2024-03-27 REL PDBj PDBj PDBj 2020-02-02 2020-06-03 2020-06-03 2024-03-27 Department of Biotechnology (DBT, India) DBT/PR12422/MED/31/287/2014 India Department of Biotechnology (DBT, India) BT/PR5081/INF/22/156/2012 India Science and Engineering Research Board (SERB) SB/S2/RJN-094/2017 India Structure of Dimethylformamidase, tetramer Arya CA Yadav S ab polypeptide, mononuclear iron, amidohydrolase, tetramer, HYDROLASE Arya CK Yadav S Fine J Casanal A Chopra G Ramanathan G Vinothkumar KR Subramanian R A 2-Tyr-1-carboxylate Mononuclear Iron Center Forms the Active Site of a Paracoccus Dimethylformamidase. Angew.Chem.Int.Ed.Engl. GE 59 16961 16966 2020 32452120 doi:10.1002/anie.202005332 1521-3773 0179 ACIEAY Vinothkumar KR Arya CK Ramanathan G Subramanian R Comparison of CryoEM and X-ray structures of dimethylformamidase Prog.Biophys.Mol.Biol. UK 160 66 78 2021 32735943 doi:10.1016/j.pbiomolbio.2020.06.008 0079-6107 0918 PBIMAC 6lvb FULLOVERLAP Dimethylformamidase Dimethylformamidase 0 1 2
Tetramer, 2x(a2b2)
Paracoccus sp. SSG05 0.4 N,N-dimethylformamidase large subunit Paracoccus sp. SSG05 0.086341758 4 Escherichia coli BL21(DE3) LEVO MKDIAIRGYCDRPSVATGETIRFYVSANETRGTFDAELVRLIHGDSNPAGPGYKEEAIKSDLEGQYPARFQRTQFGSYVE VADPDAGLQPDGAFSVHLFLWSTTPSRGRQGIASRWNDERQSGWNLAIEDGRVVFTIGDGSGATSSVVSDRPLFQQIWYS ITGVYDPEKKQLRLYQKSVVNRTNSRFGLVVPLDSDCAVSADATVKAADSETSLLIAGLGEAAAQDGRTWCIAHYNGKVD APKIYGCALGQDDAEKLSRGEIVRPISRLAHWDFSAGIGLNGIPTDHVVDASGYGHHGRCMNQPSRGSTGWNWDGHEENF IHCPEQYGALWFHEDCLDDCRWEKDFEFTVPEGLKSDFYAVKIRYEDTEDYIPFFVLPPRGTATAPILVIASTLSYLAYA NEQIMHKADIGQAVAGHTPVLNENDVELHKNLSYYGLSTYDGHIDGRGVQYTSWRRPIMNLRPKHRQGFGSIWELPADLH LIDWLNHNGFEYDVATEHDLNDQGAELLRRYKVVLTGSHPEYQTWANADAWEDYLADGGRGMYLAANGMYWIVEVHPEKP WVMEVRKELGVTAWEAPPGEYHYSTNGRRGGRFRGRARATQKIWGTGMSSFGFDHSGYFVQMPDSQDERVAWIMEGIDPE ERIGDGGLVGGGAGGYELDRYDLALGTPPNTLLLASSVEHSVVYTVIPDDKAFPHPGMNGGEHPFVRADITYFSTANGGG MFATSSISWLGSLSWNDYDNNVSKMTKNVLNQFIKDEPAPRVKLAAALEHHHHHH I6NT79 3.5.1.56 N,N-dimethylformamidase small subunit Paracoccus sp. SSG05 0.016083823 4 Escherichia coli BL21(DE3) LEVO MTEASESCVRDPSNYRDRSADWYAFYDERRRKEIIDIIDEHPEIVEEHAANPFGYRKHPSPYLQRVHNYFRMQPTFGRYY IYSEREWDAYRIATIREFGELPELGDERFKTEEEAMHAVFLRRIEDVRAELA I6NWZ0 3.5.1.56 FE (III) ION 5.5845e-05 4 FE water 1.8015e-05 4 HOH singleParticle particle 3 7.2 50.0 Tris-Cl 200.0 NaCl Quantifoil R0.6/1 GOLD 300 CARBON HOLEY GLOW DISCHARGE AIR
Glow discharge was carried out in Quorum Glocube instrument at 25mA for 90 seconds.
 ETHANE 100 291 FEI VITROBOT MARK IV
Blot force was 0 and blotting was done for 3.5 seconds.
Sample at higher salt exists mostly as tetramer
 FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 50.0 2.7 0.9315 0.9315 4.1457 4.1457 75000.0 130841.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN 77.7 77.7 FEI FALCON III (4k x 4k) COUNTING 4096 4096 1 793 60.0 27.0
A total of 25 frames were saved from the 60 second exposure, resulting in ~1.08 electron/frame
 1 89183
Two rounds of 2D classification was performed prior to angular assignment and reconstruction
The model was obtained from the 2D class averages of the data.
 C2 BACK PROJECTION 2.8 FSC 0.143 CUT-OFF RELION 3.0 59191 MAXIMUM LIKELIHOOD RELION 3.0 MAXIMUM LIKELIHOOD RELION 3.0 RELION 3.0 emd_0988.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 320 320 320 0 0 0 320 320 320 342.40002 342.40002 342.40002 90.0 90.0 90.0 X Y Z -0.22288269 0.42321292 0.000010709005 0.013759637 1.07 1.07 1.07 0.07 AUTHOR One of the primary map from the refinement in Relion OTHER REAL 38.799999999999997 emd_0988_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 320 320 320 0 0 0 320 320 320 342.40002 342.40002 342.40002 90.0 90.0 90.0 X Y Z -0.040447418 0.13497369 0.000010890596 0.0053306967 1.07 1.07 1.07 AUTHOR One of the half map from the refinement in Relion emd_0988_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 320 320 320 0 0 0 320 320 320 342.40002 342.40002 342.40002 90.0 90.0 90.0 X Y Z -0.039019134 0.13327363 0.000010526343 0.005331446 1.07 1.07 1.07 AUTHOR One of the half map from the refinement in Relion