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- PDB-8qhn: Streptococcus pyogenes GapN in complex with NADPH and erythrose-4... -

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Basic information

Entry
Database: PDB / ID: 8qhn
TitleStreptococcus pyogenes GapN in complex with NADPH and erythrose-4-phosphate
Components(NADP-dependent glyceraldehyde-3-phosphate ...) x 2
KeywordsOXIDOREDUCTASE / GapN / NADPH / G3H / Substrate
Function / homology
Function and homology information


glyceraldehyde-3-phosphate dehydrogenase (NADP+) / glyceraldehyde-3-phosphate dehydrogenase (NADP+) (non-phosphorylating) activity / lactaldehyde dehydrogenase (NAD+) activity
Similarity search - Function
: / Aldehyde dehydrogenase, cysteine active site / Aldehyde dehydrogenases cysteine active site. / Aldehyde dehydrogenase domain / Aldehyde dehydrogenase family / Aldehyde dehydrogenase, C-terminal / Aldehyde dehydrogenase, N-terminal / Aldehyde/histidinol dehydrogenase
Similarity search - Domain/homology
ERYTHOSE-4-PHOSPHATE / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / NADP-dependent glyceraldehyde-3-phosphate dehydrogenase
Similarity search - Component
Biological speciesStreptococcus pyogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å
AuthorsWirsing, R. / Schindelin, H.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG) Germany
Citation
Journal: To Be Published
Title: Streptococcus pyogenes GapN in complex with NADPH and erythrose-4-phosphate
Authors: Wirsing, R. / Schindelin, H.
#1: Journal: Acta Crystallogr D Biol Crystallogr / Year: 2012
Title: Towards automated crystallographic structure refinement with phenix.refine.
Authors: Afonine, P.V. / Grosse-Kunstleve, R.W. / Echols, N. / Headd, J.J. / Moriarty, N.W. / Mustyakimov, M. / Terwilliger, T.C. / Urzhumtsev, A. / Zwart, P.H. / Adams, P.D.
History
DepositionSep 8, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 4, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NADP-dependent glyceraldehyde-3-phosphate dehydrogenase
B: NADP-dependent glyceraldehyde-3-phosphate dehydrogenase
C: NADP-dependent glyceraldehyde-3-phosphate dehydrogenase
D: NADP-dependent glyceraldehyde-3-phosphate dehydrogenase
E: NADP-dependent glyceraldehyde-3-phosphate dehydrogenase
F: NADP-dependent glyceraldehyde-3-phosphate dehydrogenase
G: NADP-dependent glyceraldehyde-3-phosphate dehydrogenase
H: NADP-dependent glyceraldehyde-3-phosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)409,02130
Polymers404,2818
Non-polymers4,73922
Water49,5232749
1
A: NADP-dependent glyceraldehyde-3-phosphate dehydrogenase
B: NADP-dependent glyceraldehyde-3-phosphate dehydrogenase
C: NADP-dependent glyceraldehyde-3-phosphate dehydrogenase
D: NADP-dependent glyceraldehyde-3-phosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)204,86315
Polymers202,4394
Non-polymers2,42411
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: NADP-dependent glyceraldehyde-3-phosphate dehydrogenase
F: NADP-dependent glyceraldehyde-3-phosphate dehydrogenase
G: NADP-dependent glyceraldehyde-3-phosphate dehydrogenase
H: NADP-dependent glyceraldehyde-3-phosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)204,15715
Polymers201,8424
Non-polymers2,31611
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)97.521, 98.476, 102.981
Angle α, β, γ (deg.)77.766, 76.083, 67.792
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 2 through 11 or resid 13...
d_2ens_1(chain "C" and (resid 2 through 11 or resid 13...
d_3ens_1(chain "D" and (resid 2 through 11 or resid 13...
d_4ens_1(chain "E" and (resid 2 through 11 or resid 13...
d_5ens_1(chain "G" and (resid 2 through 11 or resid 13...
d_6ens_1(chain "H" and (resid 2 through 11 or resid 13...
d_1ens_2(chain "B" and (resid 2 through 11 or resid 13...
d_2ens_2(chain "F" and (resid 2 through 11 or resid 13...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ens_1ALAALAGLYGLYAA2 - 112 - 11
d_12ens_1TRPTRPTHRTHRAA13 - 2113 - 21
d_13ens_1TYRTYRGLYGLYAA23 - 3223 - 32
d_14ens_1VALVALALAALAAA34 - 4734 - 47
d_15ens_1ALAALATRPTRPAA49 - 5649 - 56
d_16ens_1THRTHRTYRTYRAA58 - 6158 - 61
d_17ens_1GLUGLUALAALAAA63 - 10563 - 105
d_18ens_1ILEILEGLYGLYAA107 - 115107 - 115
d_19ens_1ARGARGARGARGAA117117
d_110ens_1GLUGLUILEILEAA119 - 184119 - 184
d_111ens_1GLYGLYGLYGLYAA186 - 208186 - 208
d_112ens_1GLYGLYHISHISAA210 - 220210 - 220
d_113ens_1ALAALAGLYGLYAA222 - 235222 - 235
d_114ens_1GLYGLYGLYGLYAA237 - 243237 - 243
d_115ens_1ARGARGASPASPAA245 - 255245 - 255
d_116ens_1ALAALAARGARGAA257 - 283257 - 283
d_117ens_1THRTHRVALVALAA285 - 292285 - 292
d_118ens_1LYSLYSGLYGLYAA295 - 314295 - 314
d_119ens_1PROPROTHRTHRAA316 - 328316 - 328
d_120ens_1ALAALAILEILEAA330 - 359330 - 359
d_121ens_1PROPROTHRTHRAA361 - 369361 - 369
d_122ens_1METMETVALVALAA371 - 388371 - 388
d_123ens_1THRTHRTHRTHRAA390390
d_124ens_1GLUGLUASNASNAA392 - 432392 - 432
d_125ens_1LYSLYSTYRTYRAA434 - 459434 - 459
d_126ens_1ILEILEGLNGLNAA461 - 475461 - 475
d_21ens_1ALAALAGLYGLYCC2 - 112 - 11
d_22ens_1TRPTRPTHRTHRCC13 - 2113 - 21
d_23ens_1TYRTYRGLYGLYCC23 - 3223 - 32
d_24ens_1VALVALALAALACC34 - 4734 - 47
d_25ens_1ALAALATRPTRPCC49 - 5649 - 56
d_26ens_1THRTHRTYRTYRCC58 - 6158 - 61
d_27ens_1GLUGLUALAALACC63 - 10563 - 105
d_28ens_1ILEILEGLYGLYCC107 - 115107 - 115
d_29ens_1ARGARGARGARGCC117117
d_210ens_1GLUGLUILEILECC119 - 184119 - 184
d_211ens_1GLYGLYGLYGLYCC186 - 208186 - 208
d_212ens_1GLYGLYHISHISCC210 - 220210 - 220
d_213ens_1ALAALAGLYGLYCC222 - 235222 - 235
d_214ens_1GLYGLYGLYGLYCC237 - 243237 - 243
d_215ens_1ARGARGASPASPCC245 - 255245 - 255
d_216ens_1ALAALAARGARGCC257 - 283257 - 283
d_217ens_1THRTHRVALVALCC285 - 292285 - 292
d_218ens_1LYSLYSGLYGLYCC295 - 314295 - 314
d_219ens_1PROPROTHRTHRCC316 - 328316 - 328
d_220ens_1ALAALAILEILECC330 - 359330 - 359
d_221ens_1PROPROTHRTHRCC361 - 369361 - 369
d_222ens_1METMETVALVALCC371 - 388371 - 388
d_223ens_1THRTHRTHRTHRCC390390
d_224ens_1GLUGLUASNASNCC392 - 432392 - 432
d_225ens_1LYSLYSTYRTYRCC434 - 459434 - 459
d_226ens_1ILEILEGLNGLNCC461 - 475461 - 475
d_31ens_1ALAALAGLYGLYDD2 - 117 - 16
d_32ens_1TRPTRPTHRTHRDD13 - 2118 - 26
d_33ens_1TYRTYRGLYGLYDD23 - 3228 - 37
d_34ens_1VALVALALAALADD34 - 4739 - 52
d_35ens_1ALAALATRPTRPDD49 - 5654 - 61
d_36ens_1THRTHRTYRTYRDD58 - 6163 - 66
d_37ens_1GLUGLUALAALADD63 - 10568 - 110
d_38ens_1ILEILEGLYGLYDD107 - 115112 - 120
d_39ens_1ARGARGARGARGDD117122
d_310ens_1GLUGLUILEILEDD119 - 184124 - 189
d_311ens_1GLYGLYGLYGLYDD186 - 208191 - 213
d_312ens_1GLYGLYHISHISDD210 - 220215 - 225
d_313ens_1ALAALAGLYGLYDD222 - 235227 - 240
d_314ens_1GLYGLYGLYGLYDD237 - 243242 - 248
d_315ens_1ARGARGASPASPDD245 - 255250 - 260
d_316ens_1ALAALAARGARGDD257 - 283262 - 288
d_317ens_1THRTHRVALVALDD285 - 292290 - 297
d_318ens_1LYSLYSGLYGLYDD295 - 314300 - 319
d_319ens_1PROPROTHRTHRDD316 - 328321 - 333
d_320ens_1ALAALAILEILEDD330 - 359335 - 364
d_321ens_1PROPROTHRTHRDD361 - 369366 - 374
d_322ens_1METMETVALVALDD371 - 388376 - 393
d_323ens_1THRTHRTHRTHRDD390395
d_324ens_1GLUGLUASNASNDD392 - 432397 - 437
d_325ens_1LYSLYSTYRTYRDD434 - 459439 - 464
d_326ens_1ILEILEGLNGLNDD461 - 475466 - 480
d_41ens_1ALAALAGLYGLYEE2 - 112 - 11
d_42ens_1TRPTRPTHRTHREE13 - 2113 - 21
d_43ens_1TYRTYRGLYGLYEE23 - 3223 - 32
d_44ens_1VALVALALAALAEE34 - 4734 - 47
d_45ens_1ALAALATRPTRPEE49 - 5649 - 56
d_46ens_1THRTHRTYRTYREE58 - 6158 - 61
d_47ens_1GLUGLUALAALAEE63 - 10563 - 105
d_48ens_1ILEILEGLYGLYEE107 - 115107 - 115
d_49ens_1ARGARGARGARGEE117117
d_410ens_1GLUGLUILEILEEE119 - 184119 - 184
d_411ens_1GLYGLYGLYGLYEE186 - 208186 - 208
d_412ens_1GLYGLYHISHISEE210 - 220210 - 220
d_413ens_1ALAALAGLYGLYEE222 - 235222 - 235
d_414ens_1GLYGLYGLYGLYEE237 - 243237 - 243
d_415ens_1ARGARGASPASPEE245 - 255245 - 255
d_416ens_1ALAALAARGARGEE257 - 283257 - 283
d_417ens_1THRTHRVALVALEE285 - 292285 - 292
d_418ens_1LYSLYSGLYGLYEE295 - 314295 - 314
d_419ens_1PROPROTHRTHREE316 - 328316 - 328
d_420ens_1ALAALAILEILEEE330 - 359330 - 359
d_421ens_1PROPROTHRTHREE361 - 369361 - 369
d_422ens_1METMETVALVALEE371 - 388371 - 388
d_423ens_1THRTHRTHRTHREE390390
d_424ens_1GLUGLUASNASNEE392 - 432392 - 432
d_425ens_1LYSLYSTYRTYREE434 - 459434 - 459
d_426ens_1ILEILEGLNGLNEE461 - 475461 - 475
d_51ens_1ALAALAGLYGLYGG2 - 112 - 11
d_52ens_1TRPTRPTHRTHRGG13 - 2113 - 21
d_53ens_1TYRTYRGLYGLYGG23 - 3223 - 32
d_54ens_1VALVALALAALAGG34 - 4734 - 47
d_55ens_1ALAALATRPTRPGG49 - 5649 - 56
d_56ens_1THRTHRTYRTYRGG58 - 6158 - 61
d_57ens_1GLUGLUALAALAGG63 - 10563 - 105
d_58ens_1ILEILEGLYGLYGG107 - 115107 - 115
d_59ens_1ARGARGARGARGGG117117
d_510ens_1GLUGLUILEILEGG119 - 184119 - 184
d_511ens_1GLYGLYGLYGLYGG186 - 208186 - 208
d_512ens_1GLYGLYHISHISGG210 - 220210 - 220
d_513ens_1ALAALAGLYGLYGG222 - 235222 - 235
d_514ens_1GLYGLYGLYGLYGG237 - 243237 - 243
d_515ens_1ARGARGASPASPGG245 - 255245 - 255
d_516ens_1ALAALAARGARGGG257 - 283257 - 283
d_517ens_1THRTHRVALVALGG285 - 292285 - 292
d_518ens_1LYSLYSGLYGLYGG295 - 314295 - 314
d_519ens_1PROPROTHRTHRGG316 - 328316 - 328
d_520ens_1ALAALAILEILEGG330 - 359330 - 359
d_521ens_1PROPROTHRTHRGG361 - 369361 - 369
d_522ens_1METMETVALVALGG371 - 388371 - 388
d_523ens_1THRTHRTHRTHRGG390390
d_524ens_1GLUGLUASNASNGG392 - 432392 - 432
d_525ens_1LYSLYSTYRTYRGG434 - 459434 - 459
d_526ens_1ILEILEGLNGLNGG461 - 475461 - 475
d_61ens_1ALAALAGLYGLYHH2 - 112 - 11
d_62ens_1TRPTRPTHRTHRHH13 - 2113 - 21
d_63ens_1TYRTYRGLYGLYHH23 - 3223 - 32
d_64ens_1VALVALALAALAHH34 - 4734 - 47
d_65ens_1ALAALATRPTRPHH49 - 5649 - 56
d_66ens_1THRTHRTYRTYRHH58 - 6158 - 61
d_67ens_1GLUGLUALAALAHH63 - 10563 - 105
d_68ens_1ILEILEGLYGLYHH107 - 115107 - 115
d_69ens_1ARGARGARGARGHH117117
d_610ens_1GLUGLUILEILEHH119 - 184119 - 184
d_611ens_1GLYGLYGLYGLYHH186 - 208186 - 208
d_612ens_1GLYGLYHISHISHH210 - 220210 - 220
d_613ens_1ALAALAGLYGLYHH222 - 235222 - 235
d_614ens_1GLYGLYGLYGLYHH237 - 243237 - 243
d_615ens_1ARGARGASPASPHH245 - 255245 - 255
d_616ens_1ALAALAARGARGHH257 - 283257 - 283
d_617ens_1THRTHRVALVALHH285 - 292285 - 292
d_618ens_1LYSLYSGLYGLYHH295 - 314295 - 314
d_619ens_1PROPROTHRTHRHH316 - 328316 - 328
d_620ens_1ALAALAILEILEHH330 - 359330 - 359
d_621ens_1PROPROTHRTHRHH361 - 369361 - 369
d_622ens_1METMETVALVALHH371 - 388371 - 388
d_623ens_1THRTHRTHRTHRHH390390
d_624ens_1GLUGLUASNASNHH392 - 432392 - 432
d_625ens_1LYSLYSTYRTYRHH434 - 459434 - 459
d_626ens_1ILEILEGLNGLNHH461 - 475461 - 475
d_11ens_2ALAALAGLYGLYBB2 - 112 - 11
d_12ens_2TRPTRPALAALABB13 - 7913 - 79
d_13ens_2ILEILEGLYGLYBB82 - 23582 - 235
d_14ens_2GLYGLYASPASPBB237 - 255237 - 255
d_15ens_2ALAALAALAALABB257 - 266257 - 266
d_16ens_2ALAALAMETMETBB268 - 293268 - 293
d_17ens_2LYSLYSPROPROBB295 - 316295 - 316
d_18ens_2ASPASPILEILEBB318 - 359318 - 359
d_19ens_2PROPROVALVALBB361 - 391361 - 391
d_110ens_2GLUGLUALAALABB393 - 407393 - 407
d_111ens_2ILEILEILEILEBB409409
d_112ens_2THRTHRASNASNBB411 - 413411 - 413
d_113ens_2PROPROASNASNBB415 - 432415 - 432
d_114ens_2LYSLYSTYRTYRBB434 - 459434 - 459
d_115ens_2ILEILEGLNGLNBB461 - 475461 - 475
d_116ens_2NAPNAPNAPNAPBL501
d_117ens_2GOLGOLGOLGOLBM502
d_21ens_2ALAALAGLYGLYFF2 - 112 - 11
d_22ens_2TRPTRPALAALAFF13 - 7913 - 79
d_23ens_2ILEILEGLYGLYFF82 - 23582 - 235
d_24ens_2GLYGLYASPASPFF237 - 255237 - 255
d_25ens_2ALAALAALAALAFF257 - 266257 - 266
d_26ens_2ALAALAMETMETFF268 - 293268 - 293
d_27ens_2LYSLYSPROPROFF295 - 316295 - 316
d_28ens_2ASPASPILEILEFF318 - 359318 - 359
d_29ens_2PROPROVALVALFF361 - 391361 - 391
d_210ens_2GLUGLUALAALAFF393 - 407393 - 407
d_211ens_2ILEILEILEILEFF409409
d_212ens_2THRTHRASNASNFF411 - 413411 - 413
d_213ens_2PROPROASNASNFF415 - 432415 - 432
d_214ens_2LYSLYSTYRTYRFF434 - 459434 - 459
d_215ens_2ILEILEGLNGLNFF461 - 475461 - 475
d_216ens_2NAPNAPNAPNAPFW502
d_217ens_2GOLGOLGOLGOLFX503

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(-0.549624471812, -0.833797053807, -0.0519173675027), (-0.834090340855, 0.544200225059, 0.0902187249837), (-0.0469706640101, 0.0928901938234, -0.994567830072)-51.232156557, -23.917748381, -58.7864615684
2given(-0.422558738308, 0.252042645264, 0.870585215615), (0.272713041026, -0.880681837805, 0.387333316169), (0.86433310126, 0.401091019008, 0.303404489975)9.75617169328, -36.6532630089, 4.80731498017
3given(-0.999862637406, -0.0145757988363, -0.00789001947986), (-0.0128266420762, 0.378996125925, 0.925309361126), (-0.0104968362928, 0.925283460687, -0.379131024589)-18.8856719383, -36.5585675094, -66.3710817242
4given(0.54499374262, 0.836405217711, 0.0583792111128), (-0.338778979087, 0.283366352917, -0.897180201165), (-0.766948905621, 0.469179946097, 0.437789394968)33.0412759865, -100.091186054, -67.00989461
5given(0.417443944418, -0.253421367009, -0.872650081082), (0.907083100933, 0.0589005013409, 0.416810483247), (-0.054229155177, -0.965561153778, 0.254461897037)-28.3383352353, -45.5986819818, -101.320545492
6given(-0.999977668418, -0.000695236568112, -0.00664675198041), (-0.00644463472018, 0.363581691325, 0.931540026202), (0.00176899663598, 0.931562059328, -0.363578052516)-18.6140133773, -36.7410268302, -65.4759979165

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Components

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NADP-dependent glyceraldehyde-3-phosphate ... , 2 types, 8 molecules ABCEFGHD

#1: Protein
NADP-dependent glyceraldehyde-3-phosphate dehydrogenase


Mass: 50460.457 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pyogenes (bacteria) / Gene: E0F67_08075 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A4U9C786
#2: Protein NADP-dependent glyceraldehyde-3-phosphate dehydrogenase


Mass: 51058.055 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Strep-tag at N-terminus: -10 to -5 are visible in chain D
Source: (gene. exp.) Streptococcus pyogenes (bacteria) / Gene: E0F67_08075 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A4U9C786

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Sugars , 1 types, 1 molecules

#4: Sugar ChemComp-E4P / ERYTHOSE-4-PHOSPHATE


Type: saccharide / Mass: 200.084 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H9O7P / Feature type: SUBJECT OF INVESTIGATION

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Non-polymers , 3 types, 2770 molecules

#3: Chemical
ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H28N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2749 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 1.99 Å3/Da / Density % sol: 38.31 % / Description: Prism
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: Precipitant: 0.01 M PBS buffer 0.16-0.185 M (NH4)3-citrate 18-21% (w/v) PEG 3350 1 mM E4P Protein concentration: 8 mg/ml in PBS buffer

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 12M / Detector: PIXEL / Date: Mar 9, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.989→48.404 Å / Num. obs: 186084 / % possible obs: 79.35 % / Redundancy: 3.72 % / Biso Wilson estimate: 20.31 Å2 / CC1/2: 0.9977 / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.055 / Rrim(I) all: 0.108 / Net I/σ(I): 7.403
Reflection shellResolution: 1.989→2.112 Å / Redundancy: 3.73 % / Rmerge(I) obs: 0.564 / Mean I/σ(I) obs: 1.545 / Num. unique obs: 9305 / CC1/2: 0.7575 / Rpim(I) all: 0.336 / Rrim(I) all: 0.658 / % possible all: 24.01

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDSdata reduction
XDSdata scaling
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.99→41.15 Å / SU ML: 0.2219 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 22.0939
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2108 9019 4.85 %
Rwork0.1662 177012 -
obs0.1684 186031 79.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.82 Å2
Refinement stepCycle: LAST / Resolution: 1.99→41.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms28387 0 306 2749 31442
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003629479
X-RAY DIFFRACTIONf_angle_d0.544540081
X-RAY DIFFRACTIONf_chiral_restr0.04394722
X-RAY DIFFRACTIONf_plane_restr0.00545159
X-RAY DIFFRACTIONf_dihedral_angle_d11.920811039
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS0.564589575548
ens_1d_3AAX-RAY DIFFRACTIONTorsion NCS0.495871335837
ens_1d_4AAX-RAY DIFFRACTIONTorsion NCS0.443592846889
ens_1d_5AAX-RAY DIFFRACTIONTorsion NCS0.600864214554
ens_1d_6AAX-RAY DIFFRACTIONTorsion NCS0.605352266243
ens_2d_2BBX-RAY DIFFRACTIONTorsion NCS0.937334275133
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.99-2.010.2788210.2169306X-RAY DIFFRACTION4.19
2.01-2.030.2647290.2255670X-RAY DIFFRACTION8.95
2.03-2.060.2517980.20241625X-RAY DIFFRACTION21.97
2.06-2.090.27451460.20242626X-RAY DIFFRACTION35.88
2.09-2.110.24281780.19253778X-RAY DIFFRACTION50.59
2.11-2.140.24552890.19334864X-RAY DIFFRACTION65.35
2.14-2.170.26453330.20255763X-RAY DIFFRACTION78.31
2.17-2.210.25433530.19826332X-RAY DIFFRACTION86.17
2.21-2.240.22233310.18976734X-RAY DIFFRACTION89.1
2.24-2.280.25293100.18386738X-RAY DIFFRACTION90.72
2.28-2.320.2563200.18836945X-RAY DIFFRACTION93.45
2.32-2.360.23623420.17886976X-RAY DIFFRACTION93.4
2.36-2.40.24793430.17616911X-RAY DIFFRACTION92.96
2.4-2.450.24383400.17536885X-RAY DIFFRACTION92.11
2.45-2.510.22083550.18016750X-RAY DIFFRACTION90.95
2.51-2.560.24463420.18556622X-RAY DIFFRACTION89.2
2.56-2.630.25853610.18746182X-RAY DIFFRACTION83.69
2.63-2.70.2413500.17357113X-RAY DIFFRACTION95.51
2.7-2.780.23313200.17217138X-RAY DIFFRACTION95.22
2.78-2.870.24473390.17197126X-RAY DIFFRACTION95.11
2.87-2.970.2243640.17567040X-RAY DIFFRACTION94.96
2.97-3.090.23153690.16437036X-RAY DIFFRACTION94.69
3.09-3.230.19513400.16186992X-RAY DIFFRACTION94.1
3.23-3.40.21013460.16196911X-RAY DIFFRACTION92.86
3.4-3.610.19713320.1526790X-RAY DIFFRACTION91.02
3.61-3.890.17972850.14816364X-RAY DIFFRACTION85.12
3.89-4.280.16453650.13267131X-RAY DIFFRACTION95.65
4.28-4.90.15624260.12747003X-RAY DIFFRACTION94.81
4.9-6.170.18183410.16066846X-RAY DIFFRACTION92.35
6.17-41.150.19033510.1796815X-RAY DIFFRACTION91.7
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)
10.293987045680.0741255560443-0.05831433324020.134200837458-0.05669207841580.39580021025-0.01266914714510.1016045709860.0283005720776-0.03905566487520.051609754897-0.00129891156896-0.1062011381-0.02988102754080.01159454394390.168548546672-0.00655414093439-0.0075254201060.1560469178390.0157395399820.102608968588-15.2927253582-10.3354724925-50.752288289
22.00001502512.000001292232.000000777722.000030242312.000007919082.00003029809-0.000610390713708-1.125587010162.714486274675.682818099990.2831197510172.52876650385-1.24891294476-2.26324865513-0.281625337730.562493137898-0.0369633651541-0.01282391167220.5867101395360.05077005755190.56495720562316.2468971183-64.4113022908-96.3693333106
30.281283187379-0.032947042118-0.0490133896460.1816099003770.02390231281250.2040609727970.009665518193550.030642799682-0.0378609867032-0.0159640766506-0.0176232323587-0.001930319668550.0293745213536-0.01543073677141.28780400327E-60.1160100990930.0092201499640.00379750159030.0948212752436-0.002581188694910.11887177975612.1851827156-81.259080538-103.428570282
40.2932094118780.02782744642540.06454557513060.07132875931470.01157285466170.162735456533-0.01193581518480.06848785530260.000342135019732-0.02226697454920.0206475608612-0.0185186875556-0.0307395643560.0557396265306-5.127125297E-70.102435245798-0.0133826480098-0.002722042290.130204360159-0.004804258030230.095087164720910.0201801926-29.8263187389-34.195705747
50.1538679275710.0118860661017-0.01828468660650.1558177002160.0222706777040.284085002628-0.01911673780090.006602398546750.02651890691510.0200470752933-0.007561075915750.00806562798118-0.0264432419833-0.01789838910091.66324536686E-60.1121040509370.00202239271827-0.001145736091480.109295365909-0.008553097465950.129289252504-31.5316136396-21.2796573683-8.52653221052
60.2319804845950.1142469863690.0006798680340250.245987722164-0.05109768928120.12981123277-0.01416825961250.0198890191278-0.029239585393-0.01955029068770.00108198342519-0.01911642185540.0108624779096-0.01917063470314.84784353505E-80.0960526521193-0.002129752266350.007966472703440.105279581544-0.01701390937650.110827230124-29.8711127717-50.808461976-27.995694548
70.228695612972-0.0934059582417-0.1720071297250.341016716170.004194030674130.586656657814-0.0992225266667-0.106697856806-0.04730173054020.1327048810670.04158882014160.07844947607910.157167375517-0.0217245113035-0.1969630924690.1862226041680.02330781870850.03816402880950.1257004583250.04960517880850.102233879531-3.01334052568-87.2223956551-56.4991202808
80.31853139508-0.17616789647-0.0472806080040.1316678354310.02443119921260.127149870175-0.0168113081777-0.0371651090733-0.09527086010970.0259531858694-0.001504535329820.08158826910650.0245864481642-0.0313080959743-1.33348849819E-50.105490453506-0.01070013649810.0101596695040.110365893850.01394971736970.172890659949-28.3246189247-79.3829769997-80.7435760674
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11(chain 'A' and resid 2 through 475)AA2 - 4751 - 474
22(chain 'G' and resid 2 through 475)GG2 - 475
33(chain 'H' and resid 2 through 475)HH2 - 4751 - 474
44(chain 'B' and resid 2 through 475)BE2 - 4751 - 474
55(chain 'C' and resid 2 through 475)CI2 - 4751 - 474
66(chain 'D' and resid -10 through 475)DL-10 - 4751 - 480
77(chain 'E' and resid 2 through 475)EP2 - 4751 - 474
88(chain 'F' and resid 2 through 475)FT2 - 4751 - 474

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