5F4W | pdb_00005f4w

Tagatose-1,6-bisphosphate aldolase from Streptococcus pyogenes in complex with TBP

PDB DOI: https://doi.org/10.2210/pdb5F4W/pdb

Classification: LYASE
Organism(s): Streptococcus pyogenes serotype M1
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2015-12-03 Released: 2017-02-01
Deposition Author(s): LowKam, C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.66 Å
R-Value Free:
0.206 (Depositor), 0.210 (DCC)
R-Value Work:
0.173 (Depositor), 0.185 (DCC)
R-Value Observed:
0.174 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

NON-STEREOSPECIFIC SUBSTRATE CLEAVAGE BY TAGATOSE-BISPHOSPHATE CLASS I ALDOLASE

LowKam, C., Liotard, B., Sygusch, J.

To be published.

Macromolecule Content

Total Structure Weight: 147.29 kDa
Atom Count: 11,921
Modeled Residue Count: 1,302
Deposited Residue Count: 1,308
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tagatose 1,6-diphosphate aldolase 2	A, B, C, D	327	Streptococcus pyogenes serotype M1	Mutation(s): 0 Gene Names: lacD2, lacD.2, SPy_1919, M5005_Spy1635 EC: 4.1.2.40
UniProt
Find proteins for P63705 (Streptococcus pyogenes serotype M1) Explore P63705 Go to UniProtKB: P63705
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P63705
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
P6T Query on P6T Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	1,6-di-O-phosphono-D-tagatose C₆ H₁₄ O₁₂ P₂ XPYBSIWDXQFNMH-PQLUHFTBSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
13P Query on 13P Download:Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	1,3-DIHYDROXYACETONEPHOSPHATE C₃ H₇ O₆ P GNGACRATGGDKBX-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain K [auth C] SDF format, chain M [auth D] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain K [auth C] MOL2 format, chain M [auth D] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain K [auth C] mmCIF format, chain M [auth D]	H [auth A], I [auth A], K [auth C], M [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain K [auth C] Focus chain M [auth D] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain K [auth C] Focus chain M [auth D]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain J [auth B] SDF format, chain L [auth C] SDF format, chain N [auth D] MOL2 format, chain F [auth A] MOL2 format, chain J [auth B] MOL2 format, chain L [auth C] MOL2 format, chain N [auth D] mmCIF format, chain F [auth A] mmCIF format, chain J [auth B] mmCIF format, chain L [auth C] mmCIF format, chain N [auth D]	F [auth A], J [auth B], L [auth C], N [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain F [auth A] Focus chain J [auth B] Focus chain L [auth C] Focus chain N [auth D] Interactions & Density Focus chain F [auth A] Focus chain J [auth B] Focus chain L [auth C] Focus chain N [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.66 Å
R-Value Free: 0.206 (Depositor), 0.210 (DCC)
R-Value Work: 0.173 (Depositor), 0.185 (DCC)
R-Value Observed: 0.174 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.955	α = 90
b = 107.373	β = 90
c = 237.73	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2017-02-01

Deposition Author(s):

LowKam, C.

Revision History (Full details and data files)

Version 1.0: 2017-02-01
Type: Initial release
Version 1.1: 2023-09-27
Changes: Data collection, Database references, Derived calculations, Refinement description

5F4W | pdb_00005f4w

Tagatose-1,6-bisphosphate aldolase from Streptococcus pyogenes in complex with TBP

Literature

NON-STEREOSPECIFIC SUBSTRATE CLEAVAGE BY TAGATOSE-BISPHOSPHATE CLASS I ALDOLASE

Biological Assembly 1

Biological Assembly 2

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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