6TGH | pdb_00006tgh

SHMT from Streptococcus thermophilus Tyr55Thr variant in complex with D-Serine both as external aldimine and as non-covalent complex

PDB DOI: https://doi.org/10.2210/pdb6TGH/pdb

Classification: TRANSFERASE
Organism(s): Streptococcus thermophilus
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2019-11-15 Released: 2020-06-03
Deposition Author(s): Petrillo, G., Hernandez, K., Bujons, J., Clapes, P., Uson, I.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.12 Å
R-Value Free:
0.284 (Depositor), 0.284 (DCC)
R-Value Work:
0.237 (Depositor), 0.239 (DCC)
R-Value Observed:
0.239 (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

Structural insights into nucleophile substrate specificity in variants of N-Serine hydroxymethyltransferase from Streptococcus thermophilus

Petrillo, G., Hernandez, K., Bujons, J., Clapes, P., Uson, I.

To be published.

Macromolecule Content

Total Structure Weight: 181.22 kDa
Atom Count: 12,968
Modeled Residue Count: 1,640
Deposited Residue Count: 1,660
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine hydroxymethyltransferase	A, B [auth C], C [auth B], D	415	Streptococcus thermophilus	Mutation(s): 1 Gene Names: glyA, CDA68_00974, DID82_07515 EC: 2.1.2.1
UniProt
Find proteins for Q5M0B4 (Streptococcus thermophilus (strain CNRZ 1066)) Explore Q5M0B4 Go to UniProtKB: Q5M0B4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5M0B4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EVM (Subject of Investigation/LOI) Query on EVM Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain K [auth B] MOL2 format, chain F [auth A] MOL2 format, chain K [auth B] mmCIF format, chain F [auth A] mmCIF format, chain K [auth B]	F [auth A], K [auth B]	L-Serine, N-[[3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]-4-pyridinyl]methylene] C₁₁ H₁₄ N₂ O₈ P JFLJYKRWFQAEDK-QLKAYGNNSA-N		Interactions Focus chain F [auth A] Focus chain K [auth B] Interactions & Density Focus chain F [auth A] Focus chain K [auth B]
PLP (Subject of Investigation/LOI) Query on PLP Download:Ideal Coordinates CCD File SDF format, chain M [auth D] SDF format, chain I [auth C] MOL2 format, chain M [auth D] MOL2 format, chain I [auth C] mmCIF format, chain M [auth D] mmCIF format, chain I [auth C]	I [auth C], M [auth D]	PYRIDOXAL-5'-PHOSPHATE C₈ H₁₀ N O₆ P NGVDGCNFYWLIFO-UHFFFAOYSA-N		Interactions Focus chain I [auth C] Focus chain M [auth D] Interactions & Density Focus chain I [auth C] Focus chain M [auth D]
DSN (Subject of Investigation/LOI) Query on DSN Download:Ideal Coordinates CCD File SDF format, chain H [auth C] SDF format, chain L [auth D] MOL2 format, chain H [auth C] MOL2 format, chain L [auth D] mmCIF format, chain H [auth C] mmCIF format, chain L [auth D]	H [auth C], L [auth D]	D-SERINE C₃ H₇ N O₃ MTCFGRXMJLQNBG-UWTATZPHSA-N		Interactions Focus chain H [auth C] Focus chain L [auth D] Interactions & Density Focus chain H [auth C] Focus chain L [auth D]
NA (Subject of Investigation/LOI) Query on NA Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain J [auth B] SDF format, chain G [auth C] MOL2 format, chain E [auth A] MOL2 format, chain J [auth B] MOL2 format, chain G [auth C] mmCIF format, chain E [auth A] mmCIF format, chain J [auth B] mmCIF format, chain G [auth C]	E [auth A], G [auth C], J [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain G [auth C] Focus chain J [auth B] Interactions & Density Focus chain E [auth A] Focus chain G [auth C] Focus chain J [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.12 Å
R-Value Free: 0.284 (Depositor), 0.284 (DCC)
R-Value Work: 0.237 (Depositor), 0.239 (DCC)
R-Value Observed: 0.239 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 200.795	α = 90
b = 112.93	β = 93.1
c = 131.918	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
iMOSFLM	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2020-06-03

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2020-06-03
Type: Initial release
Version 1.1: 2024-01-24
Changes: Data collection, Database references, Derived calculations, Refinement description

6TGH | pdb_00006tgh

SHMT from Streptococcus thermophilus Tyr55Thr variant in complex with D-Serine both as external aldimine and as non-covalent complex

Literature

Structural insights into nucleophile substrate specificity in variants of N-Serine hydroxymethyltransferase from Streptococcus thermophilus

Biological Assembly 1

Biological Assembly 2

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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