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PDBsum entry 2a7b

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protein metals links
Endocytosis/exocytosis PDB id
2a7b
Jmol
Contents
Protein chain
120 a.a. *
Metals
_XE ×2
Waters ×87
* Residue conservation analysis
PDB id:
2a7b
Name: Endocytosis/exocytosis
Title: On the routine use of soft x-rays in macromolecular crystallography, part iii- the optimal data collection wavelength
Structure: Gamma-adaptin appendage domain. Chain: a. Engineered: yes
Source: Mus musculus. House mouse. Organism_taxid: 10090. Gene: ap1g1, adtg, clapg1. Expressed in: escherichia coli. Expression_system_taxid: 562
Resolution:
1.65Å     R-factor:   0.183     R-free:   0.228
Authors: C.Mueller-Dieckmann,S.Panjikar,P.A.Tucker,M.S.Weiss
Key ref:
C.Mueller-Dieckmann et al. (2005). On the routine use of soft X-rays in macromolecular crystallography. Part III. The optimal data-collection wavelength. Acta Crystallogr D Biol Crystallogr, 61, 1263-1272. PubMed id: 16131760 DOI: 10.1107/S0907444905021475
Date:
05-Jul-05     Release date:   19-Jul-05    
PROCHECK
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 Headers
 References

Protein chain
Pfam   ArchSchema ?
P22892  (AP1G1_MOUSE) -  AP-1 complex subunit gamma-1
Seq:
Struc:
 
Seq:
Struc:
822 a.a.
120 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     clathrin adaptor complex   1 term 
  Biological process     vesicle-mediated transport   2 terms 

 

 
DOI no: 10.1107/S0907444905021475 Acta Crystallogr D Biol Crystallogr 61:1263-1272 (2005)
PubMed id: 16131760  
 
 
On the routine use of soft X-rays in macromolecular crystallography. Part III. The optimal data-collection wavelength.
C.Mueller-Dieckmann, S.Panjikar, P.A.Tucker, M.S.Weiss.
 
  ABSTRACT  
 
Complete and highly redundant data sets were collected at different wavelengths between 0.80 and 2.65 A for a total of ten different protein and DNA model systems. The magnitude of the anomalous signal-to-noise ratio as assessed by the quotient R(anom)/R(r.i.m.) was found to be influenced by the data-collection wavelength and the nature of the anomalously scattering substructure. By utilizing simple empirical correlations, for instance between the estimated deltaF/F and the expected R(anom) or the data-collection wavelength and the expected R(r.i.m.), the wavelength at which the highest anomalous signal-to-noise ratio can be expected could be estimated even before the experiment. Almost independent of the nature of the anomalously scattering substructure and provided that no elemental X-ray absorption edge is nearby, this optimal wavelength is 2.1 A.
 
  Selected figure(s)  
 
Figure 1.
Figure 1 Estimated anomalous diffraction ratio [Delta] F/F in the wavelength range 0.5-3.0 for the ten model systems described in this paper. The estimate is for zero scattering angle and assumes resolved and independent anomalous scatterers. The ten systems are separated into two groups (Xe group and P/S/Ca group) and sorted in decreasing strength of the anomalous signal. Black lines, ConA-Xe, adaptin-Xe, PPE-Xe and HEL-Xe; blue line, thermolysin; green lines, DNA, HEL, trypsin, thaumatin and PPE-Ca. The experimentally determined anomalously scattering substructures for the ten systems were (1) ConA-Xe: two protein S atoms, one Mn2+ and one Ca^2+ ion, both fully occupied, as well as six Xe atoms with occupancies (q) of 0.40, 0.30, 0.20, 0.15, 0.15 and 0.10; (2) adaptin-Xe: four protein S atoms and two Xe atoms (q = 0.32 and 0.10); (3) PPE-Xe: ten protein S atoms, one Xe atom (q = 0.72) and two SO[4]^2- ions (q = 0.70 and 0.50); (4) HEL-Xe: ten S atoms, two Xe atoms (q = 0.24 and 0.08), the first one being situated on a crystallographic twofold axis, and eight Cl- ions (q = 0.68, 0.58, 0.52, 0.37, 0.37, 0.34, 0.31 and 0.28); (5) DNA: eight P atoms; (6) HEL: ten S atoms and seven Cl- ions (q = 0.80, 0.77, 0.70, 0.60, 0.57, 0.37 and 0.25); (7) thermolysin: two protein S atoms, six Ca^2+ ions (q = 1.00, 1.00, 1.00, 1.00, 0.50 and 0.25), one fully occupied Zn2+ ion and two DMSO molecules (q = 0.50 and 0.40); (8) trypsin: 14 protein S atoms, one fully occupied Ca^2+ ion and two partially occupied Cl- ions (q = 0.40 and 0.25); (9) thaumatin: 17 protein S atoms and (10) PPE-Ca: ten protein S atoms, one Ca^2+ ion (q = 0.81) and one Cl- ion (q = 0.30).
Figure 4.
Figure 4 Dependence of the observed R*[r.i.m] values on the data-collection wavelength. The data distribution can be fitted with the exponential function R*[r.i.m] = 3.78 + 0.0002exp(3.76 [lambda] ) and an R2 value of 0.57. The three outliers (DNA data sets collected at [lambda] = 2.10, 2.30 and 2.50 , respectively) not obeying the exponential fit are shown as open circles.
 
  The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2005, 61, 1263-1272) copyright 2005.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21525641 C.Homer, L.Cooper, and A.Gonzalez (2011).
Energy dependence of site-specific radiation damage in protein crystals.
  J Synchrotron Radiat, 18, 338-345.  
21460444 G.Evans, D.Axford, and R.L.Owen (2011).
The design of macromolecular crystallography diffraction experiments.
  Acta Crystallogr D Biol Crystallogr, 67, 261-270.  
20029111 J.Brandao-Neto, S.P.Thompson, A.R.Lennie, F.F.Ferreira, and C.C.Tang (2010).
Characterization of wax as a potential diffraction intensity standard for macromolecular crystallography beamlines.
  J Synchrotron Radiat, 17, 53-60.  
20693684 M.W.Bowler, M.Guijarro, S.Petitdemange, I.Baker, O.Svensson, M.Burghammer, C.Mueller-Dieckmann, E.J.Gordon, D.Flot, S.M.McSweeney, and G.A.Leonard (2010).
Diffraction cartography: applying microbeams to macromolecular crystallography sample evaluation and data collection.
  Acta Crystallogr D Biol Crystallogr, 66, 855-864.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time.