3PGY | pdb_00003pgy

Serine hydroxymethyltransferase from Staphylococcus aureus, S95P mutant.

PDB DOI: https://doi.org/10.2210/pdb3PGY/pdb

Classification: TRANSFERASE
Organism(s): Staphylococcus aureus subsp. aureus COL
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2010-11-02 Released: 2010-11-17
Deposition Author(s): Osipiuk, J., Makowska-Grzyska, M., Kwon, K., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.92 Å
R-Value Free:
0.208 (Depositor), 0.214 (DCC)
R-Value Work:
0.166 (Depositor), 0.173 (DCC)
R-Value Observed:
0.168 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Serine hydroxymethyltransferase from Staphylococcus aureus, S95P mutant

Osipiuk, J., Makowska-Grzyska, M., Kwon, K., Anderson, W.F., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 183.94 kDa
Atom Count: 13,941
Modeled Residue Count: 1,606
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, C, D	415	Staphylococcus aureus subsp. aureus COL	Mutation(s): 1 Gene Names: glyA EC: 2.1.2.1
UniProt
Find proteins for Q5HE87 (Staphylococcus aureus (strain COL)) Explore Q5HE87 Go to UniProtKB: Q5HE87
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5HE87
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CIT Query on CIT Download:Ideal Coordinates CCD File SDF format, chain Q [auth D] SDF format, chain P [auth D] SDF format, chain O [auth D] SDF format, chain L [auth C] SDF format, chain I [auth B] SDF format, chain H [auth B] SDF format, chain G [auth B] SDF format, chain E [auth A] MOL2 format, chain Q [auth D] MOL2 format, chain P [auth D] MOL2 format, chain O [auth D] MOL2 format, chain L [auth C] MOL2 format, chain I [auth B] MOL2 format, chain H [auth B] MOL2 format, chain G [auth B] MOL2 format, chain E [auth A] mmCIF format, chain Q [auth D] mmCIF format, chain P [auth D] mmCIF format, chain O [auth D] mmCIF format, chain L [auth C] mmCIF format, chain I [auth B] mmCIF format, chain H [auth B] mmCIF format, chain G [auth B] mmCIF format, chain E [auth A]	E [auth A] G [auth B] H [auth B] I [auth B] L [auth C] E [auth A], G [auth B], H [auth B], I [auth B], L [auth C], O [auth D], P [auth D], Q [auth D]	CITRIC ACID C₆ H₈ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B] Focus chain L [auth C] Focus chain O [auth D] Focus chain P [auth D] Focus chain Q [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B] Focus chain L [auth C] Focus chain O [auth D] Focus chain P [auth D] Focus chain Q [auth D]
GLY Query on GLY Download:Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain J [auth B] SDF format, chain F [auth A] MOL2 format, chain K [auth B] MOL2 format, chain J [auth B] MOL2 format, chain F [auth A] mmCIF format, chain K [auth B] mmCIF format, chain J [auth B] mmCIF format, chain F [auth A]	F [auth A], J [auth B], K [auth B]	GLYCINE C₂ H₅ N O₂ DHMQDGOQFOQNFH-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain J [auth B] Focus chain K [auth B] Interactions & Density Focus chain F [auth A] Focus chain J [auth B] Focus chain K [auth B]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain N [auth C] SDF format, chain M [auth C] MOL2 format, chain N [auth C] MOL2 format, chain M [auth C] mmCIF format, chain N [auth C] mmCIF format, chain M [auth C]	M [auth C], N [auth C]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain M [auth C] Focus chain N [auth C] Interactions & Density Focus chain M [auth C] Focus chain N [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.92 Å
R-Value Free: 0.208 (Depositor), 0.214 (DCC)
R-Value Work: 0.166 (Depositor), 0.173 (DCC)
R-Value Observed: 0.168 (Depositor)

Diffraction Data:

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.081	α = 90
b = 86.531	β = 90
c = 301.806	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
MOLREP	phasing
HKL-3000	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2010-11-17

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2010-11-17
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-11-08
Changes: Refinement description
Version 1.3: 2023-09-06
Changes: Data collection, Database references, Derived calculations, Refinement description