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- PDB-8s3b: Crystal structure of Medicago truncatula glutamate dehydrogenase ... -

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Basic information

Entry
Database: PDB / ID: 8s3b
TitleCrystal structure of Medicago truncatula glutamate dehydrogenase 2 in complex with 3-(1H-Tetrazol-5-yl)benzoic acid and NAD
ComponentsGlutamate dehydrogenase
KeywordsOXIDOREDUCTASE / glutamic acid / NAD cofactor / nitrogen metabolism
Function / homology
Function and homology information


glutamate dehydrogenase (NAD+) activity / L-glutamate catabolic process / nucleotide binding / mitochondrion / metal ion binding
Similarity search - Function
Glutamate dehydrogenase / NAD(P) binding domain of glutamate dehydrogenase / Leu/Phe/Val dehydrogenases active site / Glu / Leu / Phe / Val dehydrogenases active site. / Glutamate/phenylalanine/leucine/valine dehydrogenase / Glutamate/phenylalanine/leucine/valine dehydrogenase, dimerisation domain / Glu/Leu/Phe/Val dehydrogenase, dimerisation domain / Glutamate/Leucine/Phenylalanine/Valine dehydrogenase / Glutamate/phenylalanine/leucine/valine dehydrogenase, C-terminal / Glutamate/Leucine/Phenylalanine/Valine dehydrogenase ...Glutamate dehydrogenase / NAD(P) binding domain of glutamate dehydrogenase / Leu/Phe/Val dehydrogenases active site / Glu / Leu / Phe / Val dehydrogenases active site. / Glutamate/phenylalanine/leucine/valine dehydrogenase / Glutamate/phenylalanine/leucine/valine dehydrogenase, dimerisation domain / Glu/Leu/Phe/Val dehydrogenase, dimerisation domain / Glutamate/Leucine/Phenylalanine/Valine dehydrogenase / Glutamate/phenylalanine/leucine/valine dehydrogenase, C-terminal / Glutamate/Leucine/Phenylalanine/Valine dehydrogenase / Aminoacid dehydrogenase-like, N-terminal domain superfamily / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
: / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Glutamate dehydrogenase
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsGrzechowiak, M. / Ruszkowski, M.
Funding support Poland, 1items
OrganizationGrant numberCountry
Polish National Science Centre Poland
CitationJournal: Int.J.Biol.Macromol. / Year: 2024
Title: Legume-type glutamate dehydrogenase: Structure, activity, and inhibition studies.
Authors: Grzechowiak, M. / Sliwiak, J. / Link, A. / Ruszkowski, M.
History
DepositionFeb 19, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 4, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glutamate dehydrogenase
B: Glutamate dehydrogenase
C: Glutamate dehydrogenase
D: Glutamate dehydrogenase
E: Glutamate dehydrogenase
F: Glutamate dehydrogenase
G: Glutamate dehydrogenase
H: Glutamate dehydrogenase
I: Glutamate dehydrogenase
J: Glutamate dehydrogenase
K: Glutamate dehydrogenase
L: Glutamate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)552,22891
Polymers538,72812
Non-polymers13,50079
Water21,7621208
1
A: Glutamate dehydrogenase
C: Glutamate dehydrogenase
D: Glutamate dehydrogenase
E: Glutamate dehydrogenase
H: Glutamate dehydrogenase
I: Glutamate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)276,42548
Polymers269,3646
Non-polymers7,06142
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glutamate dehydrogenase
F: Glutamate dehydrogenase
G: Glutamate dehydrogenase
J: Glutamate dehydrogenase
K: Glutamate dehydrogenase
L: Glutamate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)275,80343
Polymers269,3646
Non-polymers6,43937
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)99.809, 109.861, 156.366
Angle α, β, γ (deg.)78.998, 78.482, 72.219
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 6 through 8 or resid 10...
d_2ens_1(chain "B" and (resid 6 through 8 or resid 10...
d_3ens_1(chain "C" and (resid 6 through 8 or resid 10...
d_4ens_1(chain "D" and (resid 6 through 8 or resid 10...
d_5ens_1(chain "E" and (resid 6 through 8 or resid 10...
d_6ens_1(chain "F" and (resid 6 through 8 or resid 10...
d_7ens_1(chain "G" and (resid 6 through 8 or resid 10...
d_8ens_1(chain "H" and (resid 6 through 8 or resid 10...
d_9ens_1(chain "I" and (resid 6 through 8 or resid 10...
d_10ens_1(chain "J" and (resid 6 through 8 or resid 10...
d_11ens_1(chain "K" and (resid 6 through 8 or resid 10...
d_12ens_1(chain "L" and (resid 6 through 8 or resid 10...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1ALAASNA5 - 7
d_12ens_1ASNSERA9 - 14
d_13ens_1ILEPROA16 - 72
d_14ens_1VALASPA74 - 77
d_15ens_1VALALAA79 - 83
d_16ens_1LEUPROA86 - 109
d_17ens_1ASPASPA111 - 142
d_18ens_1GLYARGA144 - 181
d_19ens_1ALAGLYA183 - 230
d_110ens_1VALPROA232 - 245
d_111ens_1GLYLEUA247 - 254
d_112ens_1HISLEUA256 - 263
d_113ens_1ASPHISA265 - 280
d_114ens_1CYSLYSA282 - 296
d_115ens_1ALAASNA299 - 300
d_116ens_1VALVALA302
d_117ens_1ALAALAA304
d_118ens_1PHEASPA306 - 320
d_119ens_1ILESERA322 - 324
d_120ens_1LYSGLUA326 - 359
d_121ens_1LYSTHRA361 - 371
d_122ens_1ALACYSA373 - 381
d_123ens_1THRALAA383 - 401
d_124ens_1ALAALAA403 - 411
d_125ens_1NADNADB
d_21ens_1ALAASNJ5 - 7
d_22ens_1ASNSERJ9 - 14
d_23ens_1ILEPROJ16 - 72
d_24ens_1VALASPJ74 - 77
d_25ens_1VALALAJ79 - 83
d_26ens_1LEUPROJ85 - 108
d_27ens_1ASPASPJ110 - 141
d_28ens_1GLYARGJ143 - 180
d_29ens_1ALAGLYJ182 - 229
d_210ens_1VALPROJ231 - 244
d_211ens_1GLYLEUJ246 - 253
d_212ens_1HISLEUJ255 - 262
d_213ens_1ASPHISJ264 - 279
d_214ens_1CYSLYSJ281 - 295
d_215ens_1ALAASNJ298 - 299
d_216ens_1VALVALJ301
d_217ens_1ALAALAJ303
d_218ens_1PHEASPJ305 - 319
d_219ens_1ILESERJ321 - 323
d_220ens_1LYSGLUJ325 - 358
d_221ens_1LYSTHRJ360 - 370
d_222ens_1ALACYSJ372 - 380
d_223ens_1THRALAJ382 - 400
d_224ens_1ALAALAJ402 - 410
d_225ens_1NADNADK
d_31ens_1ALAASNT5 - 7
d_32ens_1ASNSERT9 - 14
d_33ens_1ILEPROT16 - 72
d_34ens_1VALASPT74 - 77
d_35ens_1VALALAT79 - 83
d_36ens_1LEUPROT85 - 108
d_37ens_1ASPASPT110 - 141
d_38ens_1GLYARGT143 - 180
d_39ens_1ALAGLYT182 - 229
d_310ens_1VALPROT231 - 244
d_311ens_1GLYLEUT246 - 253
d_312ens_1HISLEUT255 - 262
d_313ens_1ASPHIST264 - 279
d_314ens_1CYSLYST281 - 295
d_315ens_1ALAASNT298 - 299
d_316ens_1VALVALT301
d_317ens_1ALAALAT303
d_318ens_1PHEASPT305 - 319
d_319ens_1ILESERT321 - 323
d_320ens_1LYSGLUT325 - 358
d_321ens_1LYSTHRT360 - 370
d_322ens_1ALACYST372 - 380
d_323ens_1THRALAT382 - 400
d_324ens_1ALAALAT402 - 410
d_325ens_1NADNADU
d_41ens_1ALAASND7 - 9
d_42ens_1ASNSERD11 - 16
d_43ens_1ILEPROD18 - 74
d_44ens_1VALASPD76 - 79
d_45ens_1VALALAD81 - 85
d_46ens_1LEUPROD87 - 110
d_47ens_1ASPASPD112 - 143
d_48ens_1GLYARGD145 - 182
d_49ens_1ALAGLYD184 - 231
d_410ens_1VALPROD233 - 246
d_411ens_1GLYLEUD248 - 255
d_412ens_1HISLEUD257 - 264
d_413ens_1ASPHISD266 - 281
d_414ens_1CYSLYSD283 - 297
d_415ens_1ALAASND300 - 301
d_416ens_1VALVALD303
d_417ens_1ALAALAD305
d_418ens_1PHEASPD307 - 321
d_419ens_1ILESERD323 - 325
d_420ens_1LYSGLUD327 - 360
d_421ens_1LYSTHRD362 - 372
d_422ens_1ALACYSD374 - 382
d_423ens_1THRALAD384 - 402
d_424ens_1ALAALAD404 - 412
d_425ens_1NADNADE
d_51ens_1ALAASNF4 - 6
d_52ens_1ASNSERF8 - 13
d_53ens_1ILEPROF15 - 71
d_54ens_1VALASPF73 - 76
d_55ens_1VALALAF78 - 82
d_56ens_1LEUPROF84 - 107
d_57ens_1ASPASPF109 - 140
d_58ens_1GLYARGF142 - 179
d_59ens_1ALAGLYF181 - 228
d_510ens_1VALPROF230 - 243
d_511ens_1GLYLEUF245 - 252
d_512ens_1HISLEUF254 - 261
d_513ens_1ASPHISF263 - 278
d_514ens_1CYSLYSF280 - 294
d_515ens_1ALAASNF297 - 298
d_516ens_1VALVALF300
d_517ens_1ALAALAF302
d_518ens_1PHEASPF304 - 318
d_519ens_1ILESERF320 - 322
d_520ens_1LYSGLUF324 - 357
d_521ens_1LYSTHRF359 - 369
d_522ens_1ALACYSF371 - 379
d_523ens_1THRALAF381 - 399
d_524ens_1ALAALAF401 - 409
d_525ens_1NADNADF
d_61ens_1ALAASNG5 - 7
d_62ens_1ASNSERG9 - 14
d_63ens_1ILEPROG16 - 72
d_64ens_1VALASPG74 - 77
d_65ens_1VALALAG79 - 83
d_66ens_1LEUPROG85 - 108
d_67ens_1ASPASPG110 - 141
d_68ens_1GLYARGG143 - 180
d_69ens_1ALAGLYG182 - 229
d_610ens_1VALPROG231 - 244
d_611ens_1GLYLEUG246 - 253
d_612ens_1HISLEUG255 - 262
d_613ens_1ASPHISG264 - 279
d_614ens_1CYSLYSG281 - 295
d_615ens_1ALAASNG298 - 299
d_616ens_1VALVALG301
d_617ens_1ALAALAG303
d_618ens_1PHEASPG305 - 319
d_619ens_1ILESERG321 - 323
d_620ens_1LYSGLUG325 - 358
d_621ens_1LYSTHRG360 - 370
d_622ens_1ALACYSG372 - 380
d_623ens_1THRALAG382 - 400
d_624ens_1ALAALAG402 - 410
d_625ens_1NADNADG
d_71ens_1ALAASNH5 - 7
d_72ens_1ASNSERH9 - 14
d_73ens_1ILEPROH16 - 72
d_74ens_1VALASPH74 - 77
d_75ens_1VALALAH79 - 83
d_76ens_1LEUPROH86 - 109
d_77ens_1ASPASPH111 - 142
d_78ens_1GLYARGH144 - 181
d_79ens_1ALAGLYH183 - 230
d_710ens_1VALPROH232 - 245
d_711ens_1GLYLEUH247 - 254
d_712ens_1HISLEUH256 - 263
d_713ens_1ASPHISH265 - 280
d_714ens_1CYSLYSH282 - 296
d_715ens_1ALAASNH299 - 300
d_716ens_1VALVALH302
d_717ens_1ALAALAH304
d_718ens_1PHEASPH306 - 320
d_719ens_1ILESERH322 - 324
d_720ens_1LYSGLUH326 - 359
d_721ens_1LYSTHRH361 - 371
d_722ens_1ALACYSH373 - 381
d_723ens_1THRALAH383 - 401
d_724ens_1ALAALAH403 - 411
d_725ens_1NADNADH
d_81ens_1ALAASNI5 - 7
d_82ens_1ASNSERI9 - 14
d_83ens_1ILEPROI16 - 72
d_84ens_1VALASPI74 - 77
d_85ens_1VALALAI79 - 83
d_86ens_1LEUPROI85 - 108
d_87ens_1ASPASPI110 - 141
d_88ens_1GLYARGI143 - 180
d_89ens_1ALAGLYI182 - 229
d_810ens_1VALPROI231 - 244
d_811ens_1GLYLEUI246 - 253
d_812ens_1HISLEUI255 - 262
d_813ens_1ASPHISI264 - 279
d_814ens_1CYSLYSI281 - 295
d_815ens_1ALAASNI298 - 299
d_816ens_1VALVALI301
d_817ens_1ALAALAI303
d_818ens_1PHEASPI305 - 319
d_819ens_1ILESERI321 - 323
d_820ens_1LYSGLUI325 - 358
d_821ens_1LYSTHRI360 - 370
d_822ens_1ALACYSI372 - 380
d_823ens_1THRALAI382 - 400
d_824ens_1ALAALAI403 - 411
d_825ens_1NADNADI
d_91ens_1ALAASNK4 - 6
d_92ens_1ASNSERK8 - 13
d_93ens_1ILEPROK15 - 71
d_94ens_1VALASPK73 - 76
d_95ens_1VALALAK78 - 82
d_96ens_1LEUPROK84 - 107
d_97ens_1ASPASPK109 - 140
d_98ens_1GLYARGK142 - 179
d_99ens_1ALAGLYK181 - 228
d_910ens_1VALPROK230 - 243
d_911ens_1GLYLEUK245 - 252
d_912ens_1HISLEUK254 - 261
d_913ens_1ASPHISK263 - 278
d_914ens_1CYSLYSK280 - 294
d_915ens_1ALAASNK297 - 298
d_916ens_1VALVALK300
d_917ens_1ALAALAK302
d_918ens_1PHEASPK304 - 318
d_919ens_1ILESERK320 - 322
d_920ens_1LYSGLUK324 - 357
d_921ens_1LYSTHRK359 - 369
d_922ens_1ALACYSK371 - 379
d_923ens_1THRALAK381 - 399
d_924ens_1ALAALAK401 - 409
d_925ens_1NADNADK
d_101ens_1ALAASNL4 - 6
d_102ens_1ASNSERL8 - 13
d_103ens_1ILEPROL15 - 71
d_104ens_1VALASPL73 - 76
d_105ens_1VALALAL78 - 82
d_106ens_1LEUPROL84 - 107
d_107ens_1ASPASPL109 - 140
d_108ens_1GLYARGL142 - 179
d_109ens_1ALAGLYL181 - 228
d_1010ens_1VALPROL230 - 243
d_1011ens_1GLYLEUL245 - 252
d_1012ens_1HISLEUL254 - 261
d_1013ens_1ASPHISL263 - 278
d_1014ens_1CYSLYSL280 - 294
d_1015ens_1ALAASNL297 - 298
d_1016ens_1VALVALL300
d_1017ens_1ALAALAL302
d_1018ens_1PHEASPL304 - 318
d_1019ens_1ILESERL320 - 322
d_1020ens_1LYSGLUL324 - 357
d_1021ens_1LYSTHRL359 - 369
d_1022ens_1ALACYSL371 - 379
d_1023ens_1THRALAL381 - 399
d_1024ens_1ALAALAL401 - 409
d_1025ens_1NADNADL
d_111ens_1ALAASNN3 - 5
d_112ens_1ASNSERN7 - 12
d_113ens_1ILEPRON14 - 70
d_114ens_1VALASPN72 - 75
d_115ens_1VALALAN77 - 81
d_116ens_1LEUPRON83 - 106
d_117ens_1ASPASPN108 - 139
d_118ens_1GLYARGN141 - 178
d_119ens_1ALAGLYN180 - 227
d_1110ens_1VALPRON229 - 242
d_1111ens_1GLYLEUN244 - 251
d_1112ens_1HISLEUN253 - 260
d_1113ens_1ASPHISN262 - 277
d_1114ens_1CYSLYSN279 - 293
d_1115ens_1ALAASNN296 - 297
d_1116ens_1VALVALN299
d_1117ens_1ALAALAN301
d_1118ens_1PHEASPN303 - 317
d_1119ens_1ILESERN319 - 321
d_1120ens_1LYSGLUN323 - 356
d_1121ens_1LYSTHRN358 - 368
d_1122ens_1ALACYSN370 - 378
d_1123ens_1THRALAN380 - 398
d_1124ens_1ALAALAN400 - 408
d_1125ens_1NADNADN
d_121ens_1ALAASNM4 - 6
d_122ens_1ASNSERM8 - 13
d_123ens_1ILEPROM15 - 71
d_124ens_1VALASPM73 - 76
d_125ens_1VALALAM78 - 82
d_126ens_1LEUPROM84 - 107
d_127ens_1ASPASPM109 - 140
d_128ens_1GLYARGM142 - 179
d_129ens_1ALAGLYM181 - 228
d_1210ens_1VALPROM230 - 243
d_1211ens_1GLYLEUM245 - 252
d_1212ens_1HISLEUM254 - 261
d_1213ens_1ASPHISM263 - 278
d_1214ens_1CYSLYSM280 - 294
d_1215ens_1ALAASNM297 - 298
d_1216ens_1VALVALM300
d_1217ens_1ALAALAM302
d_1218ens_1PHEASPM304 - 318
d_1219ens_1ILESERM320 - 322
d_1220ens_1LYSGLUM324 - 357
d_1221ens_1LYSTHRM359 - 369
d_1222ens_1ALACYSM371 - 379
d_1223ens_1THRALAM381 - 399
d_1224ens_1ALAALAM401 - 409
d_1225ens_1NADNADM

NCS oper:
IDCodeMatrixVector
1given(-0.800089237914, 0.597480526509, -0.0536118626501), (0.597016481914, 0.801805747293, 0.026055017387), (0.0585536651025, -0.0111608266233, -0.998221871255)124.187235097, -16.9349997109, 145.952796894
2given(0.433852609752, -0.46843858538, 0.769634461766), (-0.465557986257, -0.84789556234, -0.253631379754), (0.771380369496, -0.248270834152, -0.585947027013)-8.00267549833, 156.611722962, 108.891779201
3given(-0.99996445992, 0.00791532977438, -0.00290283500498), (-0.00614080455869, -0.919729526705, -0.392504634656), (-0.00577662668651, -0.392472859267, 0.919745445937)201.494864841, 128.999669552, 26.7074729336
4given(-0.428433269028, 0.113407229393, 0.896428320788), (0.465485781884, 0.878017384612, 0.111393263639), (-0.774446848308, 0.464999217893, -0.428961311198)39.2241709123, -53.7450888776, 216.169071118
5given(-0.669119238105, -0.112732606036, -0.734554834396), (-0.0924145461723, -0.968132931674, 0.232762063628), (-0.737386599318, 0.223629126334, 0.637378237)218.031963585, 107.820924464, 34.4646142928
6given(0.667021218176, 0.393659460317, -0.632546380755), (0.0985694391142, 0.79492044527, 0.598653114386), (0.73848951257, -0.461664071588, 0.491426011552)49.5724261977, -29.8316838016, -67.9338046193
7given(-0.453989472257, 0.467189168425, -0.758701416887), (0.1463928867, 0.879049030828, 0.453698053912), (0.878898561726, 0.0949056494985, -0.467472176594)210.237276669, -59.694158154, 69.6163592586
8given(0.428924642911, -0.126243225, -0.89447543222), (-0.134828892031, -0.988041951658, 0.0747948637095), (-0.893221596569, 0.0885197712668, -0.44081677545)162.18486092, 93.0547292508, 246.205966646
9given(0.788525815612, -0.533623748906, -0.305733107002), (-0.610087292434, -0.741439922939, -0.279392799267), (-0.077592098333, 0.406832318377, -0.910201588111)41.5344039763, 206.953461525, 131.745138663
10given(0.387224672995, 0.133448910329, 0.912276515622), (-0.126556546266, 0.987796943253, -0.0907779681287), (-0.913258174462, -0.0803030960332, 0.399388181531)-82.4036009423, 61.0353797752, 92.1271029825
11given(-0.364639782142, -0.476803761776, 0.799809978705), (0.107177113623, -0.874732512287, -0.472605647727), (0.924959942697, -0.0866094954622, 0.370064723665)33.2706123428, 161.863730765, -90.1829271519

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Components

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Protein , 1 types, 12 molecules ABCDEFGHIJKL

#1: Protein
Glutamate dehydrogenase


Mass: 44894.016 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: 11433210, MTR_5g013470, MtrunA17_Chr5g0399821 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): -GOLD / References: UniProt: G7JYL4

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Non-polymers , 10 types, 1287 molecules

#2: Chemical
ChemComp-A1H40 / 3-(1~{H}-1,2,3,4-tetrazol-5-yl)benzoic acid


Mass: 190.159 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C8H6N4O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 29 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#6: Chemical
ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: C4H12NO3 / Comment: pH buffer*YM
#7: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#9: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#10: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1208 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.97 Å3/Da / Density % sol: 58.58 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 60mM Divalents (MgCl2, CaCl2) 0.1M Tris (base)/;Bicine pH 8.5 20% v/v PEG 500* MME; 10 % w/v PEG 20000, 10% etylene glycol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 8, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.3→75.86 Å / Num. obs: 230242 / % possible obs: 91 % / Redundancy: 1.99 % / Biso Wilson estimate: 33.63 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.073 / Rrim(I) all: 0.103 / Net I/σ(I): 8.7
Reflection shellResolution: 2.3→2.4 Å / Redundancy: 1.93 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 11515 / CC1/2: 0.72 / Rpim(I) all: 0.43 / % possible all: 62.5

-
Processing

Software
NameVersionClassification
PHENIX1.18.1_3865refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→65.69 Å / SU ML: 0.2755 / Cross valid method: FREE R-VALUE / σ(F): 1.95 / Phase error: 21.4253
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.188 1151 0.5 %
Rwork0.1685 229013 -
obs0.1686 230164 84.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 48.34 Å2
Refinement stepCycle: LAST / Resolution: 2.3→65.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms38008 0 350 1208 39566
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008139127
X-RAY DIFFRACTIONf_angle_d0.97652994
X-RAY DIFFRACTIONf_chiral_restr0.06175879
X-RAY DIFFRACTIONf_plane_restr0.00666882
X-RAY DIFFRACTIONf_dihedral_angle_d17.184114534
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.369600332508
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS0.421230121326
ens_1d_4AX-RAY DIFFRACTIONTorsion NCS0.463070540616
ens_1d_5AX-RAY DIFFRACTIONTorsion NCS0.490592434333
ens_1d_6AX-RAY DIFFRACTIONTorsion NCS0.390427016765
ens_1d_7AX-RAY DIFFRACTIONTorsion NCS0.506317424266
ens_1d_8AX-RAY DIFFRACTIONTorsion NCS0.574101485672
ens_1d_9AX-RAY DIFFRACTIONTorsion NCS0.502662833801
ens_1d_10AX-RAY DIFFRACTIONTorsion NCS0.68628245394
ens_1d_11AX-RAY DIFFRACTIONTorsion NCS0.534758978147
ens_1d_12AX-RAY DIFFRACTIONTorsion NCS0.659431875802
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.40.3169570.243111167X-RAY DIFFRACTION32.8
2.4-2.530.27861200.236524208X-RAY DIFFRACTION71.01
2.53-2.690.25191570.218931051X-RAY DIFFRACTION91.01
2.69-2.890.23291650.201832833X-RAY DIFFRACTION96.48
2.89-3.180.22511650.191132825X-RAY DIFFRACTION96.37
3.18-3.650.20161630.167932253X-RAY DIFFRACTION94.57
3.65-4.590.13221590.134732021X-RAY DIFFRACTION93.95
4.59-65.690.16061650.144932655X-RAY DIFFRACTION95.91
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.51420091196-0.1846161642220.4036404524011.567257511260.08555038896850.8000977814670.1139885300520.249939154585-0.0239780398265-0.221855716728-0.123654241003-0.02430408006790.08447861654920.04507296147690.01082828356890.208838857032-0.01054332987540.0526162368930.203494200195-0.0281860998370.203026966789102.86459605737.498586034586.2881824643
21.30495525883-0.7401638365740.1494839906282.30617688740.805160303341.562257173030.257330325440.295040998071-0.405764094894-0.555409329369-0.2852360645860.3704134279570.126169170327-0.035388874305-0.02364989980950.4424686739630.0296089858891-0.04935157919210.254160391666-0.1422639820910.38887168820698.893586297414.702988999976.6883427484
32.43985831627-1.21702290305-0.0006003540886510.637036288136-0.591897543144.567863036820.2459629568990.146267520722-0.5127122247-0.477237713025-0.1038590939830.330538121051-0.0914899815732-0.0381573774985-0.184041566380.241300718601-0.0562440584613-0.04341981847170.260983577679-0.07933312583880.39054640696681.533269272831.715064142684.2923867309
41.51629522542-0.7550323181610.3865844601051.99650049597-0.4137099054160.928249886289-0.0638075524378-0.1989254002750.09330085621530.2694400833580.004343797587320.0566094985213-0.180558548197-0.08905980669430.05785606533280.251119934997-0.04736439304530.06239631016020.336127108912-0.03970210910150.18625371226759.710169207276.763774581465.3746138005
51.363897627710.254919645012-0.1242143075320.796857937727-0.4025634101041.31911489707-0.00610488198871-0.0458335599206-0.1308491759920.006044391163650.04012862642430.08266401619950.1022971752-0.00841894198566-0.03005232466240.168389142782-0.02542255426370.04418962039980.194991304581-0.01373841735390.22104362300352.347204625156.342214950374.0329964762
61.26992682521-0.2549086172790.382526668161.48336265733-0.2009736666511.10207885638-0.0351268136194-0.2908027823730.03347358263550.2421332062540.02179423582460.0796470426798-0.0957767807661-0.1715287463340.0005276674902660.328795059663-0.03360453593910.05653741289550.291234090835-0.03757444136660.16230411739687.248980591755.7876349686128.580550887
70.4451683680.07546533671110.09311683750621.272464638651.109246119552.14016161677-0.0576049006968-0.1080259529790.1147069305660.121274141025-0.08155818575640.125790994931-0.32088677972-0.2433712528680.1275821300250.4452804076190.03495034751560.01111327952850.24964641915-0.04257085654050.25660127747884.602384855779.0404183874134.421961243
84.120617871842.44026425981-0.4306615363162.373737874240.09909735803340.841971085611-0.01924283338310.2810795798180.368373065975-0.3003799549210.0960722956631-0.0837810688289-0.1953966402070.136518377692-0.07121958249220.249113217137-0.02715819725260.06692692269980.2659173062770.04497241218320.291842378898109.97575686860.484665637883.7698325609
92.698363205780.5885664110580.4439200428451.38180773996-0.01752854627381.174314664230.001115635611030.09489394198390.086864715015-0.0636744425096-0.0130024243896-0.0332775479154-0.07465759488580.0193766503670.00648605960980.1572565732190.008576259483550.01772239421760.1529046626890.002526054707880.16286456529694.466652910261.154690049794.8130174185
102.35670557304-0.284911931941.069713701563.49107056312-0.3120524291223.50691287414-0.004828781692650.2949107393730.671762869553-0.565653146602-0.099278412993-0.0869741927995-0.66237192156-0.246364734670.06137161948460.5642315028270.06925985730420.0209864921360.2865599656660.08979556429120.483397128518101.70278706589.775889753484.8742865331
111.08411313771-0.940188697924-0.1167747485671.725941504370.05388477959161.436218554870.100795445652-0.05075752004320.367234461153-0.0383851537305-0.0812723406792-0.40741973333-0.3629375070760.162679258232-0.02093633447120.230933895585-0.07277768184270.004149804180430.200054757756-0.01081992338490.324601111173112.31768803872.8142131598.8417820682
120.901316652685-0.2969014194020.3266983356212.03434808078-0.5688078297952.30469439165-0.0036574437971-0.184880373609-0.1354043410570.3114474817330.02572504247990.2704513776420.0953319604045-0.369450613828-0.08052839905570.240052966617-0.09063307636540.07383828157820.293863543427-0.003073604984250.24080007441676.940408993836.7844327509116.889218436
131.743313824310.540549872050.06779009680632.280280126351.098593377242.643718950780.11091243491-0.107282631114-0.3988096604510.363213059518-0.3416643049120.6055261487340.732768518494-1.04897228828-0.04664545560720.405749753106-0.2859024710060.1443033054880.617079427017-0.01640279509630.54657748858869.019276940914.5605150116115.50226722
141.942394612140.1493866939490.6285790586241.43533046986-0.1584920974571.13690792525-0.001471623573950.136945613247-0.0881087159818-0.304637038996-0.134010425059-0.2178603189790.0337333008620.3227871923290.1186205611340.4064663074880.008424173747210.09835166900090.3166176673190.05760803428310.20055556707181.510348531382.091833482722.0322394126
150.629559225980.0917144399564-0.4118405218981.64817382038-1.305247617181.89180291457-0.07706148292460.1038173176980.159620949933-0.209530619387-0.316153982239-0.542247055697-0.09904406396430.5059053778790.05158754716110.408932747147-0.08292749091940.08374524858580.4362224431910.1503801052170.39619366743994.3304652742100.83677676116.0945309177
161.425546129850.4328357493391.041218501340.974083519327-0.08833546630271.805563548140.05846223394230.130526339384-0.181638565641-0.259545790122-0.0802368059239-0.1745424451340.2890263875190.265106465693-0.009339419321550.3255120958380.07111862040170.06344375137380.2638749979040.03824296710790.23187309837277.447420991861.293907244234.6157179586
171.38171720627-0.2359315708720.2731843097622.22185086050.09144501581192.704245094030.257333259553-0.0542533304774-0.516805745244-0.2663017592370.00348219880905-0.2491766318541.479353176230.470850719574-0.03784343495960.9869102716010.216315967484-0.09718664930530.350081923005-0.001361872061670.47253694478771.876978447537.841502066132.9478142921
181.68626568875-0.137382069526-0.5491193918951.28457709660.4118774627871.95983750154-0.0678182639048-0.329026072022-0.2441390500130.249953309119-0.038299013662-0.2249148507620.1539530971870.2742187033610.1128129577510.319357581829-0.0223557758531-0.04950934250330.2480399755290.09701498986680.305731877915115.64556157727.3965303333123.147680348
192.264484785780.5543444197280.05794945910311.70612460079-0.5029221296571.443313903920.0393390481539-0.599228601978-0.8558816386470.18441321485-0.152040894857-0.506550282820.5800656936230.1710743592450.02621221431630.5923331874590.0220856103089-0.03965739641720.366707238160.2252773850260.672669104954115.1076751894.45590546984120.109044038
200.88151165301-0.0921955708704-0.311375560691.11512914379-0.1502675277161.810502512330.0424169981305-0.187833099796-0.02623410269060.227020768129-0.0640338230199-0.294947422810.01064837788520.2899112801510.01442761874570.239317292583-0.0511819709146-0.06065151432580.2981343123970.03556228205690.351115973043123.76726518650.0714009129118.504953398
211.706857373720.3758997973140.3680253182041.9820227786-0.6637092611371.652781941620.0404157714939-0.1724779349230.2071347866970.45233301797-0.388438771247-0.848291605856-0.3990493208020.8123526001050.06243118065420.463937620014-0.202866847777-0.1815607897240.662197968620.07183688197990.692933861114133.37966842869.9270046226128.334815911
221.74651611892-0.723043970170.1754112881862.39215932285-0.3939884441621.09410403245-0.0847320020484-0.2836532794470.1978926006060.323759597568-0.0485418545427-0.125211995645-0.2984127271640.1679740150520.07671230095160.288729499147-0.0774071766156-0.03500598386380.313274533548-0.01861475306240.19927950401977.133363350192.835869158258.8595552335
231.737167566840.101435450548-0.8017112203052.213892817220.4695441140561.98135570060.0235608860477-0.5104658719270.7443306485780.6671543661840.17578824545-0.567213054046-0.4399178047640.7433553707290.1870695661960.705542885822-0.114715405494-0.2458255267730.564774901973-0.2193168022670.62502908322685.5046984693115.12767784761.5866675123
241.17616728431-0.00359423708011-0.6888657682281.48689814082-0.110839928642.102492872060.0161660166110.08526914665720.059276128289-0.296105829578-0.02945623655460.405613720310.0236236608258-0.4401686331360.00298695022940.291834218512-0.00693846602154-0.1131813227550.341509226012-0.05360733802660.32577299084841.401219133977.296956104329.7263542992
251.46052174638-0.710867876088-0.3939110594042.633945511270.511849927681.061429862890.09151379893010.375399869392-0.556167219493-0.407276147507-0.401680299721.435462292750.249602394504-0.68652941805-0.014617043660.447732648039-0.120362719323-0.2216263061610.704584499769-0.2312895850890.96760787637528.073959202658.075649172533.1645953034
261.243772722840.0161742140716-0.431885417851.29918936083-0.5297675440522.59987941791-0.0129661015476-0.04018898575980.134662094276-0.1811522076890.01494634476030.285128978941-0.325517389795-0.249632102411-0.005181047346270.310548789470.0614533030447-0.04340016062490.251720586609-0.05364317518190.34596821319248.3683132717100.23825851734.6141036107
272.237103371040.1892655234570.9057788769592.448653295750.7616450099131.8709374708-0.273053827485-0.1746685987871.03952426555-0.655577784195-0.231978733390.75024762041-1.00232728105-0.4856654970660.0405908868510.8583845236730.19332539811-0.2367460081980.409467508995-0.09912727000440.88189128221251.3404444408122.0976685525.4752473631
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 2 through 161 )AA2 - 1611 - 161
22chain 'A' and (resid 162 through 384 )AA162 - 384162 - 384
33chain 'A' and (resid 385 through 411 )AA385 - 411385 - 411
44chain 'B' and (resid 2 through 161 )BJ2 - 1611 - 160
55chain 'B' and (resid 162 through 411 )BJ162 - 411161 - 410
66chain 'C' and (resid 2 through 183 )CT2 - 1831 - 182
77chain 'C' and (resid 184 through 411 )CT184 - 411183 - 410
88chain 'D' and (resid 0 through 42 )DAB0 - 421 - 43
99chain 'D' and (resid 43 through 183 )DAB43 - 18344 - 184
1010chain 'D' and (resid 184 through 338 )DAB184 - 338185 - 339
1111chain 'D' and (resid 339 through 411 )DAB339 - 411340 - 412
1212chain 'E' and (resid 3 through 161 )EF3 - 1611 - 159
1313chain 'E' and (resid 162 through 411 )EF162 - 411160 - 409
1414chain 'F' and (resid 2 through 161 )FG2 - 1611 - 160
1515chain 'F' and (resid 162 through 411 )FG162 - 411161 - 410
1616chain 'G' and (resid 2 through 183 )GH2 - 1831 - 183
1717chain 'G' and (resid 184 through 411 )GH184 - 411184 - 411
1818chain 'H' and (resid 2 through 161 )HI2 - 1611 - 160
1919chain 'H' and (resid 162 through 411 )HI162 - 411161 - 411
2020chain 'I' and (resid 3 through 183 )IK3 - 1831 - 181
2121chain 'I' and (resid 184 through 411 )IK184 - 411182 - 409
2222chain 'J' and (resid 3 through 183 )JL3 - 1831 - 181
2323chain 'J' and (resid 184 through 411 )JL184 - 411182 - 409
2424chain 'K' and (resid 4 through 161 )KN4 - 1611 - 158
2525chain 'K' and (resid 162 through 411 )KN162 - 411159 - 408
2626chain 'L' and (resid 3 through 183 )LM3 - 1831 - 181
2727chain 'L' and (resid 184 through 411 )LM184 - 411182 - 409

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