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- PDB-5dyi: Structure of p97 N-D1 wild-type in complex with ADP -

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Basic information

Entry
Database: PDB / ID: 5dyi
TitleStructure of p97 N-D1 wild-type in complex with ADP
ComponentsTransitional endoplasmic reticulum ATPase
KeywordsHYDROLASE / VCP / AAA ATPase
Function / homology
Function and homology information


positive regulation of Lys63-specific deubiquitinase activity / flavin adenine dinucleotide catabolic process / positive regulation of oxidative phosphorylation / VCP-NSFL1C complex / protein-DNA covalent cross-linking repair / endosome to lysosome transport via multivesicular body sorting pathway / endoplasmic reticulum stress-induced pre-emptive quality control / cellular response to arsenite ion / BAT3 complex binding / Derlin-1 retrotranslocation complex ...positive regulation of Lys63-specific deubiquitinase activity / flavin adenine dinucleotide catabolic process / positive regulation of oxidative phosphorylation / VCP-NSFL1C complex / protein-DNA covalent cross-linking repair / endosome to lysosome transport via multivesicular body sorting pathway / endoplasmic reticulum stress-induced pre-emptive quality control / cellular response to arsenite ion / BAT3 complex binding / Derlin-1 retrotranslocation complex / positive regulation of protein K63-linked deubiquitination / deubiquitinase activator activity / mitotic spindle disassembly / VCP-NPL4-UFD1 AAA ATPase complex / aggresome assembly / regulation of protein localization to chromatin / NADH metabolic process / vesicle-fusing ATPase / cellular response to misfolded protein / : / ERAD pathway / stress granule disassembly / K48-linked polyubiquitin modification-dependent protein binding / negative regulation of protein localization to chromatin / positive regulation of mitochondrial membrane potential / ubiquitin-modified protein reader activity / retrograde protein transport, ER to cytosol / regulation of aerobic respiration / ATPase complex / regulation of synapse organization / positive regulation of ATP biosynthetic process / ubiquitin-specific protease binding / ubiquitin-like protein ligase binding / autophagosome maturation / RHOH GTPase cycle / polyubiquitin modification-dependent protein binding / HSF1 activation / translesion synthesis / endoplasmic reticulum to Golgi vesicle-mediated transport / MHC class I protein binding / Protein methylation / interstrand cross-link repair / negative regulation of smoothened signaling pathway / Attachment and Entry / ATP metabolic process / : / endoplasmic reticulum unfolded protein response / proteasome complex / lipid droplet / viral genome replication / Josephin domain DUBs / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / proteasomal protein catabolic process / ADP binding / Hh mutants are degraded by ERAD / positive regulation of protein-containing complex assembly / Defective CFTR causes cystic fibrosis / Hedgehog ligand biogenesis / macroautophagy / Translesion Synthesis by POLH / ABC-family proteins mediated transport / establishment of protein localization / autophagy / Aggrephagy / cytoplasmic stress granule / positive regulation of non-canonical NF-kappaB signal transduction / positive regulation of protein catabolic process / positive regulation of canonical Wnt signaling pathway / activation of cysteine-type endopeptidase activity involved in apoptotic process / KEAP1-NFE2L2 pathway / azurophil granule lumen / double-strand break repair / Ovarian tumor domain proteases / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / E3 ubiquitin ligases ubiquitinate target proteins / site of double-strand break / cellular response to heat / Neddylation / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / protein phosphatase binding / regulation of apoptotic process / secretory granule lumen / ficolin-1-rich granule lumen / Attachment and Entry / protein ubiquitination / protein domain specific binding / DNA repair / intracellular membrane-bounded organelle / lipid binding / glutamatergic synapse / DNA damage response / ubiquitin protein ligase binding / Neutrophil degranulation / endoplasmic reticulum membrane / perinuclear region of cytoplasm / endoplasmic reticulum / ATP hydrolysis activity / protein-containing complex / RNA binding
Similarity search - Function
Vcp-like ATPase; Chain A, domain 2 - #10 / Vcp-like ATPase; Chain A, domain 2 / Barwin-like endoglucanases - #20 / Helicase, Ruva Protein; domain 3 - #60 / AAA ATPase, CDC48 family / Barwin-like endoglucanases / Cell division protein 48 (CDC48), N-terminal domain / CDC48, N-terminal subdomain / Cell division protein 48 (CDC48) N-terminal domain / CDC48, domain 2 ...Vcp-like ATPase; Chain A, domain 2 - #10 / Vcp-like ATPase; Chain A, domain 2 / Barwin-like endoglucanases - #20 / Helicase, Ruva Protein; domain 3 - #60 / AAA ATPase, CDC48 family / Barwin-like endoglucanases / Cell division protein 48 (CDC48), N-terminal domain / CDC48, N-terminal subdomain / Cell division protein 48 (CDC48) N-terminal domain / CDC48, domain 2 / Cell division protein 48 (CDC48), domain 2 / Cell division protein 48 (CDC48) domain 2 / CDC48 domain 2-like superfamily / Aspartate decarboxylase-like domain superfamily / AAA ATPase, AAA+ lid domain / AAA+ lid domain / ATPase, AAA-type, conserved site / AAA-protein family signature. / Helicase, Ruva Protein; domain 3 / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Roll / Beta Barrel / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Transitional endoplasmic reticulum ATPase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.71 Å
AuthorsTang, W.K. / Xia, D.
CitationJournal: Sci Rep / Year: 2016
Title: Role of the D1-D2 Linker of Human VCP/p97 in the Asymmetry and ATPase Activity of the D1-domain.
Authors: Tang, W.K. / Xia, D.
History
DepositionSep 24, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 10, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transitional endoplasmic reticulum ATPase
B: Transitional endoplasmic reticulum ATPase
C: Transitional endoplasmic reticulum ATPase
D: Transitional endoplasmic reticulum ATPase
E: Transitional endoplasmic reticulum ATPase
F: Transitional endoplasmic reticulum ATPase
G: Transitional endoplasmic reticulum ATPase
H: Transitional endoplasmic reticulum ATPase
I: Transitional endoplasmic reticulum ATPase
J: Transitional endoplasmic reticulum ATPase
K: Transitional endoplasmic reticulum ATPase
L: Transitional endoplasmic reticulum ATPase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)660,10224
Polymers654,97612
Non-polymers5,12612
Water0
1
A: Transitional endoplasmic reticulum ATPase
B: Transitional endoplasmic reticulum ATPase
C: Transitional endoplasmic reticulum ATPase
D: Transitional endoplasmic reticulum ATPase
E: Transitional endoplasmic reticulum ATPase
F: Transitional endoplasmic reticulum ATPase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)330,05112
Polymers327,4886
Non-polymers2,5636
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23910 Å2
ΔGint-113 kcal/mol
Surface area110050 Å2
MethodPISA
2
G: Transitional endoplasmic reticulum ATPase
H: Transitional endoplasmic reticulum ATPase
I: Transitional endoplasmic reticulum ATPase
J: Transitional endoplasmic reticulum ATPase
K: Transitional endoplasmic reticulum ATPase
L: Transitional endoplasmic reticulum ATPase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)330,05112
Polymers327,4886
Non-polymers2,5636
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24030 Å2
ΔGint-110 kcal/mol
Surface area110040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)146.440, 176.210, 256.870
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G
81H
91I
101J
111L
121K
12A
22B
32C
42D
52E
62F
72G
82H
92I
102J
112K
122L
13A
23B
33C
43D
53E
63F
73G
83H
93I
103J
113K
123L

NCS domain segments:

Refine code: 1

Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111ASNASNLYSLYSAA21 - 6321 - 63
211ASNASNLYSLYSBB21 - 6321 - 63
311ASNASNLYSLYSCC21 - 6321 - 63
411ASNASNLYSLYSDD21 - 6321 - 63
511ASNASNLYSLYSEE21 - 6321 - 63
611ASNASNLYSLYSFF21 - 6321 - 63
711ASNASNLYSLYSGG21 - 6321 - 63
811ASNASNLYSLYSHH21 - 6321 - 63
911ASNASNLYSLYSII21 - 6321 - 63
1011ASNASNLYSLYSJJ21 - 6321 - 63
1111ASNASNLYSLYSLL21 - 6321 - 63
1211ASNASNLYSLYSKK21 - 6321 - 63
121ILEILEARGARGAA114 - 147114 - 147
221ILEILEARGARGBB114 - 147114 - 147
321ILEILEARGARGCC114 - 147114 - 147
421ILEILEARGARGDD114 - 147114 - 147
521ILEILEARGARGEE114 - 147114 - 147
621ILEILEARGARGFF114 - 147114 - 147
721ILEILEARGARGGG114 - 147114 - 147
821ILEILEARGARGHH114 - 147114 - 147
921ILEILEARGARGII114 - 147114 - 147
1021ILEILEARGARGJJ114 - 147114 - 147
1121ILEILEARGARGLL114 - 147114 - 147
1221ILEILEARGARGKK114 - 147114 - 147
131GLYGLYASNASNAA149 - 199149 - 199
231GLYGLYASNASNBB149 - 199149 - 199
331GLYGLYASNASNCC149 - 199149 - 199
431GLYGLYASNASNDD149 - 199149 - 199
531GLYGLYASNASNEE149 - 199149 - 199
631GLYGLYASNASNFF149 - 199149 - 199
731GLYGLYASNASNGG149 - 199149 - 199
831GLYGLYASNASNHH149 - 199149 - 199
931GLYGLYASNASNII149 - 199149 - 199
1031GLYGLYASNASNJJ149 - 199149 - 199
1131GLYGLYASNASNLL149 - 199149 - 199
1231GLYGLYASNASNKK149 - 199149 - 199
141ARGARGLYSLYSAA65 - 11265 - 112
241ARGARGLYSLYSBB65 - 11265 - 112
341ARGARGLYSLYSCC65 - 11265 - 112
441ARGARGLYSLYSDD65 - 11265 - 112
541ARGARGLYSLYSEE65 - 11265 - 112
641ARGARGLYSLYSFF65 - 11265 - 112
741ARGARGLYSLYSGG65 - 11265 - 112
841ARGARGLYSLYSHH65 - 11265 - 112
941ARGARGLYSLYSII65 - 11265 - 112
1041ARGARGLYSLYSJJ65 - 11265 - 112
1141ARGARGLYSLYSLL65 - 11265 - 112
1241ARGARGLYSLYSKK65 - 11265 - 112
112GLUGLUCYSCYSAA200 - 209200 - 209
212GLUGLUCYSCYSBB200 - 209200 - 209
312GLUGLUCYSCYSCC200 - 209200 - 209
412GLUGLUCYSCYSDD200 - 209200 - 209
512GLUGLUCYSCYSEE200 - 209200 - 209
612GLUGLUCYSCYSFF200 - 209200 - 209
712GLUGLUCYSCYSGG200 - 209200 - 209
812GLUGLUCYSCYSHH200 - 209200 - 209
912GLUGLUCYSCYSII200 - 209200 - 209
1012GLUGLUCYSCYSJJ200 - 209200 - 209
1112GLUGLUCYSCYSKK200 - 209200 - 209
1212GLUGLUCYSCYSLL200 - 209200 - 209
122GLNGLNGLYGLYAA212 - 370212 - 370
222GLNGLNGLYGLYBB212 - 370212 - 370
322GLNGLNGLYGLYCC212 - 370212 - 370
422GLNGLNGLYGLYDD212 - 370212 - 370
522GLNGLNGLYGLYEE212 - 370212 - 370
622GLNGLNGLYGLYFF212 - 370212 - 370
722GLNGLNGLYGLYGG212 - 370212 - 370
822GLNGLNGLYGLYHH212 - 370212 - 370
922GLNGLNGLYGLYII212 - 370212 - 370
1022GLNGLNGLYGLYJJ212 - 370212 - 370
1122GLNGLNGLYGLYKK212 - 370212 - 370
1222GLNGLNGLYGLYLL212 - 370212 - 370
113ILEILETHRTHRAA371 - 403371 - 403
213ILEILETHRTHRBB371 - 403371 - 403
313ILEILETHRTHRCC371 - 403371 - 403
413ILEILETHRTHRDD371 - 403371 - 403
513ILEILETHRTHREE371 - 403371 - 403
613ILEILETHRTHRFF371 - 403371 - 403
713ILEILETHRTHRGG371 - 403371 - 403
813ILEILETHRTHRHH371 - 403371 - 403
913ILEILETHRTHRII371 - 403371 - 403
1013ILEILETHRTHRJJ371 - 403371 - 403
1113ILEILETHRTHRKK371 - 403371 - 403
1213ILEILETHRTHRLL371 - 403371 - 403
123VALVALADPADPAA - M407 - 800407
223VALVALADPADPBB - N407 - 800407
323VALVALADPADPCC - O407 - 800407
423VALVALADPADPDD - P407 - 800407
523VALVALADPADPEE - Q407 - 800407
623VALVALADPADPFF - R407 - 800407
723VALVALADPADPGG - S407 - 800407
823VALVALADPADPHH - T407 - 800407
923VALVALADPADPII - U407 - 800407
1023VALVALADPADPJJ - V407 - 800407
1123VALVALADPADPKK - W407 - 800407
1223VALVALADPADPLL - X407 - 800407

NCS ensembles :
ID
1
2
3

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.551987, -0.050203, 0.83234), (-0.175118, 0.968946, 0.174576), (-0.815257, -0.242121, 0.526054)-81.46857, -20.73938, -21.47482
3given(-0.439546, -0.206886, 0.874069), (-0.344894, 0.937391, 0.048436), (-0.829366, -0.280172, -0.48338)-138.511, -20.15041, 45.8543
4given(-0.980484, -0.196504, -0.00611), (-0.195622, 0.978237, -0.069165), (0.019568, -0.06662, -0.997587)-100.12651, -0.71625, 134.61647
5given(-0.491803, -0.240156, -0.836932), (-0.131331, 0.970673, -0.20136), (0.860745, 0.010886, -0.50892)-24.78069, 6.152, 141.73474
6given(0.491615, -0.157791, -0.856398), (0.048246, 0.986871, -0.154135), (0.869475, 0.034457, 0.492774)25.46204, 10.92739, 74.65029
7given(-0.92801, -0.052511, 0.368835), (0.093444, -0.991178, 0.093995), (0.360646, 0.121694, 0.92473)-108.56269, -93.65288, 30.77656
8given(-0.15097, 0.087191, 0.984686), (0.250292, -0.960274, 0.123403), (0.956327, 0.265089, 0.12315)-108.02319, -89.0003, 108.84141
9given(0.734534, 0.31259, 0.602285), (0.408954, -0.912204, -0.025313), (0.541494, 0.2649, -0.79788)-40.78196, -71.17594, 146.47615
10given(0.887192, 0.237236, -0.395738), (0.245141, -0.968982, -0.031308), (-0.390891, -0.069236, -0.917829)23.63136, -78.64913, 105.62397
11given(-0.776637, 0.076527, -0.625283), (-0.091125, -0.995802, -0.008691), (-0.623322, 0.050229, 0.78035)-38.56246, -97.86588, -5.34829
12given(0.119378, 0.16116, -0.979682), (0.063422, -0.985961, -0.154465), (-0.990821, -0.043694, -0.127923)24.0239, -81.8044, 32.02054
13given(1), (1), (1)
14given(0.513883, -0.02138, 0.857594), (-0.163624, 0.978894, 0.12245), (-0.842111, -0.203249, 0.499539)-81.90866, -15.56269, -16.461
15given(-0.459153, -0.194604, 0.86678), (-0.290206, 0.955038, 0.06069), (-0.839618, -0.223679, -0.494983)-137.57318, -18.13224, 50.84983
16given(-0.969504, -0.244669, 0.014106), (-0.245071, 0.968205, -0.050198), (-0.001376, -0.052124, -0.99864)-104.53783, -7.25985, 134.13371
17given(-0.481962, -0.18964, -0.855423), (-0.136829, 0.980609, -0.1403), (0.865442, 0.049427, -0.498565)-19.00977, 3.37332, 144.70621
18given(0.511282, -0.127779, -0.849861), (0.018501, 0.990292, -0.137763), (0.859214, 0.054712, 0.508683)28.43859, 9.19388, 75.51876
19given(-0.919818, -0.043631, 0.389911), (0.077573, -0.994403, 0.071725), (0.3846, 0.096221, 0.918055)-108.50462, -94.26031, 32.41102
20given(-0.12801, 0.059141, 0.990008), (0.23664, -0.967568, 0.088398), (0.963128, 0.245591, 0.109864)-107.79413, -87.14413, 110.24301
21given(0.758083, 0.28893, 0.584662), (0.357575, -0.933882, -0.00213), (0.54539, 0.210676, -0.811274)-38.79326, -75.6298, 147.0369
22given(0.881949, 0.267817, -0.387866), (0.270136, -0.96154, -0.049682), (-0.386254, -0.060959, -0.920376)23.88871, -77.59416, 105.80286
23given(0.101986, 0.098044, -0.989942), (0.090764, -0.991898, -0.088887), (-0.990637, -0.080785, -0.110058)22.56467, -83.26202, 30.89696
24given(-0.808769, 0.015409, -0.587924), (-0.010698, -0.999877, -0.01149), (-0.588029, -0.003003, 0.808834)-42.74069, -93.26448, -5.02406
25given(1), (1), (1)
26given(0.523312, -0.053484, 0.850461), (-0.160754, 0.973912, 0.160164), (-0.836841, -0.220531, 0.501062)-83.54804, -18.95009, -17.89763
27given(-0.465676, -0.215875, 0.858222), (-0.311685, 0.947659, 0.06925), (-0.82825, -0.235247, -0.508587)-138.64627, -20.2962, 51.90207
28given(-0.97043, -0.241153, -0.010561), (-0.240385, 0.969464, -0.04852), (0.02194, -0.044546, -0.998766)-102.27466, -7.04921, 136.4299
29given(-0.471153, -0.232787, -0.850779), (-0.146153, 0.971816, -0.184967), (0.869859, 0.037196, -0.491897)-21.75395, 4.24316, 143.56549
30given(0.512415, -0.150193, -0.845502), (0.037724, 0.987573, -0.152568), (0.857909, 0.046282, 0.511712)26.66148, 10.46104, 74.62125
31given(-0.916757, -0.034015, 0.397994), (0.067617, -0.995203, 0.070696), (0.39368, 0.091722, 0.91466)-108.55981, -94.97082, 33.18823
32given(-0.130046, 0.081024, 0.988192), (0.258532, -0.959408, 0.112687), (0.957209, 0.270133, 0.10382)-107.35251, -87.61891, 110.87753
33given(0.746291, 0.320658, 0.583291), (0.392328, -0.919818, 0.003696), (0.537706, 0.226083, -0.812255)-38.4814, -74.70379, 146.98178
34given(0.878334, 0.256913, -0.403145), (0.269248, -0.962695, -0.026887), (-0.395013, -0.084931, -0.914741)24.61031, -79.12782, 104.92518
35given(0.09921, 0.12488, -0.987199), (0.075931, -0.990151, -0.117622), (-0.992165, -0.06329, -0.107715)22.90652, -82.37713, 31.02101
36given(-0.808223, 0.059673, -0.585845), (-0.045443, -0.998206, -0.038984), (-0.58712, -0.004885, 0.809485)-41.86206, -94.25135, -5.14019

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Components

#1: Protein
Transitional endoplasmic reticulum ATPase / TER ATPase / 15S Mg(2+)-ATPase p97 subunit / Valosin-containing protein / VCP


Mass: 54581.312 Da / Num. of mol.: 12 / Fragment: UNP residues 1-481
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VCP / Production host: Escherichia coli (E. coli) / References: UniProt: P55072, vesicle-fusing ATPase
#2: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.53 Å3/Da / Density % sol: 51.38 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.1 M sodium citrate, pH 6.0, 0.3 M NaCl, 15.2 % PEG3350, 20 % glycerol, 2 % benzamidine

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300HS / Detector: CCD / Date: Mar 1, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.71→50 Å / Num. obs: 62997 / % possible obs: 88.8 % / Redundancy: 4.9 % / Net I/σ(I): 7.12

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Processing

Software
NameVersionClassification
REFMAC5.8.0124refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementResolution: 3.71→50 Å / Cor.coef. Fo:Fc: 0.879 / Cor.coef. Fo:Fc free: 0.833 / SU B: 172.044 / SU ML: 0.957 / Cross valid method: THROUGHOUT / ESU R Free: 1.164 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28527 2448 5.1 %RANDOM
Rwork0.24855 ---
obs0.25037 45977 68.08 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 140.215 Å2
Baniso -1Baniso -2Baniso -3
1--3.59 Å20 Å20 Å2
2--2.14 Å20 Å2
3---1.45 Å2
Refinement stepCycle: 1 / Resolution: 3.71→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms41255 0 324 0 41579
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01942240
X-RAY DIFFRACTIONr_bond_other_d0.0030.0241575
X-RAY DIFFRACTIONr_angle_refined_deg1.6351.99357118
X-RAY DIFFRACTIONr_angle_other_deg1.173395756
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.92155253
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.87124.1521970
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.582157736
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.7715396
X-RAY DIFFRACTIONr_chiral_restr0.0810.26513
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02147188
X-RAY DIFFRACTIONr_gen_planes_other0.0030.028964
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.2987.22621048
X-RAY DIFFRACTIONr_mcbond_other2.2987.22621047
X-RAY DIFFRACTIONr_mcangle_it4.12810.83626289
X-RAY DIFFRACTIONr_mcangle_other4.12810.83626290
X-RAY DIFFRACTIONr_scbond_it1.837.41121192
X-RAY DIFFRACTIONr_scbond_other1.837.41121193
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.44511.04430830
X-RAY DIFFRACTIONr_long_range_B_refined9.93967.801170732
X-RAY DIFFRACTIONr_long_range_B_other9.93967.801170733
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: tight thermal / Weight position: 0.5

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A27958.1
11B279510.31
11C279510.4
11D27959.18
11E279510.44
11F279510.77
11G27958.83
11H279510.48
11I27957.42
11J27958.79
11K279517.58
11L279513.72
22A26377.21
22B26376.28
22C26378.31
22D26378.39
22E263716.81
22F263710.71
22G26377.68
22H26378.6
22I26379.09
22J26377.96
22K26376.83
22L26378.6
33A13309.82
33B13308.99
33C133011.16
33D133010.39
33E13308.38
33F13309.21
33G13307.04
33H13307.76
33I13308.32
33J13309.73
33K13308.95
33L133010.24
LS refinement shellResolution: 3.71→3.805 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.57 33 -
Rwork0.463 681 -
obs--13.78 %
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)
14.54591.55513.8315.22091.49517.95870.06420.30130.2014-0.2989-0.1075-0.5431-0.29390.20210.04330.3133-0.11470.33740.24340.13760.80399.4683-58.846436.183
27.1485-3.3193-4.42827.35343.192410.4379-0.0634-0.07340.93640.1090.0456-0.1848-0.40960.77610.01780.1754-0.075-0.28340.5437-0.11150.67829.8619-55.442699.3618
36.935-0.4382-1.18324.79822.06853.40280.0184-1.09830.16530.44830.01520.1326-0.174-0.0931-0.03371.26860.03850.05941.1045-0.22090.5673-43.6788-64.1677132.136
45.5096-1.18052.95776.1177-3.25769.3983-0.2902-0.2440.08090.59160.35450.06840.0013-0.3986-0.06430.22480.07950.23440.7068-0.34840.6828-98.0126-71.8353101.5424
55.80641.557-3.75045.033-2.49586.87420.5287-0.43181.2921-0.3334-0.12191.0483-0.3473-0.7907-0.40670.8845-0.0024-0.39140.6788-0.19121.1625-99.157-72.45938.1499
69.22571.15970.56983.46551.09822.95840.10590.5426-0.017-0.5665-0.10.0175-0.27990.1058-0.00591.2261-0.0741-0.08890.48280.3020.3764-44.6793-67.65085.5035
75.2921.44190.25314.6565-2.02099.028-0.19630.3981-0.4915-0.25510.10880.41740.113-0.57790.08760.7448-0.14840.07720.3578-0.20861.0655-104.3289-40.038851.8029
87.6939-2.59283.02295.4235-1.26274.85780.0809-0.6144-0.92240.4606-0.18530.58820.6414-0.8470.10441.5446-0.18820.38170.62310.12460.5656-79.6733-37.9759110.4684
99.2167-0.7608-1.43846.46611.39595.5989-0.2654-0.8413-0.45950.4621-0.1076-0.05570.26640.25970.3731.02480.0369-0.50450.55680.04840.3192-17.7773-24.7605117.9484
103.0368-1.1919-0.55855.76961.34935.6974-0.0972-0.8295-0.29150.19220.3165-0.89620.46360.8971-0.21930.79870.1374-0.17910.9486-0.04071.178319.429-17.747668.719
118.8104-0.24841.42537.31810.25893.33530.09920.37740.13590.0751-0.2025-0.8763-0.21030.12030.10330.6165-0.06760.22690.4311-0.0680.2229-4.4067-25.167510.2011
127.2813.46-2.04847.9202-1.05815.7431-0.37170.06840.3306-0.21840.0629-0.08140.05760.19640.30880.60110.1949-0.30440.4814-0.15070.2069-66.749-33.09712.0351
136.7978-1.46211.92412.3410.11475.962-0.08770.05620.28430.06050.0718-0.01670.1164-0.2590.01590.2061-0.0370.14820.09080.08350.2781-13.811-67.180151.1632
143.4741-0.0150.98933.7005-1.60418.1-0.2046-0.17470.16390.02470.1427-0.0925-0.0227-0.02810.06190.04150.0786-0.10050.2515-0.11780.4175-13.3847-65.984585.8089
156.2132.0536-1.77324.2961-1.39426.82890.1303-0.29140.03620.1741-0.06880.1828-0.018-0.2439-0.06150.30510.1961-0.12560.5578-0.11520.2498-42.7691-71.1589104.0898
168.34542.49791.44783.50960.9793.5848-0.21090.0311-0.0324-0.2555-0.0363-0.00760.2991-0.09190.24710.23760.02240.22730.449-0.14450.3879-73.1113-75.785987.0306
174.4541-0.0851-1.67792.81581.84556.9172-0.0114-1.13210.8377-0.09850.104-0.1458-0.1563-0.0788-0.09260.4612-0.2089-0.17430.7748-0.11720.7166-73.7402-75.024452.2141
187.666-0.19280.09162.21821.54075.956-0.02-0.66640.2251-0.1043-0.1231-0.02450.0995-0.59070.14310.6717-0.0833-0.16080.2050.11330.2549-44.0106-71.725134.0817
196.129-0.922-1.62282.86350.9666.24070.01550.27940.20430.06950.06590.247-0.1272-0.0837-0.08150.50710.0604-0.06260.1944-0.15620.2146-77.7655-29.261656.0372
204.70840.58860.61853.34541.66626.4923-0.25180.1957-0.03480.22710.0186-0.07470.2853-0.26920.23320.71190.04650.13780.1657-0.07430.0793-64.2601-28.050488.307
216.52061.81390.40854.13510.20044.7819-0.1981-0.11250.1781-0.190.0515-0.0553-0.06810.08040.14660.92410.1012-0.26740.2215-0.05670.0913-30.4574-20.597392.3403
223.95342.3585-1.85063.5486-1.17236.65850.2389-0.4072-0.01550.11620.0157-0.10480.21950.2841-0.25460.5459-0.0057-0.20950.3576-0.15970.3648-9.4079-16.905264.2056
236.1167-0.00190.71542.9072-0.7766.11440.093-0.28430.04120.09310.05770.1097-0.41620.0138-0.15070.5269-0.0750.10790.1348-0.09680.0872-22.3248-20.856532.4127
247.2137-0.70140.0052.6782-0.75634.52130.04860.0325-0.03140.2619-0.00030.1518-0.27550.2095-0.04830.68390.0879-0.09880.182-0.07130.0472-56.6574-25.517328.1277
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A21 - 200
2X-RAY DIFFRACTION2B21 - 200
3X-RAY DIFFRACTION3C21 - 200
4X-RAY DIFFRACTION4D21 - 200
5X-RAY DIFFRACTION5E21 - 200
6X-RAY DIFFRACTION6F21 - 200
7X-RAY DIFFRACTION7G21 - 200
8X-RAY DIFFRACTION8H21 - 200
9X-RAY DIFFRACTION9I21 - 200
10X-RAY DIFFRACTION10J21 - 200
11X-RAY DIFFRACTION11K21 - 200
12X-RAY DIFFRACTION12L21 - 200
13X-RAY DIFFRACTION13A201 - 460
14X-RAY DIFFRACTION13A800
15X-RAY DIFFRACTION14B201 - 458
16X-RAY DIFFRACTION14B800
17X-RAY DIFFRACTION15C201 - 458
18X-RAY DIFFRACTION15C800
19X-RAY DIFFRACTION16D201 - 459
20X-RAY DIFFRACTION16D800
21X-RAY DIFFRACTION17E201 - 458
22X-RAY DIFFRACTION17E800
23X-RAY DIFFRACTION18F201 - 458
24X-RAY DIFFRACTION18F800
25X-RAY DIFFRACTION19G201 - 458
26X-RAY DIFFRACTION19G800
27X-RAY DIFFRACTION20H201 - 459
28X-RAY DIFFRACTION20H800
29X-RAY DIFFRACTION21I201 - 459
30X-RAY DIFFRACTION21I800
31X-RAY DIFFRACTION22J201 - 461
32X-RAY DIFFRACTION22J800
33X-RAY DIFFRACTION23K201 - 459
34X-RAY DIFFRACTION23K800
35X-RAY DIFFRACTION24L201 - 458
36X-RAY DIFFRACTION24L800

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