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Materials and Methods: FDPS + minodronate (3B7L)

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StructureFDPS + minodronate
PDB Code3B7L
Ligandsminodronate
Entry clone accessiongi|4503685
Entry clone sourceMGC
SGC clone accessionIMAGE:4132071
TagN-terminal tag: mgsshhhhhhssgrenlyfqghm
Construct sequenceghmNGDQNSDVYAQEKQDFVQHFSQIVRVLTEDEMGHPEIGDAIARLKEVLEYNAIGGKYNRGLTVVVAFRELVEPRKQDADSLQRAWTVGWCVELLQAFFLVADDIMDSSLTRRGQICWYQKPGVG
LDAINDANLLEACIYRLLKLYCREQPYYLNLIELFLQSSYQTEIGQTLDLLTAPQGNVDLVRFTEKRYKSIVKYKTAFYSFYLPIAAAMYMAGIDGEKEHANAKKILLEMGEFFQIQDDYLDLFGDP
SVTGKIGTDIQDNKCSWLVVQCLQRATPEQYQILKENYGQKEAEKVARVKALYEELDLPAVFLQYEEDSYSHIMALIEQYAAPLPPAVFLGLARKIYKRRK
Vectorp11
Expression hostBL21(DE3)
Growth methodOvernight cultures in LB (10 mL with100 ug/mL ampicillin) were used to inoculate 1 litre of LB medium containing 100 ug/mL ampicillin. Cultures were grown at 37°C until they reached an OD600 of 0.6-0.8 and then induced with 1 mM IPTG. The temperature was adjusted to 18°C and expression was allowed to continue overnight. The cells were collected by centrifugation.
Extraction procedureThe cell pellet was resuspended in 50 mM HEPES pH 7.5, 5 mM imidazole, 500 mM NaCl, 5% glycerol.and lysed using a high pressure cell disruptor. The lysate was centrifuged at 17,000 RPM for 30 minutes at 4°C and the supernatant was collected.
Purification buffersBinding: 50 mM HEPES pH 7.5, 5 mM imidazole, 500 mM NaCl, 5% glycerol, 0.5 mM TCEPWash: 50 mM HEPES pH 7.5, 500 mM NaCl, 30 mM imidazole, 5% glycerol, 0.5 mM TCEP Elution: 50 mM HEPES pH 7.5, 500 mM NaCl, 250 mM imidazole, 5% glycerol, 0.5 mM TCEPColumn 2 buffer: 10 mM Hepes pH 7.5, 500 mM NaCl, 5% glycerol, 0.5 mM TCEP
Purification procedureColumn 1 : 2mL Ni-NTA agaroseApproximately 75mLs of bacterial lysate was loaded by gravity onto a 2mL Ni-NTA agarose columns pre-equilebrated with binding buffer. The columns were then washed twice with 30mL binding buffer, then twice with 12.5mL of wash buffer. Protein was then eluted with 12.5 mL of elution buffer and collected as 1.5mL fractions. Fractions containing purified protein were pooled and concentrated to a volume of less than 5mLs using a Vivaspin concentrator with 10 kD MW cutoff.Enzymatic treatment : His-tagged TEV protease was added (50 ug per mg FDPSA) and incubated at 4°C for 24 hours to remove the hexahistidine tag. The TEV protease and any uncleaved protein was removed by passing the solution over Ni-NTA agarose beads. The cleaved FDPSA was concentrated to 60mg/mL using a Vivaspin concentrator with 10 kD MW cutoff. Final protein buffer: 10 mM Hepes pH 7.5, 500 mM NaCl, 5% glycerol, 0.5 mM TCEP.Column 2 : Hiload 16/60 Superdex 200 prep grade 120 mLThe concentrated TEV cleaved protein was loaded onto the column at 1 mL/min using an AKTA purifier system. Eluted protein was collected in 1 mL fractions.
Protein stock concentrationAll fractions containing pure protein were pooled. concentrated to 47.9mg/ml using a Vivaspin concentrator with 10 kD MW cutoff.
Mass specCharacterisation of the protein by mass spectrometry revealed MW of 42.96kDa uncleaved and 40.727kDa after TEV cleavage, coinciding with the predicted mass.
CrystallizationMinodronate was prepared as a 100 mM stock solution in 100mM Tris HCl pH 7.7. MgCl2 was prepared as a 100mM aquaeus stock solution. Minodronate and MgCl2 were added to the protein to a final concentration of 2 mM each and a final protein concentration of 15mg/mL. Crystals were grown at 20°C in 300 nl sitting drops by mixing 100 nl of protein solution and 200 nl of precipitant consisting of 0.2M NH4Cl pH6.3, 20% PEG 6000, 10% Ethylene glycol. Crystals were mounted using 20% ethylene glycol as a cryoprotectant before flash freezing.
Data collectionResolution: 2.0Å; X-ray source: Rotating anode, FR-E superbright.

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