5W16

Crystal structure of glutamate racemase from Thermus thermophilus in complex with D-glutamate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.91 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.187 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Crystal structure of glutamate racemase from Thermus Thermophilus in complex with D-glutamate

Cooling, G.T.Vance, N.R.Spies, M.A.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Glutamate racemaseA, B, C, D278Thermus thermophilusMutation(s): 0 
Gene Names: murITTHA1643TTMY_1945
EC: 5.1.1.3
UniProt
Find proteins for A0A1J1ER74 (Thermus thermophilus)
Explore A0A1J1ER74 
Go to UniProtKB:  A0A1J1ER74
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1J1ER74
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DGL
Query on DGL

Download Ideal Coordinates CCD File 
E [auth A],
L [auth B],
Q [auth C],
Z [auth D]
D-GLUTAMIC ACID
C5 H9 N O4
WHUUTDBJXJRKMK-GSVOUGTGSA-N
 Ligand Interaction
NO3
Query on NO3

Download Ideal Coordinates CCD File 
AA [auth D],
BA [auth D],
CA [auth D],
DA [auth D],
F [auth A],
AA [auth D],
BA [auth D],
CA [auth D],
DA [auth D],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
M [auth B],
N [auth B],
R [auth C],
S [auth C],
T [auth C],
U [auth C],
V [auth C]
NITRATE ION
N O3
NHNBFGGVMKEFGY-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
EA [auth D],
FA [auth D],
K [auth A],
O [auth B],
P [auth B],
EA [auth D],
FA [auth D],
K [auth A],
O [auth B],
P [auth B],
W [auth C],
X [auth C],
Y [auth C]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.91 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.187 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.677α = 90
b = 96.728β = 90
c = 179.066γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01 GM097373

Revision History  (Full details and data files)

  • Version 1.0: 2018-06-06
    Type: Initial release
  • Version 1.1: 2020-01-01
    Changes: Author supporting evidence