4RL6 | pdb_00004rl6

Crystal Structure of the Q04L03_STRP2 protein from Streptococcus pneumoniae. Northeast Structural Genomics Consortium Target SpR105

• PDB DOI: https://doi.org/10.2210/pdb4RL6/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Streptococcus pneumoniae D39
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2014-10-15 Released: 2014-11-05 
• Deposition Author(s): Vorobiev, S., Neely, H.M., Odukwe, C.D., Seetharaman, J., Mao, L., Xiao, R., Kohan, E., Wang, D., Everett, J.K., Acton, T.B., Montelione, G.T., Tong, L., Hunt, J.F., Northeast Structural Genomics Consortium (NESG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.79 Å
• R-Value Free: 
  0.204 (Depositor), 0.225 (DCC) 
• R-Value Work: 
  0.179 (Depositor), 0.202 (DCC) 
• R-Value Observed: 
  0.180 (Depositor) 

Literature

Crystal Structure of the Q04L03_STRP2 protein from Streptococcus pneumoniae.

Vorobiev, S., Neely, H.M., Odukwe, C.D., Seetharaman, J., Mao, L., Xiao, R., Kohan, E., Wang, D., Everett, J.K., Acton, T.B., Montelione, G.T., Tong, L., Hunt, J.F.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 98.59 kDa 
• Atom Count: 6,511 
• Modeled Residue Count: 810 
• Deposited Residue Count: 854 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Saccharopine dehydrogenase	A, B	427	Streptococcus pneumoniae D39	Mutation(s): 0  Gene Names: lys1, SPD_0812 EC: 1.5.1.7
UniProt
Find proteins for A0A0H2ZP94 (Streptococcus pneumoniae serotype 2 (strain D39 / NCTC 7466)) Explore A0A0H2ZP94  Go to UniProtKB:  A0A0H2ZP94

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NDP	C [auth A], D [auth B]	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H30 N7 O17 P3 ACFIXJIJDZMPPO-NNYOXOHSSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.79 Å
• R-Value Free:  0.204 (Depositor), 0.225 (DCC) 
• R-Value Work:  0.179 (Depositor), 0.202 (DCC) 
• R-Value Observed: 0.180 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.705	α = 90
b = 120.845	β = 90
c = 154.042	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
AutoSol	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-11-05 
Deposition Author(s): Vorobiev, S., Neely, H.M., Odukwe, C.D., Seetharaman, J., Mao, L., Xiao, R., Kohan, E., Wang, D., Everett, J.K., Acton, T.B., Montelione, G.T., Tong, L., Hunt, J.F., Northeast Structural Genomics Consortium (NESG)

Revision History  

• Version 1.0: 2014-11-05
  Type: Initial release
  
• Version 1.1: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary