Value Observed: 0.149

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Crystal structure of tagatose 1,6-diphosphate aldolase from Staphylococcus aureus

Chang, C., Marshall, N., Cobb, G., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 37.91 kDa
Atom Count: 3,204
Modelled Residue Count: 325
Deposited Residue Count: 329
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tagatose 1,6-diphosphate aldolase	A	329	Staphylococcus aureus subsp. aureus Mu50	Mutation(s): 0 Gene Names: lacD, SAV2192, Staphylococcus aureus subsp. aureus Mu50 EC: 4.1.2.40
UniProt
Find proteins for P0A009 (Staphylococcus aureus (strain Mu50 / ATCC 700699)) Explore P0A009 Go to UniProtKB: P0A009
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0A009
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] SDF format, chain H [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain H [auth A]	B [auth A], C [auth A], H [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain B [auth A] Focus chain C [auth A] Focus chain H [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A] Focus chain H [auth A]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] MOL2 format, chain G [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A]	G [auth A], I [auth A], J [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain I [auth A] Focus chain J [auth A] Interactions & Density Focus chain G [auth A] Focus chain I [auth A] Focus chain J [auth A]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A]	D [auth A], E [auth A], F [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.171
R-Value Work: 0.148
R-Value Observed: 0.149
Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.704	α = 90
b = 84.704	β = 90
c = 202.759	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
HKL-3000	phasing
SHELXD	phasing
SHELXE	model building
MLPHARE	phasing
DM	model building
RESOLVE	model building
Coot	model building
ARP/wARP	model building
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
DM	phasing
RESOLVE	phasing