8G22 | pdb_00008g22

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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.00 Å
R-Value Free:
0.143 (Depositor), 0.150 (DCC)
R-Value Work:
0.125 (Depositor), 0.133 (DCC)
R-Value Observed:
0.126 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.1 of the entry. See complete history.

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.

Macromolecule Content

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

Macromolecules

Find similar proteins by:

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O54665
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.00 Å
R-Value Free: 0.143 (Depositor), 0.150 (DCC)
R-Value Work: 0.125 (Depositor), 0.133 (DCC)
R-Value Observed: 0.126 (Depositor)

Diffraction Data:

Space Group: H 3

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

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Entry History

& Funding Information

Deposition Data

Released Date: 2023-02-22

Deposition Author(s):

Brunzelle, J.S.

Satchell, K.J.F.

Center for Structural Biology of Infectious Diseases (CSBID)

Center for Structural Genomics of Infectious Diseases (CSGID)

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 (Full details and data files)

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

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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.