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)

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)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

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.

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

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| 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A0H2ZP94
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NDP Query on NDP Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B]	C [auth A], D [auth B]	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₃₀ N₇ O₁₇ P₃ ACFIXJIJDZMPPO-NNYOXOHSSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [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: 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

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2014-11-05

Deposition Author(s):

Northeast Structural Genomics Consortium (NESG)

Revision History (Full details and data files)

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