3JRK | pdb_00003jrk

A putative tagatose 1,6-diphosphate aldolase from Streptococcus pyogenes

PDB DOI: https://doi.org/10.2210/pdb3JRK/pdb

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

Deposited: 2009-09-08 Released: 2009-09-22
Deposition Author(s): Fan, Y., Volkart, L., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.97 Å
R-Value Free:
0.230 (Depositor), 0.238 (DCC)
R-Value Work:
0.188 (Depositor), 0.200 (DCC)
R-Value Observed:
0.190 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

The crystal structure of a putative tagatose 1,6-diphosphate aldolase from Streptococcus pyogenes

Fan, Y., Volkart, L., Clancy, S., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 291.57 kDa
Atom Count: 21,833
Modeled Residue Count: 2,572
Deposited Residue Count: 2,576
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 2	A, B, C, D, E A, B, C, D, E, F, G, H	322	Streptococcus pyogenes serotype M1	Mutation(s): 0 Gene Names: lacD.2, lacD2, M5005_Spy1635, SPy_1919 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P63705
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain Q [auth F] SDF format, chain P [auth E] SDF format, chain O [auth D] SDF format, chain N [auth D] SDF format, chain M [auth C] SDF format, chain L [auth B] SDF format, chain K [auth B] SDF format, chain J [auth A] SDF format, chain I [auth A] MOL2 format, chain Q [auth F] MOL2 format, chain P [auth E] MOL2 format, chain O [auth D] MOL2 format, chain N [auth D] MOL2 format, chain M [auth C] MOL2 format, chain L [auth B] MOL2 format, chain K [auth B] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] mmCIF format, chain Q [auth F] mmCIF format, chain P [auth E] mmCIF format, chain O [auth D] mmCIF format, chain N [auth D] mmCIF format, chain M [auth C] mmCIF format, chain L [auth B] mmCIF format, chain K [auth B] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A]	I [auth A] J [auth A] K [auth B] L [auth B] M [auth C] I [auth A], J [auth A], K [auth B], L [auth B], M [auth C], N [auth D], O [auth D], P [auth E], Q [auth F]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth C] Focus chain N [auth D] Focus chain O [auth D] Focus chain P [auth E] Focus chain Q [auth F] Interactions & Density Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth C] Focus chain N [auth D] Focus chain O [auth D] Focus chain P [auth E] Focus chain Q [auth F]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.97 Å
R-Value Free: 0.230 (Depositor), 0.238 (DCC)
R-Value Work: 0.188 (Depositor), 0.200 (DCC)
R-Value Observed: 0.190 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.517	α = 90
b = 169.729	β = 94.09
c = 167.054	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
SHELXD	phasing
MLPHARE	phasing
ARP	model building
WARP	model building
HKL-3000	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2009-09-22

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2009-09-22
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Refinement description, Version format compliance
Version 1.2: 2017-11-01
Changes: Refinement description
Version 1.3: 2024-10-16
Changes: Data collection, Database references, Derived calculations, Structure summary

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Deposit Data

Help and Resources

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A putative tagatose 1,6-diphosphate aldolase from Streptococcus pyogenes

The crystal structure of a putative tagatose 1,6-diphosphate aldolase from Streptococcus pyogenes

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)

3JRK | pdb_00003jrk