7JZC | pdb_00007jzc

Dihydrodipicolinate synthase S48W mutant with lysine in the allosteric site, and pyruvate in the catalytic site

• PDB DOI: https://doi.org/10.2210/pdb7JZC/pdb

• Classification: LYASE
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2020-09-02 Released: 2021-09-22 
• Deposition Author(s): Board, A.J., Dobson, R.C.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.07 Å
• R-Value Free: 
  0.209 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.172 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.174 (Depositor) 

Starting Model: experimental

Literature

Mapping the uncharted water channel of DHDPS

Board, A.J., Dobson, R.C.J.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: mass spectrometry

Macromolecule Content 

• Total Structure Weight: 63.02 kDa 
• Atom Count: 4,616 
• Modeled Residue Count: 584 
• Deposited Residue Count: 584 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
4-hydroxy-tetrahydrodipicolinate synthase	A, B	292	Escherichia coli	Mutation(s): 1  Gene Names:  dapA, A6V01_06140, A8C65_04230, ACU57_04510, AM464_03890, AML07_10805, APZ14_05880, AUQ13_12840, AUS26_08890, AW106_01920, BANRA_01022, BANRA_04600, BMA87_04055, BUE81_00170, BvCms2454_00575, BvCmsKSP026_00126, BvCmsSINP011_00590, BW690_08395, BZL31_19835, C5N07_10510, C9306_12515, C9Z39_22035, C9Z89_01665, CG692_24655, CI693_08805, CIG45_08195, COD30_00655, D2185_06295, D3821_11825, D4638_04510, D4718_03620, D5H35_00590, D6004_00600, D9610_05430, D9D44_02140, D9I18_08280, D9J52_02245, D9S45_15015, DAH30_02905, DAH32_09095, DIV22_31750, DJ503_11770, DL326_03925, DL530_01595, DL800_18800, DLW60_01905, DMY83_09445, DNW42_05980, DQF71_00895, DS143_00895, DT034_06790, DTL43_01515, DVB38_05855, E2119_05140, E2134_09475, E2135_00560, E2855_03226, E2863_03133, E5P22_02280, E5S42_08940, EAI42_12285, EAI52_02575, EAM59_02025, EAN70_00660, EBM08_03910, EC3234A_44c00840, EC95NR1_01697, ECTO6_01408, ED307_17520, ED600_00625, EEP23_23010, EG599_00615, EH412_01980, EHJ36_02055, EI028_07440, EIZ93_19645, EKI52_22350, EL75_1173, EL79_1184, EL80_1189, EPT01_15155, ERS150876_00779, EYD11_06580, F1E19_01790, F7F00_00605, F7F23_09350, F7F26_01975, FQR64_06700, GHR40_11105, GKF74_08320, GKF86_10525, GKF89_17025, GP666_02180, GP935_11985, GQA06_13610, GQE30_13075, GQE34_24640, GQE51_05930, GRW80_06100, NCTC10963_01382, NCTC11126_06127, NCTC11341_00817, NCTC13216_00544, NCTC8960_04113, NCTC9045_01668, NCTC9062_01738, NCTC9962_06536, RK56_024520, SAMEA3472047_03904, SAMEA3484427_00338, SAMEA3484429_00447, SAMEA3752559_00798, SAMEA3753300_00971, SK85_02727 EC: 4.3.3.7
UniProt
Find proteins for P0A6L2 (Escherichia coli (strain K12)) Explore P0A6L2  Go to UniProtKB:  P0A6L2

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
K	C [auth A], D [auth B]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.07 Å
• R-Value Free:  0.209 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.172 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.174 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 121.129	α = 90
b = 121.129	β = 90
c = 111.271	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
Coot	model building
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-09-22 
Deposition Author(s): Board, A.J., Dobson, R.C.J.

Revision History  

• Version 1.0: 2021-09-22
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Refinement description
• Version 1.2: 2023-11-29
  Changes: Data collection