5HJL | pdb_00005hjl

Crystal structure of class I tagatose 1,6-bisphosphate aldolase LacD from Streptococcus porcinus

PDB DOI: https://doi.org/10.2210/pdb5HJL/pdb

Classification: LYASE
Organism(s): Streptococcus porcinus str. Jelinkova 176
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2016-01-13 Released: 2016-12-07
Deposition Author(s): Freichels, R., Kerff, F., Herman, R., Charlier, P., Galleni, M.
Funding Organization(s): National Fund for Scientific Research, FRS-FNRS

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free:
0.229 (Depositor), 0.234 (DCC)
R-Value Work:
0.174 (Depositor), 0.178 (DCC)

Starting Model: experimental
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This is version 1.1 of the entry. See complete history.

Literature

Structure and Characterization of a new class I Tagatose-1,6-bipshosphate aldolase from Streptococcus porcinus : switch in specificity directed by an Arginine

Freichels, R., Delmarcelle, M., Van der Heiden, E., Herman, R., Colarusso, A., Wathelet, B., Kerff, F., Galleni, M.

To be published.

Macromolecule Content

Total Structure Weight: 74.5 kDa
Atom Count: 5,054
Modeled Residue Count: 644
Deposited Residue Count: 666
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tagatose 1,6-diphosphate aldolase	A, B	333	Streptococcus porcinus str. Jelinkova 176	Mutation(s): 0 Gene Names: lacD, STRPO_0644 EC: 4.1.2.40

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain G [auth B] SDF format, chain F [auth B] SDF format, chain E [auth A] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain H [auth B] MOL2 format, chain G [auth B] MOL2 format, chain F [auth B] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain H [auth B] mmCIF format, chain G [auth B] mmCIF format, chain F [auth B] 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 B] G [auth B] C [auth A], D [auth A], E [auth A], F [auth B], G [auth B], H [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free: 0.229 (Depositor), 0.234 (DCC)
R-Value Work: 0.174 (Depositor), 0.178 (DCC)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 100.66	α = 90
b = 93.75	β = 120.58
c = 88.11	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
Coot	model building
XDS	data reduction

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2016-12-07

Deposition Author(s):

Funding Organization	Location	Grant Number
National Fund for Scientific Research	Belgium	--
FRS-FNRS	Belgium	IISN 4.4503

Revision History (Full details and data files)

Version 1.0: 2016-12-07
Type: Initial release
Version 1.1: 2024-01-10
Changes: Data collection, Database references, Refinement description

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.