3HL3 | pdb_00003hl3

2.76 Angstrom Crystal Structure of a Putative Glucose-1-Phosphate Thymidylyltransferase from Bacillus anthracis in Complex with a Sucrose.

PDB DOI: https://doi.org/10.2210/pdb3HL3/pdb

Classification: TRANSFERASE
Organism(s): Bacillus anthracis
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2009-05-26 Released: 2009-06-09
Deposition Author(s): Minasov, G., Shuvalova, L., Halavaty, A., Dubrovska, I., Winsor, J., Papazisi, L., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.76 Å
R-Value Free:
0.206 (Depositor), 0.219 (DCC)
R-Value Work:
0.173 (Depositor), 0.182 (DCC)
R-Value Observed:
0.175 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 2.1 of the entry. See complete history.

Literature

2.76 Angstrom Crystal Structure of a Putative Glucose-1-Phosphate Thymidylyltransferase from Bacillus anthracis in Complex with a Sucrose.

Minasov, G., Shuvalova, L., Halavaty, A., Dubrovska, I., Winsor, J., Papazisi, L., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Macromolecule Content

Total Structure Weight: 30.62 kDa
Atom Count: 2,053
Modeled Residue Count: 246
Deposited Residue Count: 269
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glucose-1-phosphate thymidylyltransferase	A	269	Bacillus anthracis	Mutation(s): 0 Gene Names: BA1228, BAS1135, BA_1228, GBAA1228, GBAA_1228 EC: 2.7.7.24
UniProt
Find proteins for A0A6L8PCC3 (Bacillus anthracis) Explore A0A6L8PCC3 Go to UniProtKB: A0A6L8PCC3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A6L8PCC3
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose	B	2		N/A	Interactions Focus chain B Interactions & Density Focus chain B
Glycosylation Resources
GlyTouCan: G05551OP GlyCosmos: G05551OP

Biologically Interesting Molecules (External Reference)

1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900003 Query on PRD_900003	B	sucrose	Oligosaccharide / Nutrient		Interactions Focus chain B Interactions & Density Focus chain B

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.76 Å
R-Value Free: 0.206 (Depositor), 0.219 (DCC)
R-Value Work: 0.173 (Depositor), 0.182 (DCC)
R-Value Observed: 0.175 (Depositor)

Diffraction Data:

Space Group: P 6 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 134.425	α = 90
b = 134.425	β = 90
c = 85.274	γ = 120

Software Package:

Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2009-06-09

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2009-06-09
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.2: 2017-11-01
Changes: Refinement description
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary
Version 2.1: 2023-09-06
Changes: Data collection, Database references, Refinement description, Structure summary