3GHS

Human aldose reductase in complex with NADP+ and the inhibitor IDD594. Investigation of global effects of radiation damage on protein structure. Second stage of radiation damage.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1 Å
  • R-Value Free: 0.098 
  • R-Value Work: 0.081 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

X-ray-radiation-induced cooperative atomic movements in protein.

Petrova, T.Lunin, V.Y.Ginell, S.Hazemann, I.Lazarski, K.Mitschler, A.Podjarny, A.Joachimiak, A.

(2009) J.Mol.Biol. 387: 1092-1105

  • DOI: 10.1016/j.jmb.2009.02.030
  • Primary Citation of Related Structures:  3GHR, 3GHT, 3GHU

  • PubMed Abstract: 
  • X-rays interact with biological matter and cause damage. Proteins and other macromolecules are damaged primarily by ionizing X-ray photons and secondarily by reactive radiolytic chemical species. In particular, protein molecules are damaged during X- ...

    X-rays interact with biological matter and cause damage. Proteins and other macromolecules are damaged primarily by ionizing X-ray photons and secondarily by reactive radiolytic chemical species. In particular, protein molecules are damaged during X-ray diffraction experiments with protein crystals, which is, in many cases, a serious hindrance to structure solution. The local X-ray-induced structural changes of the protein molecule have been studied using a number of model systems. However, it is still not well understood whether these local chemical changes lead to global structural changes in protein and what the mechanism is. We present experimental evidence at atomic resolution indicating the movement of large parts of the protein globule together with bound water molecules in the early stages of radiation damage to the protein crystal. The data were obtained from a crystal cryocooled to approximately 100 K and diffracting to 1 A. The movement of the protein structural elements occurs simultaneously with the decarboxylation of several glutamate and aspartate residues that mediate contacts between moving protein structural elements and with the rearrangement of the water network. The analysis of the anisotropy of atomic displacement parameters reveals that the observed atomic movements occur at different rates in different unit cells of the crystal. Thus, the examination of the cooperative atomic movement enables us to better understand how radiation-induced local chemical and structural changes of the protein molecule eventually lead to disorder in protein crystals.


    Organizational Affiliation

    Structural Biology Center, Biosciences Division, Argonne National Laboratory, Argonne, IL 60439, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Aldose reductase
A
316Homo sapiensGene Names: AKR1B1 (ALDR1)
EC: 1.1.1.21
Find proteins for P15121 (Homo sapiens)
Go to Gene View: AKR1B1
Go to UniProtKB:  P15121
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CIT
Query on CIT

Download SDF File 
Download CCD File 
A
CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N
 Ligand Interaction
LDT
Query on LDT

Download SDF File 
Download CCD File 
A
IDD594
[2-(4-BROMO-2-FLUORO-BENZYLTHIOCARBAMOYL)-5-FLUORO-PHENOXY]-ACETIC ACID
C16 H12 Br F2 N O3 S
JCZUIWYXULSXSW-UHFFFAOYSA-N
 Ligand Interaction
NDP
Query on NDP

Download SDF File 
Download CCD File 
A
NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H30 N7 O17 P3
ACFIXJIJDZMPPO-NNYOXOHSSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
LDTΔG: -31.3 - -40.9 kJ/mol (99) BINDINGDB
LDTΔH: -46.2 kJ/mol (99) BINDINGDB
LDTIC50: 3 - 30 nM (99) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1 Å
  • R-Value Free: 0.098 
  • R-Value Work: 0.081 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 49.368α = 90.00
b = 66.801β = 92.22
c = 47.355γ = 90.00
Software Package:
Software NamePurpose
HKL-3000data reduction
HKL-3000data scaling
AMoREphasing
HKL-3000data collection
SHELXL-97refinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-03-24
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance