4FHA | pdb_00004fha

Structure of Dihydrodipicolinate Synthase from Streptococcus pneumoniae,bound to pyruvate and lysine

PDB DOI: https://doi.org/10.2210/pdb4FHA/pdb

Classification: LYASE
Organism(s): Streptococcus pneumoniae SP3-BS71
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2012-06-06 Released: 2013-09-18
Deposition Author(s): Perugini, M.A., Dogovski, C., Parker, M.W., Gorman, M.A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.88 Å
R-Value Free:
0.183 (Depositor), 0.184 (DCC)
R-Value Work:
0.159 (Depositor), 0.158 (DCC)
R-Value Observed:
0.160 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Structure, Function, Stability and Knockout Phenotype of Dihydrodipicolinate Synthase from Streptococcus pneumoniae

Perugini, M.A., Dogovski, C., Parker, M.W., Gorman, M.A., Dobson, R.C.J., Jameson, G.B., Ketaren, N.E., Praszkier, J., Bailey, M.F., Bryant, G., Yang, J., Griffin, M.D.W., Pearce, F.G., Mitsakos, V.

To be published.

Macromolecule Content

Total Structure Weight: 68.37 kDa
Atom Count: 5,087
Modeled Residue Count: 614
Deposited Residue Count: 622
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dihydrodipicolinate synthase	A, B	311	Streptococcus pneumoniae SP3-BS71	Mutation(s): 0 Gene Names: CGSSp3BS71_00085 EC: 4.2.1.52

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
LYS Query on LYS Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain E [auth B] MOL2 format, chain C [auth A] MOL2 format, chain E [auth B] mmCIF format, chain C [auth A] mmCIF format, chain E [auth B]	C [auth A], E [auth B]	LYSINE C₆ H₁₅ N₂ O₂ KDXKERNSBIXSRK-YFKPBYRVSA-O		Interactions Focus chain C [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth B]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain F [auth B] MOL2 format, chain D [auth A] MOL2 format, chain F [auth B] mmCIF format, chain D [auth A] mmCIF format, chain F [auth B]	D [auth A], F [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain F [auth B] Interactions & Density Focus chain D [auth A] Focus chain F [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
KPI Query on KPI	A, B	L-PEPTIDE LINKING	C₉ H₁₆ N₂ O₄		LYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.88 Å
R-Value Free: 0.183 (Depositor), 0.184 (DCC)
R-Value Work: 0.159 (Depositor), 0.158 (DCC)
R-Value Observed: 0.160 (Depositor)

Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.381	α = 90
b = 106.368	β = 90
c = 106.232	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
Blu-Ice	data collection
XDS	data reduction
PHASER	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2013-09-18

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2013-09-18
Type: Initial release
Version 1.1: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.2: 2023-11-29
Changes: Data collection