Re: [ccp4bb] Are there any proteins capable of crystallizing at a wide range of pH having the same space group?

Thu, 19 Sep 2019 23:55:14 -0700

As far as lysozyme is concerned, the space group obtained is mainly the result of an interplay between the pI of lysozyme on the one hand and the pH of the solute and type of salt (or organic small molecule) on the other hand (Hofmeister series). The pI is about 9.5 and one should not be surprized lysozyme can crystallize in the same space group over a wide pH range (4 to 9).... Not sure you will find examples in the PDB of other protein with a more neutral pI that behave similarly. 

Overpopulating the PDB are (to name a few)
Beta-2-microglobulin (1034) <http://www.rcsb.org/pdb/search/smart.do?smartComparator=and&smartSearchSubtype_0=MacroMoleculeQuery&macromoleculeName_0=E2RN10,P01887,P01888,P07151,P21611,P61769,P61771,Q04475,Q07717,Q14U75,Q5MGS7,Q65XZ7,Q6L7B0,Q6V7J5,UNS1396664598&smartComparator=and&refine=true&tabtoshow=Current&qrid=6FAE3590&evtc=DrillDown&evta=UniProtMolecule%20Name&evtl=Results> 

 *
     o Lysozyme C (1009)
       
<http://www.rcsb.org/pdb/search/smart.do?smartComparator=and&smartSearchSubtype_0=MacroMoleculeQuery&macromoleculeName_0=P00698,P00700,P00701,P00702,P00703,P00704,P11375,P61626,Q7LZQ1&smartComparator=and&refine=true&tabtoshow=Current&qrid=6FAE3590&evtc=DrillDown&evta=UniProtMolecule%20Name&evtl=Results>
     o Carbonic anhydrase 2 (752)
       
<http://www.rcsb.org/pdb/search/smart.do?smartComparator=and&smartSearchSubtype_0=MacroMoleculeQuery&macromoleculeName_0=P00918,P00921,P45148,P61517,P9WPJ9&smartComparator=and&refine=true&tabtoshow=Current&qrid=6FAE3590&evtc=DrillDown&evta=UniProtMolecule%20Name&evtl=Results>
     o Endothiapepsin (525)
       
<http://www.rcsb.org/pdb/search/smart.do?smartComparator=and&smartSearchSubtype_0=MacroMoleculeQuery&macromoleculeName_0=P11838&smartComparator=and&refine=true&tabtoshow=Current&qrid=6FAE3590&evtc=DrillDown&evta=UniProtMolecule%20Name&evtl=Results>
 * Cationic trypsin (445)
   
<http://www.rcsb.org/pdb/search/smart.do?smartComparator=and&smartSearchSubtype_0=MacroMoleculeQuery&macromoleculeName_0=P00760&smartComparator=and&refine=true&tabtoshow=Current&qrid=6FAE3590&evtc=DrillDown&evta=UniProtMolecule%20Name&evtl=Results>
 * Myoglobin (418)
   
<http://www.rcsb.org/pdb/search/smart.do?smartComparator=and&smartSearchSubtype_0=MacroMoleculeQuery&macromoleculeName_0=H3JQV6,P02144,P02181,P02184,P02185,P02186,P02189,P02205,P56208,P68080,P68082,P68189,P68190&smartComparator=and&refine=true&tabtoshow=Current&qrid=6FAE3590&evtc=DrillDown&evta=UniProtMolecule%20Name&evtl=Results>

 * Cyclin-dependent kinase 2 (402)
   
<http://www.rcsb.org/pdb/search/smart.do?smartComparator=and&smartSearchSubtype_0=MacroMoleculeQuery&macromoleculeName_0=P24941&smartComparator=and&refine=true&tabtoshow=Current&qrid=4886BC49&evtc=DrillDown&evta=UniProtMolecule%20Name&evtl=Results>
 * Prothrombin (380)
   
<http://www.rcsb.org/pdb/search/smart.do?smartComparator=and&smartSearchSubtype_0=MacroMoleculeQuery&macromoleculeName_0=P00734,P00735,P19221&smartComparator=and&refine=true&tabtoshow=Current&qrid=4886BC49&evtc=DrillDown&evta=UniProtMolecule%20Name&evtl=Results>
 * Beta-secretase 1 (377)
   
<http://www.rcsb.org/pdb/search/smart.do?smartComparator=and&smartSearchSubtype_0=MacroMoleculeQuery&macromoleculeName_0=P56817&smartComparator=and&refine=true&tabtoshow=Current&qrid=4886BC49&evtc=DrillDown&evta=UniProtMolecule%20Name&evtl=Results>
 * DNA polymerase beta (318)
   
<http://www.rcsb.org/pdb/search/smart.do?smartComparator=and&smartSearchSubtype_0=MacroMoleculeQuery&macromoleculeName_0=P06746,P06766,Q9U6N3&smartComparator=and&refine=true&tabtoshow=Current&qrid=4886BC49&evtc=DrillDown&evta=UniProtMolecule%20Name&evtl=Results>

 * Beta-lactamase (552)
   
<http://www.rcsb.org/pdb/search/smart.do?smartComparator=and&smartSearchSubtype_0=MacroMoleculeQuery&macromoleculeName_0=A0A059Q5E8,A0A076YIY5,A0A077KT80,A0A0B6VPP7,A0A0F6P2I5,A0A0H2V8D3,A0A0H3H219,A0A0H3KN52,A0A0H4IUK8,A0A0T9EA39,A0A0U3IB62,A0A160YKM3,A0A175VLQ4,A0A182DW26,A0A1B3B7F6,A0A1U8YI81,A0A1Y0WMN3,A0A220QIS6,A0A2Z4BUZ1,A0A2Z4T9G7,A0A386YIZ1,A0EL75,A0QZC8,A1JML9,A2RP81,A4JN42,A4JP73,A5N1B8,A5PHA6,A7TUE6,A8DS27,A8FFI9,B1MCI3,B1PL86,B1YX81,B2FRP5,B2JET9,B4EPS2,B5LY47,B7SNP8,C0LZL5,C5HUY1,C7PJE6,C8CP57,D1ALR7,D1C5R0,D2ARB3,D3INY1,D3X610,D5DH82,E1R245,E2NI36,F6KZJ2,G3F7G9,G3G192,G5CKK8,H2ERK4,H6UQI0,H7C785,I6XA30,L7V1I2,M4JTK1,P00807,P00808,P00811,P05193,P05364,P0A5I7,P14559,P24735,P52664,P85302,P94458,P9WKD3,Q09HD0,Q0Z8S4,Q2T5A3,Q2TR58,Q3SAW3,Q46041,Q48428,Q48434,Q51400,Q51578,Q54488,Q59401,Q59517,Q5NH60,Q5VCA8,Q6BCU6,Q6DRA1,Q6JP75,Q6NCV7,Q6RFZ0,Q6XEC0,Q6ZXB6,Q76DI4,Q76LX5,Q79DR3,Q79MP6,Q7BNC2,Q7D0B8,Q7NYG4,Q840M4,Q87Z37,Q8EMP8,Q8GRH0,Q8KMX3,Q8XDQ2,Q8YU74,Q939N4,Q93CA2,Q93DC4,Q93F76,Q93LQ9,Q93PQ0,Q93T42,Q99QC1,Q9AGJ5,Q9EXV5,Q9KJY7,Q9KVZ2,Q9L387,Q9L4R5,Q9L5C7,Q9L5C8,Q9R429,Q9R435,Q9RBQ1,Q9RMI1,R4NH29,S5LVN3,T0BMH6&smartComparator=and&refine=true&tabtoshow=Current&qrid=9B9BD293&evtc=DrillDown&evta=UniProtMolecule%20Name&evtl=Results>
 * Thermonuclease (290)
   
<http://www.rcsb.org/pdb/search/smart.do?smartComparator=and&smartSearchSubtype_0=MacroMoleculeQuery&macromoleculeName_0=A5A513,A5A520,A5A523,P00644,Q5HHM4,Q8NXI6&smartComparator=and&refine=true&tabtoshow=Current&qrid=9B9BD293&evtc=DrillDown&evta=UniProtMolecule%20Name&evtl=Results>
 * Maltose/maltodextrin-bind ... (254)
   
<http://www.rcsb.org/pdb/search/smart.do?smartComparator=and&smartSearchSubtype_0=MacroMoleculeQuery&macromoleculeName_0=P0AEX9,P0AEY0,P19576&smartComparator=and&refine=true&tabtoshow=Current&qrid=9B9BD293&evtc=DrillDown&evta=UniProtMolecule%20Name&evtl=Results>
 * Dihydrofolate reductase (213)
   
<http://www.rcsb.org/pdb/search/smart.do?smartComparator=and&smartSearchSubtype_0=MacroMoleculeQuery&macromoleculeName_0=A0A0M3KKX1,A0A384KYY5,A0QP85,A5U6B6,B1XC49,C3TR70,G4VJD6,I7FC10,O30463,P00374,P00375,P00378,P00381,P04382,P0A017,P0ABQ4,P0ABQ5,P16184,P22906,P9WNX0,P9WNX1,Q03E11,Q1RGF0,Q54801,Q5KZ26,Q60034,Q70YQ6,Q81R22,Q834R2,Q83AB2,U5M636,U6N356,W7NDF6&smartComparator=and&refine=true&tabtoshow=Current&qrid=9B9BD293&evtc=DrillDown&evta=UniProtMolecule%20Name&evtl=Results>


Jeroen

Am 20.09.19 um 01:03 schrieb Murpholino Peligro:
A quick glance at the entries of hen egg white lysozyme in the PDB show that it can be crystallized at different pH values, but the space group is not always the same. I still have to refine the analysis but I was wondering that maybe there are a few proteins that can crystallize at a wide range (maybe not that wide) of pH values and still have the same space group?
To refine the analysis a wee further: By any chance do you know any proteins overpopulating the PDB (i.e. besides HEWL)? 

Lots of thanks as always.

Murphy


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--
*Dr.math. et dis. nat.Jeroen R. Mesters*
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