8G22

Crystal Structure of the dTDP-4-dehydrorhamnose Reductase from Streptococcus pneumoniae.

• PDB DOI: https://doi.org/10.2210/pdb8G22/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Streptococcus pneumoniae Taiwan19F-14
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2023-02-03 Released: 2023-02-22 
• Deposition Author(s): Minasov, G., Shuvalova, L., Brunzelle, J.S., Kiryukhina, O., Satchell, K.J.F., Center for Structural Biology of Infectious Diseases (CSBID), Center for Structural Genomics of Infectious Diseases (CSGID)
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.00 Å
• R-Value Free: 0.143 
• R-Value Work: 0.125 
• R-Value Observed: 0.126 

Starting Model: experimental

Literature

Crystal Structure of the dTDP-4-dehydrorhamnose Reductase from Streptococcus pneumoniae.

Minasov, G., Shuvalova, L., Brunzelle, J.S., Kiryukhina, O., Satchell, K.J.F., Center for Structural Biology of Infectious Diseases (CSBID), Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 32.61 kDa 
• Atom Count: 3,320 
• Modelled Residue Count: 286 
• Deposited Residue Count: 286 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
dTDP-4-dehydrorhamnose reductase	A	286	Streptococcus pneumoniae Taiwan19F-14	Mutation(s): 0  Gene Names: rmlD EC: 1.1.1.133
UniProt
Find proteins for O54665 (Streptococcus pneumoniae) Explore O54665  Go to UniProtKB:  O54665

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.00 Å
• R-Value Free: 0.143 
• R-Value Work: 0.125 
• R-Value Observed: 0.126 
• Space Group: H 3
• Diffraction Data: https://doi.org/10.18430/m38g22

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 120.178	α = 90
b = 120.178	β = 90
c = 48.075	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-02-22 
Deposition Author(s): Minasov, G., Shuvalova, L., Brunzelle, J.S., Kiryukhina, O., Satchell, K.J.F., Center for Structural Biology of Infectious Diseases (CSBID), Center for Structural Genomics of Infectious Diseases (CSGID)

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	75N93022C00035
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	HHSN272201700060C

Revision History  

• Version 1.0: 2023-02-22
  Type: Initial release
  
• Version 1.1: 2024-05-22
  Changes: Data collection