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PDBsum entry 1gwg

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protein metals links
Ferritin PDB id
1gwg
Jmol
Contents
Protein chain
168 a.a. *
Metals
IOD ×9
_CD ×2
Waters ×152
* Residue conservation analysis
PDB id:
1gwg
Name: Ferritin
Title: Tri-iodide derivative of apoferritin
Structure: Ferritin light chain. Chain: a. Fragment: l-chain residues 1-174. Synonym: ferritin l subunit, ferritin. Engineered: yes
Source: Equus caballus. Horse. Organism_taxid: 9796. Organ: spleen. Expressed in: escherichia coli. Expression_system_taxid: 562
Biol. unit: 24mer (from PDB file)
Resolution:
2.01Å     R-factor:   0.169     R-free:   0.208
Authors: G.Evans,G.Bricogne
Key ref:
G.Evans and G.Bricogne (2002). Triiodide derivatization and combinatorial counter-ion replacement: two methods for enhancing phasing signal using laboratory Cu Kalpha X-ray equipment. Acta Crystallogr D Biol Crystallogr, 58, 976-991. PubMed id: 12037300 DOI: 10.1107/S0907444902005486
Date:
15-Mar-02     Release date:   06-Jun-02    
PROCHECK
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 Headers
 References

Protein chain
Pfam   ArchSchema ?
P02791  (FRIL_HORSE) -  Ferritin light chain
Seq:
Struc:
175 a.a.
168 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     intracellular ferritin complex   1 term 
  Biological process     iron ion transport   2 terms 
  Biochemical function     metal ion binding     3 terms  

 

 
DOI no: 10.1107/S0907444902005486 Acta Crystallogr D Biol Crystallogr 58:976-991 (2002)
PubMed id: 12037300  
 
 
Triiodide derivatization and combinatorial counter-ion replacement: two methods for enhancing phasing signal using laboratory Cu Kalpha X-ray equipment.
G.Evans, G.Bricogne.
 
  ABSTRACT  
 
A series of experiments performed at Cu Kalpha wavelength on in-house X-ray equipment are presented which investigate two possibilities for enhancing the experimental phasing signal by means of (i) triiodide/iodide soaks using KI/I(2) and (ii) combinations of counter-ions introduced using the short cryosoak method. Triiodide-derivative crystal structures for five test proteins have been refined and reveal that iodine can bind as polyiodide and single iodide ions through hydrophobic and hydrogen-bonding interactions both at the molecular surface and in intramolecular and intermolecular cavities. In three cases, the structures could be automatically determined with autoSHARP using in-house SAD and SIRAS data. The investigation of combinatorial counter-ion replacement using multiple salts with Na(+) and Cs(+) as cations and I(-) and Cl(-) as anions reveals that, for the case of hen egg-white lysozyme, significant improvement in phasing signal is obtained by the combined use of salts compared with SIRAS methods using native and single short-soak derivative data sets.
 
  Selected figure(s)  
 
Figure 2.
Figure 2 Region of the elastase molecule showing the common binding site for (a) iodine and (b) xenon.
Figure 6.
Figure 6 Example of a pentaiodide molecule (sites B21-B25) binding in a partially solvent-exposed pocket formed between two symmetry-related molecules of XI. The pentaiodide is tethered at each end by hydrogen bonds (yellow dashes) formed with Gln234 NE2 and Lys240 NZ. The central three atoms contact through van der Waals interactions. The symmetry-related protein molecule is shown in green. The anomalous difference Fourier map contoured at 4 is shown in red mesh.
 
  The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2002, 58, 976-991) copyright 2002.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19181667 D.W.Abbott, M.S.Macauley, D.J.Vocadlo, and A.B.Boraston (2009).
Streptococcus pneumoniae Endohexosaminidase D, Structural and Mechanistic Insight into Substrate-assisted Catalysis in Family 85 Glycoside Hydrolases.
  J Biol Chem, 284, 11676-11689.
PDB codes: 2w91 2w92
19422833 E.Ficko-Blean, and A.B.Boraston (2009).
N-acetylglucosamine recognition by a family 32 carbohydrate-binding module from Clostridium perfringens NagH.
  J Mol Biol, 390, 208-220.
PDB codes: 2w1q 2w1s 2w1u 2wdb
19285508 M.A.Higgins, D.W.Abbott, M.J.Boulanger, and A.B.Boraston (2009).
Blood group antigen recognition by a solute-binding protein from a serotype 3 strain of Streptococcus pneumoniae.
  J Mol Biol, 388, 299-309.
PDB code: 2w7y
19608744 M.A.Higgins, G.E.Whitworth, N.El Warry, M.Randriantsoa, E.Samain, R.D.Burke, D.J.Vocadlo, and A.B.Boraston (2009).
Differential recognition and hydrolysis of host carbohydrate antigens by Streptococcus pneumoniae family 98 glycoside hydrolases.
  J Biol Chem, 284, 26161-26173.
PDB codes: 2wmf 2wmg 2wmh 2wmi 2wmj 2wmk
18292090 K.J.Gregg, R.Finn, D.W.Abbott, and A.B.Boraston (2008).
Divergent modes of glycan recognition by a new family of carbohydrate-binding modules.
  J Biol Chem, 283, 12604-12613.
PDB codes: 2vmg 2vmh 2vmi 2vng 2vno 2vnr
18462685 M.Rossmann, R.Schultz-Heienbrok, J.Behlke, N.Remmel, C.Alings, K.Sandhoff, W.Saenger, and T.Maier (2008).
Crystal structures of human saposins C andD: implications for lipid recognition and membrane interactions.
  Structure, 16, 809-817.
PDB codes: 2qyp 2r0r 2r1q 2rb3 2z9a
17187076 A.L.van Bueren, M.Higgins, D.Wang, R.D.Burke, and A.B.Boraston (2007).
Identification and structural basis of binding to host lung glycogen by streptococcal virulence factors.
  Nat Struct Mol Biol, 14, 76-84.
PDB codes: 2j43 2j44
16230347 A.B.Boraston, M.Healey, J.Klassen, E.Ficko-Blean, A.Lammerts van Bueren, and V.Law (2006).
A structural and functional analysis of alpha-glucan recognition by family 25 and 26 carbohydrate-binding modules reveals a conserved mode of starch recognition.
  J Biol Chem, 281, 587-598.
PDB codes: 2c3g 2c3h 2c3v 2c3w 2c3x
17044043 C.E.Stevenson, N.Burton, M.M.Costa, U.Nath, R.A.Dixon, E.S.Coen, and D.M.Lawson (2006).
Crystal structure of the MYB domain of the RAD transcription factor from Antirrhinum majus.
  Proteins, 65, 1041-1045.
PDB code: 2cjj
16732286 W.A.Barton, D.Tzvetkova-Robev, E.P.Miranda, M.V.Kolev, K.R.Rajashankar, J.P.Himanen, and D.B.Nikolov (2006).
Crystal structures of the Tie2 receptor ectodomain and the angiopoietin-2-Tie2 complex.
  Nat Struct Mol Biol, 13, 524-532.
PDB codes: 2gy5 2gy7
16823037 W.A.Barton, D.Tzvetkova-Robev, H.Erdjument-Bromage, P.Tempst, and D.B.Nikolov (2006).
Highly efficient selenomethionine labeling of recombinant proteins produced in mammalian cells.
  Protein Sci, 15, 2008-2013.  
16152643 R.L.Crowther, and M.M.Georgiadis (2005).
The crystal structure of 5-keto-4-deoxyuronate isomerase from Escherichia coli.
  Proteins, 61, 680-684.
PDB code: 1xru
15893672 W.A.Barton, D.Tzvetkova, and D.B.Nikolov (2005).
Structure of the angiopoietin-2 receptor binding domain and identification of surfaces involved in Tie2 recognition.
  Structure, 13, 825-832.
PDB codes: 1z3s 1z3u
14695519 M.Salmain, B.Caro, F.Le Guen-Robin, J.C.Blais, and G.Jaouen (2004).
Solution- and crystal-phase covalent modification of lysozyme by a purpose-designed organoruthenium complex. A MALDI-TOF MS study of its metal binding sites.
  Chembiochem, 5, 99.  
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. Where a reference describes a PDB structure, the PDB codes are shown on the right.