3L21

The crystal structure of a dimeric mutant of dihydrodipicolinate synthase (DAPA, RV2753C) from Mycobacterium Tuberculosis - DHDPS-A204R


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.179 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

A dimeric mutant of DHDPS from Mycobacterium tuberculosis

Evans, G.L.Schuldt, L.Griffin, M.D.Perugini, M.A.Jamerson, G.B.Devenish, S.R.Weiss, M.S.Gerrard, J.A.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Dihydrodipicolinate synthase
A, B, C, D, E, F
A, B, C, D, E, F
304Mycobacterium tuberculosisMutation(s): 1 
Gene Names: dapAMT2823MTV002.18cRv2753c
EC: 4.2.1.52 (PDB Primary Data), 4.3.3.7 (UniProt)
UniProt
Find proteins for P9WP25 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WP25 
Go to UniProtKB:  P9WP25
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WP25
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
FA [auth C],
FB [auth F],
G [auth A],
GA [auth C],
GB [auth F],
FA [auth C],
FB [auth F],
G [auth A],
GA [auth C],
GB [auth F],
H [auth A],
HA [auth C],
I [auth A],
OA [auth D],
PA [auth D],
R [auth B],
S [auth B],
T [auth B],
WA [auth E],
XA [auth E],
YA [auth E]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
CA [auth B],
CB [auth E],
DB [auth E],
EA [auth B],
IA [auth C],
CA [auth B],
CB [auth E],
DB [auth E],
EA [auth B],
IA [auth C],
IB [auth F],
J [auth A],
JA [auth C],
JB [auth F],
K [auth A],
KA [auth C],
KB [auth F],
LA [auth C],
LB [auth F],
NA [auth C],
O [auth A],
P [auth A],
QA [auth D],
RA [auth D],
SA [auth D],
TA [auth D],
U [auth B],
V [auth B],
W [auth B],
Z [auth B],
ZA [auth E]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
PYR
Query on PYR

Download Ideal Coordinates CCD File 
DA [auth B]PYRUVIC ACID
C3 H4 O3
LCTONWCANYUPML-UHFFFAOYSA-N
 Ligand Interaction
BME
Query on BME

Download Ideal Coordinates CCD File 
Q [auth A]BETA-MERCAPTOETHANOL
C2 H6 O S
DGVVWUTYPXICAM-UHFFFAOYSA-N
 Ligand Interaction
ACT
Query on ACT

Download Ideal Coordinates CCD File 
AA [auth B],
AB [auth E],
BA [auth B],
BB [auth E],
HB [auth F],
AA [auth B],
AB [auth E],
BA [auth B],
BB [auth E],
HB [auth F],
L [auth A],
M [auth A],
MA [auth C],
N [auth A],
X [auth B],
Y [auth B]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
EB [auth E],
UA [auth D],
VA [auth D]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
CME
Query on CME
A, B, C, D, E, F
A, B, C, D, E, F
L-PEPTIDE LINKINGC5 H11 N O3 S2CYS
KPI
Query on KPI
A, B, C, D, E, F
A, B, C, D, E, F
L-PEPTIDE LINKINGC9 H16 N2 O4LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.179 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 188.83α = 90
b = 188.83β = 90
c = 130.43γ = 90
Software Package:
Software NamePurpose
MxCuBEdata collection
MOLREPphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-12-15
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2018-05-16
    Changes: Data collection, Refinement description