1FUB

FIRST PROTEIN STRUCTURE DETERMINED FROM X-RAY POWDER DIFFRACTION DATA


Experimental Data Snapshot

  • Method: POWDER DIFFRACTION

wwPDB Validation 3D Report Full Report


This is version 2.0 of the entry. See complete history

Literature

The first protein crystal structure determined from high-resolution X-ray powder diffraction data: a variant of T3R3 human insulin-zinc complex produced by grinding.

Von Dreele, R.B.Stephens, P.W.Smith, G.D.Blessing, R.H.

(2000) Acta Crystallogr.,Sect.D 56: 1549-1553

  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • X-ray diffraction analysis of protein structure is often limited by the availability of suitable crystals. However, the absence of single crystals need not present an insurmountable obstacle in protein crystallography any more than it does in materia ...

    X-ray diffraction analysis of protein structure is often limited by the availability of suitable crystals. However, the absence of single crystals need not present an insurmountable obstacle in protein crystallography any more than it does in materials science, where powder diffraction techniques have developed to the point where complex oxide, zeolite and small organic molecular structures can often be solved from powder data alone. Here, that fact is demonstrated with the structure solution and refinement of a new variant of the T(3)R(3) Zn-human insulin complex produced by mechanical grinding of a polycrystalline sample. High-resolution synchrotron X-ray powder diffraction data were used to solve this crystal structure by molecular replacement adapted for Rietveld refinement. A complete Rietveld refinement of the 1630-atom protein was achieved by combining 7981 stereochemical restraints with a 4800-step (d(min) = 3.24 A) powder diffraction pattern and yielded the residuals R(wp) = 3.73%, R(p) = 2.84%, R(F)(2) = 8.25%. It was determined that the grinding-induced phase change is accompanied by 9.5 and 17.2 degrees rotations of the two T(3)R(3) complexes that comprise the crystal structure. The material reverts over 2-3 d to recover the original T(3)R(3) crystal structure. A Rietveld refinement of this 815-atom protein by combining 3886 stereochemical restraints with a 6000-step (d(min) = 3.06 A) powder diffraction pattern yielded the residuals R(wp) = 3.46%, R(p) = 2.64%, R(F)(2) = 7.10%. The demonstrated ability to solve and refine a protein crystal structure from powder diffraction data suggests that this approach can be employed, for example, to examine structural changes in a series of protein derivatives in which the structure of one member is known from a single-crystal study.


    Related Citations: 
    • Combined Rietveld and Stereochemical Restraint Refinement of a Protein Crystal Structure
      Von Dreele, R.B.
      (1999) J.Appl.Crystallogr. 32: 1084
    • Crystallographic Evidence for Dual Coordinate Aroun in the T3R3 Human Insulin Hexamer
      Smith, G.D.,Ciszak, E.
      (1994) Biochemistry 33: 1512


    Organizational Affiliation

    Manuel Lujan Jr Neutron Scattering Center, MS H805, Los Alamos National Laboratory, Los Alamos, NM 87545, USA. vondreele@lanl.gov




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
INSULIN, A CHAIN
A, C
21Homo sapiensMutation(s): 0 
Gene Names: INS
Find proteins for P01308 (Homo sapiens)
Go to Gene View: INS
Go to UniProtKB:  P01308
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
INSULIN, B CHAIN
B, D
30Homo sapiensMutation(s): 0 
Gene Names: INS
Find proteins for P01308 (Homo sapiens)
Go to Gene View: INS
Go to UniProtKB:  P01308
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
B, D
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

Download SDF File 
Download CCD File 
B
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download SDF File 
Download CCD File 
B, D
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: POWDER DIFFRACTION

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-10-16
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance
  • Version 2.0: 2018-10-03
    Type: Atomic model, Data collection