3E58 | pdb_00003e58

Crystal structure of putative beta-phosphoglucomutase from Streptococcus thermophilus

PDB DOI: https://doi.org/10.2210/pdb3E58/pdb

Classification: ISOMERASE
Organism(s): Streptococcus thermophilus LMG 18311
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2008-08-13 Released: 2008-08-26
Deposition Author(s): Chang, C., Tesar, C., Souvong, K., Cobb, G., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.86 Å
R-Value Free:
0.199 (Depositor), 0.199 (DCC)
R-Value Work:
0.170 (Depositor), 0.169 (DCC)
R-Value Observed:
0.171 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 3E58

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

Literature

Crystal structure of putative beta-phosphoglucomutase from Streptococcus thermophilus

Chang, C., Tesar, C., Souvong, K., Cobb, G., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 49.14 kDa
Atom Count: 3,822
Modeled Residue Count: 419
Deposited Residue Count: 428
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
putative Beta-phosphoglucomutase	A, B	214	Streptococcus thermophilus LMG 18311	Mutation(s): 3 Gene Names: stu0379
UniProt
Find proteins for Q5M5S4 (Streptococcus thermophilus (strain ATCC BAA-250 / LMG 18311)) Explore Q5M5S4 Go to UniProtKB: Q5M5S4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5M5S4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain F [auth B] SDF format, chain D [auth A] MOL2 format, chain C [auth A] MOL2 format, chain F [auth B] MOL2 format, chain D [auth A] mmCIF format, chain C [auth A] mmCIF format, chain F [auth B] mmCIF format, chain D [auth A]	C [auth A], D [auth A], F [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain F [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain F [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain H [auth B] SDF format, chain E [auth A] MOL2 format, chain G [auth B] MOL2 format, chain H [auth B] MOL2 format, chain E [auth A] mmCIF format, chain G [auth B] mmCIF format, chain H [auth B] mmCIF format, chain E [auth A]	E [auth A], G [auth B], H [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain H [auth B] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain H [auth B]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.86 Å
R-Value Free: 0.199 (Depositor), 0.199 (DCC)
R-Value Work: 0.170 (Depositor), 0.169 (DCC)
R-Value Observed: 0.171 (Depositor)

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.784	α = 90
b = 88.784	β = 90
c = 118.846	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2008-08-26

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2008-08-26
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.2: 2021-10-20
Changes: Database references, Derived calculations
Version 1.3: 2024-10-30
Changes: Data collection, Structure summary

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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.