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)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Dihydrodipicolinate synthaseA, B, C, D, E, F304Mycobacterium 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
Protein Feature View
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  • 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] , H [auth A] , HA [auth C] , I [auth A] , 
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

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CA [auth B] , CB [auth E] , DB [auth E] , EA [auth B] , IA [auth C] , IB [auth F] , J [auth A] , JA [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

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DA [auth B]PYRUVIC ACID
C3 H4 O3
LCTONWCANYUPML-UHFFFAOYSA-N
 Ligand Interaction
BME
Query on BME

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

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AA [auth B] , AB [auth E] , BA [auth B] , BB [auth E] , HB [auth F] , L [auth A] , M [auth A] , MA [auth C] , 
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, FL-PEPTIDE LINKINGC5 H11 N O3 S2CYS
KPI
Query on KPI
A, B, C, D, E, FL-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