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- PDB-6hwf: Yeast 20S proteasome beta2-G45A mutant in complex with ONX 0914 -

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Basic information

Entry
Database: PDB / ID: 6hwf
TitleYeast 20S proteasome beta2-G45A mutant in complex with ONX 0914
Components
  • (Proteasome subunit alpha type- ...) x 6
  • (Proteasome subunit beta type- ...) x 7
  • Probable proteasome subunit alpha type-7
KeywordsHYDROLASE / Proteasome / Mutant / Inhibitor / Binding Analysis
Function / homology
Function and homology information


proteasome core complex assembly / nuclear outer membrane-endoplasmic reticulum membrane network / Cross-presentation of soluble exogenous antigens (endosomes) / TNFR2 non-canonical NF-kB pathway / proteasomal ubiquitin-independent protein catabolic process / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Regulation of PTEN stability and activity / CDK-mediated phosphorylation and removal of Cdc6 / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / KEAP1-NFE2L2 pathway ...proteasome core complex assembly / nuclear outer membrane-endoplasmic reticulum membrane network / Cross-presentation of soluble exogenous antigens (endosomes) / TNFR2 non-canonical NF-kB pathway / proteasomal ubiquitin-independent protein catabolic process / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Regulation of PTEN stability and activity / CDK-mediated phosphorylation and removal of Cdc6 / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / KEAP1-NFE2L2 pathway / Neddylation / Orc1 removal from chromatin / MAPK6/MAPK4 signaling / proteasome storage granule / Antigen processing: Ubiquitination & Proteasome degradation / endopeptidase activator activity / proteasome assembly / proteasome endopeptidase complex / proteasome core complex, beta-subunit complex / proteasome core complex, alpha-subunit complex / Ub-specific processing proteases / threonine-type endopeptidase activity / Neutrophil degranulation / proteasome complex / peroxisome / proteasome-mediated ubiquitin-dependent protein catabolic process / endopeptidase activity / mRNA binding / endoplasmic reticulum membrane / mitochondrion / nucleus / cytosol
Similarity search - Function
Aminohydrolase, N-terminal nucleophile (Ntn) domain / Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 / Proteasome beta subunit, C-terminal / Proteasome beta subunits C terminal / Proteasome subunit beta 4 / Proteasome subunit beta 2 / Proteasome beta 3 subunit / Proteasome subunit alpha6 / Proteasome subunit alpha5 / Proteasome beta-type subunits signature. ...Aminohydrolase, N-terminal nucleophile (Ntn) domain / Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 / Proteasome beta subunit, C-terminal / Proteasome beta subunits C terminal / Proteasome subunit beta 4 / Proteasome subunit beta 2 / Proteasome beta 3 subunit / Proteasome subunit alpha6 / Proteasome subunit alpha5 / Proteasome beta-type subunits signature. / Peptidase T1A, proteasome beta-subunit / Proteasome beta-type subunit, conserved site / Proteasome subunit A N-terminal signature / Proteasome alpha-type subunits signature. / Proteasome alpha-subunit, N-terminal domain / Proteasome subunit A N-terminal signature Add an annotation / : / Proteasome alpha-type subunit / Proteasome alpha-type subunit profile. / Proteasome B-type subunit / Proteasome beta-type subunit profile. / Proteasome subunit / Proteasome, subunit alpha/beta / Nucleophile aminohydrolases, N-terminal / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-GQK / Probable proteasome subunit alpha type-7 / Proteasome subunit alpha type-1 / Proteasome subunit beta type-4 / Proteasome subunit alpha type-3 / Proteasome subunit alpha type-2 / Proteasome subunit beta type-6 / Proteasome subunit beta type-2 / Proteasome subunit beta type-3 / Proteasome subunit beta type-5 ...Chem-GQK / Probable proteasome subunit alpha type-7 / Proteasome subunit alpha type-1 / Proteasome subunit beta type-4 / Proteasome subunit alpha type-3 / Proteasome subunit alpha type-2 / Proteasome subunit beta type-6 / Proteasome subunit beta type-2 / Proteasome subunit beta type-3 / Proteasome subunit beta type-5 / Proteasome subunit beta type-7 / Proteasome subunit alpha type-5 / Proteasome subunit beta type-1 / Proteasome subunit alpha type-6 / Proteasome subunit alpha type-4
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsHuber, E.M. / Groll, M.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationGR1861/10-1 Germany
CitationJournal: J.Med.Chem. / Year: 2019
Title: Structure-Based Design of Inhibitors Selective for Human Proteasome beta 2c or beta 2i Subunits.
Authors: Xin, B.T. / Huber, E.M. / de Bruin, G. / Heinemeyer, W. / Maurits, E. / Espinal, C. / Du, Y. / Janssens, M. / Weyburne, E.S. / Kisselev, A.F. / Florea, B.I. / Driessen, C. / van der Marel, G. ...Authors: Xin, B.T. / Huber, E.M. / de Bruin, G. / Heinemeyer, W. / Maurits, E. / Espinal, C. / Du, Y. / Janssens, M. / Weyburne, E.S. / Kisselev, A.F. / Florea, B.I. / Driessen, C. / van der Marel, G.A. / Groll, M. / Overkleeft, H.S.
History
DepositionOct 11, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 30, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 24, 2019Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc / pdbx_seq_map_depositor_info
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name / _pdbx_seq_map_depositor_info.one_letter_code / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 1.2Jan 24, 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_initial_refinement_model / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Proteasome subunit alpha type-2
B: Proteasome subunit alpha type-3
C: Proteasome subunit alpha type-4
D: Proteasome subunit alpha type-5
E: Proteasome subunit alpha type-6
F: Probable proteasome subunit alpha type-7
G: Proteasome subunit alpha type-1
H: Proteasome subunit beta type-2
I: Proteasome subunit beta type-3
J: Proteasome subunit beta type-4
K: Proteasome subunit beta type-5
L: Proteasome subunit beta type-6
M: Proteasome subunit beta type-7
N: Proteasome subunit beta type-1
O: Proteasome subunit alpha type-2
P: Proteasome subunit alpha type-3
Q: Proteasome subunit alpha type-4
R: Proteasome subunit alpha type-5
S: Proteasome subunit alpha type-6
T: Probable proteasome subunit alpha type-7
U: Proteasome subunit alpha type-1
V: Proteasome subunit beta type-2
W: Proteasome subunit beta type-3
X: Proteasome subunit beta type-4
Y: Proteasome subunit beta type-5
Z: Proteasome subunit beta type-6
a: Proteasome subunit beta type-7
b: Proteasome subunit beta type-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)735,82550
Polymers731,07928
Non-polymers4,74722
Water19,2761070
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)136.630, 299.660, 145.150
Angle α, β, γ (deg.)90.00, 113.39, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21O
12B
22P
13C
23Q
14D
24R
15E
25S
16F
26T
17G
27U
18H
28V
19I
29W
110J
210X
111K
211Y
112L
212Z
113M
213a
114N
214b

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A1 - 300
2111O1 - 300
1121B1 - 300
2121P1 - 300
1131C1 - 300
2131Q1 - 300
1141D1 - 300
2141R1 - 300
1151E1 - 300
2151S1 - 300
1161F1 - 300
2161T1 - 300
1171G1 - 300
2171U1 - 300
1181H1 - 300
2181V1 - 300
1191I1 - 300
2191W1 - 300
11101J1 - 300
21101X1 - 300
11111K1 - 300
21111Y1 - 300
11121L1 - 300
21121Z1 - 300
11131M1 - 300
21131a1 - 300
11141N1 - 300
21141b1 - 300

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.999798, -4.7E-5, 0.020105), (-0.003403, -0.985171, -0.17154), (0.019815, -0.171574, 0.984972)68.46854, -288.02203, -25.24154
3given(1), (1), (1)
4given(-0.999677, 0.011446, 0.022669), (-0.014978, -0.986621, -0.162344), (0.020507, -0.162631, 0.986474)70.85352, -288.13834, -23.47442
5given(1), (1), (1)
6given(-0.999994, -0.003263, -0.00123), (0.003422, -0.98611, -0.166058), (-0.000671, -0.166061, 0.986115)68.19105, -288.44434, -23.584
7given(1), (1), (1)
8given(-0.999996, 0.002992, -1.0E-5), (-0.002949, -0.986027, -0.166559), (-0.000508, -0.166558, 0.986031)69.50803, -288.16467, -23.57161
9given(1), (1), (1)
10given(-0.999923, -0.001922, 0.012265), (-0.000238, -0.984799, -0.173698), (0.012412, -0.173687, 0.984723)68.40633, -287.99023, -25.65235
11given(1), (1), (1)
12given(-0.999949, 0.002924, 0.009628), (-0.004598, -0.983883, -0.178755), (0.00895, -0.17879, 0.983847)69.52219, -287.30917, -26.38431
13given(1), (1), (1)
14given(-0.999887, -0.002905, 0.014764), (7.9E-5, -0.982186, -0.187911), (0.015047, -0.187889, 0.982075)68.05318, -286.76697, -28.39641
15given(1), (1), (1)
16given(-0.999925, 0.000699, 0.012211), (-0.002791, -0.985062, -0.172175), (0.011908, -0.172197, 0.984991)68.89643, -288.04913, -25.40336
17given(1), (1), (1)
18given(-0.999922, -1.3E-5, 0.012471), (-0.002142, -0.984957, -0.172786), (0.012286, -0.172799, 0.98488)68.79907, -287.97113, -25.41383
19given(1), (1), (1)
20given(-0.99995, -0.000111, 0.01005), (-0.00165, -0.984563, -0.175023), (0.009914, -0.17503, 0.984513)68.8185, -287.90198, -25.71947
21given(1), (1), (1)
22given(-0.999958, -0.001782, 0.008951), (0.000212, -0.98501, -0.172497), (0.009124, -0.172488, 0.984969)68.56322, -288.06757, -25.30986
23given(1), (1), (1)
24given(-0.999933, -0.000969, 0.011542), (-0.001045, -0.984881, -0.173229), (0.011536, -0.173229, 0.984814)68.63574, -287.9697, -25.55739
25given(1), (1), (1)
26given(-0.999922, -0.000917, 0.012471), (-0.001245, -0.985046, -0.172288), (0.012443, -0.17229, 0.984968)68.59829, -288.0365, -25.44392
27given(1), (1), (1)
28given(-0.999912, -0.001245, 0.013211), (-0.001049, -0.98506, -0.172209), (0.013228, -0.172207, 0.984972)68.50024, -288.07111, -25.43444

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Components

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Proteasome subunit alpha type- ... , 6 types, 12 molecules AOBPCQDRESGU

#1: Protein Proteasome subunit alpha type-2 / Macropain subunit Y7 / Multicatalytic endopeptidase complex subunit Y7 / Proteasome component Y7 / ...Macropain subunit Y7 / Multicatalytic endopeptidase complex subunit Y7 / Proteasome component Y7 / Proteinase YSCE subunit 7


Mass: 27191.828 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P23639, proteasome endopeptidase complex
#2: Protein Proteasome subunit alpha type-3 / Macropain subunit Y13 / Multicatalytic endopeptidase complex subunit Y13 / Proteasome component Y13 ...Macropain subunit Y13 / Multicatalytic endopeptidase complex subunit Y13 / Proteasome component Y13 / Proteinase YSCE subunit 13


Mass: 28748.230 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P23638, proteasome endopeptidase complex
#3: Protein Proteasome subunit alpha type-4 / Macropain subunit PRE6 / Multicatalytic endopeptidase complex subunit PRE6 / Proteasome component ...Macropain subunit PRE6 / Multicatalytic endopeptidase complex subunit PRE6 / Proteasome component PRE6 / Proteinase YSCE subunit PRE6


Mass: 28478.111 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P40303, proteasome endopeptidase complex
#4: Protein Proteasome subunit alpha type-5 / Macropain subunit PUP2 / Multicatalytic endopeptidase complex subunit PUP2 / Proteasome component ...Macropain subunit PUP2 / Multicatalytic endopeptidase complex subunit PUP2 / Proteasome component PUP2 / Proteinase YSCE subunit PUP2


Mass: 28649.086 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P32379, proteasome endopeptidase complex
#5: Protein Proteasome subunit alpha type-6 / Macropain subunit PRE5 / Multicatalytic endopeptidase complex subunit PRE5 / Proteasome component ...Macropain subunit PRE5 / Multicatalytic endopeptidase complex subunit PRE5 / Proteasome component PRE5 / Proteinase YSCE subunit PRE5


Mass: 25634.000 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P40302, proteasome endopeptidase complex
#7: Protein Proteasome subunit alpha type-1 / Macropain subunit C7-alpha / Multicatalytic endopeptidase complex C7 / Proteasome component C7- ...Macropain subunit C7-alpha / Multicatalytic endopeptidase complex C7 / Proteasome component C7-alpha / Proteasome component Y8 / Proteinase YSCE subunit 7 / SCL1 suppressor protein


Mass: 28033.830 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P21243, proteasome endopeptidase complex

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Protein , 1 types, 2 molecules FT

#6: Protein Probable proteasome subunit alpha type-7 / Macropain subunit C1 / Multicatalytic endopeptidase complex subunit C1 / Proteasome component C1 / ...Macropain subunit C1 / Multicatalytic endopeptidase complex subunit C1 / Proteasome component C1 / Proteinase YSCE subunit 1


Mass: 31575.068 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P21242, proteasome endopeptidase complex

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Proteasome subunit beta type- ... , 7 types, 14 molecules HVIWJXKYLZMaNb

#8: Protein Proteasome subunit beta type-2 / Macropain subunit PUP1 / Multicatalytic endopeptidase complex subunit PUP1 / Proteasome component ...Macropain subunit PUP1 / Multicatalytic endopeptidase complex subunit PUP1 / Proteasome component PUP1 / Proteinase YSCE subunit PUP1


Mass: 25128.486 Da / Num. of mol.: 2 / Mutation: G45A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Gene: PUP1, YOR157C
Production host: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P25043, proteasome endopeptidase complex
#9: Protein Proteasome subunit beta type-3 / Macropain subunit PUP3 / Multicatalytic endopeptidase complex subunit PUP3 / Proteasome component PUP3


Mass: 22627.842 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P25451, proteasome endopeptidase complex
#10: Protein Proteasome subunit beta type-4 / Macropain subunit C11 / Multicatalytic endopeptidase complex subunit C11 / Proteasome component C11 ...Macropain subunit C11 / Multicatalytic endopeptidase complex subunit C11 / Proteasome component C11 / Proteinase YSCE subunit 11


Mass: 22545.676 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P22141, proteasome endopeptidase complex
#11: Protein Proteasome subunit beta type-5 / Macropain subunit PRE2 / Multicatalytic endopeptidase complex subunit PRE2 / Proteasome component ...Macropain subunit PRE2 / Multicatalytic endopeptidase complex subunit PRE2 / Proteasome component PRE2 / Proteinase YSCE subunit PRE2


Mass: 23325.248 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P30656, proteasome endopeptidase complex
#12: Protein Proteasome subunit beta type-6 / Multicatalytic endopeptidase complex subunit C5 / Proteasome component C5


Mass: 24883.928 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P23724, proteasome endopeptidase complex
#13: Protein Proteasome subunit beta type-7 / Macropain subunit PRE4 / Multicatalytic endopeptidase complex subunit PRE4 / Proteasome component ...Macropain subunit PRE4 / Multicatalytic endopeptidase complex subunit PRE4 / Proteasome component PRE4 / Proteinase YSCE subunit PRE4


Mass: 27200.893 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P30657, proteasome endopeptidase complex
#14: Protein Proteasome subunit beta type-1 / Macropain subunit PRE3 / Multicatalytic endopeptidase complex subunit PRE3 / Proteasome component ...Macropain subunit PRE3 / Multicatalytic endopeptidase complex subunit PRE3 / Proteasome component PRE3 / Proteinase YSCE subunit PRE3


Mass: 21517.186 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P38624, proteasome endopeptidase complex

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Non-polymers , 6 types, 1092 molecules

#15: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#16: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#17: Chemical
ChemComp-GQK / (2~{S})-3-(4-methoxyphenyl)-~{N}-[(2~{S},3~{R})-4-methyl-3,4-bis(oxidanyl)-1-phenyl-pentan-2-yl]-2-[[(2~{S})-2-(2-morpholin-4-ylethanoylamino)propanoyl]amino]propanamide


Mass: 584.704 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C31H44N4O7
#18: Chemical
ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#19: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#20: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1070 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 3.67 Å3/Da / Density % sol: 66.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.8 / Details: 20 mM MgAC2, 13% MPD, 0.1 M MES / PH range: 6.8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 19, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 359000 / % possible obs: 97.5 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 12
Reflection shellResolution: 2.5→2.6 Å / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 2.4 / % possible all: 99.1

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
REFMACphasing
REFMAC5.8.0158refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5CZ4

5cz4


Resolution: 2.5→15 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.943 / SU B: 20.044 / SU ML: 0.185 / Cross valid method: THROUGHOUT / ESU R Free: 0.214 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21577 17869 5 %RANDOM
Rwork0.18854 ---
obs0.1899 339515 97.16 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 58.254 Å2
Baniso -1Baniso -2Baniso -3
1-1.6 Å2-0 Å2-0.53 Å2
2---2.98 Å2-0 Å2
3---1.33 Å2
Refinement stepCycle: LAST / Resolution: 2.5→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms49378 0 320 1070 50768
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01950608
X-RAY DIFFRACTIONr_bond_other_d0.0020.0247162
X-RAY DIFFRACTIONr_angle_refined_deg1.2741.9768486
X-RAY DIFFRACTIONr_angle_other_deg0.9683.003109454
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.42356314
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.78324.4232252
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.917158752
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.36715284
X-RAY DIFFRACTIONr_chiral_restr0.0730.27704
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0256340
X-RAY DIFFRACTIONr_gen_planes_other0.0010.0210136
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_it1.7534.0625346
X-RAY DIFFRACTIONr_mcbond_other1.7534.0625345
X-RAY DIFFRACTIONr_mcangle_it2.0686.07731630
X-RAY DIFFRACTIONr_mcangle_other2.0686.07831631
X-RAY DIFFRACTIONr_scbond_it1.854.51825262
X-RAY DIFFRACTIONr_scbond_other1.8494.51725254
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.8796.58736845
X-RAY DIFFRACTIONr_long_range_B_refined2.65846.86853654
X-RAY DIFFRACTIONr_long_range_B_other2.55846.78853522
X-RAY DIFFRACTIONr_rigid_bond_restr1.966397770
X-RAY DIFFRACTIONr_sphericity_free31.1795775
X-RAY DIFFRACTIONr_sphericity_bonded4.488597155
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1010A3063tight positional0.010.05
1111A3246tight positional0.030.05
1212A3389tight positional0.010.05
1313A3564tight positional0.010.05
1414A3002tight positional0.020.05
11A3765tight thermal4.570.5
22B3714tight thermal4.20.5
33C3685tight thermal8.840.5
44D3538tight thermal4.250.5
55E3459tight thermal4.50.5
66F3693tight thermal3.540.5
77G3724tight thermal3.340.5
88H3437tight thermal3.410.5
99I3091tight thermal3.070.5
1010J3063tight thermal30.5
1111K3246tight thermal2.380.5
1212L3389tight thermal2.680.5
1313M3564tight thermal3.220.5
1414N3002tight thermal2.360.5
LS refinement shellResolution: 2.5→2.563 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.338 1307 -
Rwork0.31 24833 -
obs--99.11 %
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)
10.3346-0.05750.07620.2249-0.06810.21590.00060.03450.0120.01770.004-0.0845-0.05220.006-0.00460.2425-0.0395-0.02250.025-0.03010.242967.4096-91.743546.1167
20.2941-0.0017-0.08530.22840.11060.41-0.03430.00550.0297-0.07560.015-0.0313-0.04610.06660.01920.262-0.03780.0210.04210.03970.212960.4137-87.569916.4593
30.46610.21090.01030.2195-0.06650.375-0.00440.07610.0766-0.07870.07520.0090.00190.0487-0.07080.3219-0.0089-0.01460.06340.04490.216833.1286-86.98651.0009
40.22860.113-0.04340.29680.02970.255-0.0227-0.02920.0601-0.06990.00480.1806-0.04060.00410.01780.25020.0516-0.08920.03030.04470.32373.9217-89.465713.4308
50.3110.06710.11930.18-0.0260.3914-0.0238-0.02220.03520.03660.01910.1629-0.0756-0.07070.00470.20040.06410.02260.02720.00160.3346-2.6495-93.715545.38
60.47430.0258-0.03140.18280.08890.10990.0268-0.03980.04440.0871-0.03350.0869-0.0140.00150.00670.30780.02760.06350.028-0.04080.212315.6975-94.379969.6637
70.13290.16210.06020.35470.03650.26480.01680.0071-0.00170.0955-0.0077-0.0541-0.0179-0.0183-0.00910.332-0.0151-0.02120.0197-0.04070.176448.0844-93.02471.0936
80.0178-0.0031-0.00580.10070.03370.01680.01540.02920.02310.04870.0115-0.1244-0.0003-0.0096-0.0270.2601-0.0096-0.04820.0733-0.0190.272467.8798-129.244947.547
90.33050.0096-0.0030.64330.070.04110.01680.018-0.0088-0.0579-0.0249-0.1424-0.0603-0.02530.00810.2221-0.01470.02510.04520.00050.241168.7267-127.210221.0616
100.3650.18290.00580.5771-0.00880.0047-0.00560.01380.0341-0.15740.01680.0075-0.02460.002-0.01130.3050.00820.01380.06090.01880.142645.3178-126.1814-0.5613
110.2340.1487-0.00390.56660.12870.04370.0126-0.050.0106-0.0722-0.01460.1485-0.0110.0020.0020.29040.0221-0.10360.04380.03160.232611.5722-130.1722.3829
120.1465-0.00390.11360.41930.04720.31150.032-0.01720.0004-0.00410.00630.1686-0.02330.0245-0.03830.17110.0168-0.04450.03070.04120.3147-4.0384-133.546528.4472
130.1912-0.10790.07380.58540.01680.07120.0229-0.01790.0210.1218-0.01530.1055-0.01720.0182-0.00760.2423-0.00330.04710.0394-0.00080.23318.0877-137.186860.2574
140.36560.0926-0.02040.3026-0.01440.00310.03290.05510.01640.1116-0.0251-0.0342-0.0030.0076-0.00780.3503-0.0038-0.03050.0682-0.02110.146740.1116-133.627270.554
150.5171-0.0831-0.15740.22540.1650.2563-0.00180.0537-0.01370.0245-0.01040.09230.0931-0.03340.01230.2383-0.0584-0.06790.02350.04320.27761.8011-205.611136.6024
160.31120.07480.15290.303-0.10920.2232-0.06850.00470.0028-0.08160.02890.00970.0094-0.06160.03950.273-0.0254-0.09790.0401-0.04650.22638.2447-204.50166.6018
170.5648-0.00010.15370.22960.02580.17460.08030.0646-0.1287-0.2141-0.02760.1390.01760.0548-0.05280.41090.0364-0.11420.0396-0.08190.219835.7381-202.6334-9.158
180.1468-0.07020.21420.5371-0.03010.32520.0413-0.01480.0248-0.2115-0.0394-0.13250.0341-0.0207-0.00190.32140.0770.06120.0435-0.05680.255264.9792-202.28523.3883
190.42170.33480.03980.32590.00090.47930.02860.0655-0.16890.06130.0634-0.22860.05880.0762-0.0920.18940.0704-0.07930.0392-0.06580.373771.8848-203.521735.3301
200.5160.1986-0.05970.1745-0.07840.11070.0763-0.0715-0.1410.0645-0.0492-0.1401-0.0003-0.0154-0.02710.30250.0028-0.14980.0340.06980.2753.7887-207.146159.4899
210.03970.0066-0.06730.22-0.06920.1348-0.0062-0.0044-0.00950.07550.03620.0512-0.0063-0.0074-0.02990.3181-0.0104-0.06510.01320.04760.238721.4753-208.934861.0137
220.0258-0.0230.01570.0904-0.01050.00980.01830.0302-0.02580.0297-0.00790.1540.01290.0196-0.01040.2471-0.023-0.01920.06210.040.32141.438-168.992444.508
230.39950.00870.00980.4288-0.06840.07610.00750.01280.017-0.05030.00630.13820.05020.0284-0.01380.2146-0.0179-0.10080.02330.00130.27960.2956-166.375418.0012
240.39340.0091-0.06020.3366-0.0490.04070.02530.0203-0.0563-0.1515-0.00490.02980.00340.027-0.02040.3210.011-0.09820.0409-0.02750.15623.4781-163.627-3.7696
250.09850.11320.00830.5287-0.01960.00530.0191-0.0674-0.0176-0.0969-0.0064-0.12270.0201-0.0051-0.01280.30670.0380.0390.083-0.03150.206757.2726-160.2058-0.4702
260.04210.0321-0.08090.4739-0.01710.31640.0373-0.0078-0.01890.0087-0.0227-0.16390.0239-0.0161-0.01460.18020.0299-0.00530.0652-0.03640.276873.1294-161.370525.5901
270.1559-0.07350.02650.59320.03890.08990.00330.0111-0.03280.1138-0.0021-0.09780.01-0.0108-0.00110.24710.0058-0.09140.04370.00380.212861.3792-163.299257.6628
280.2098-0.0210.10640.45870.0130.07680.05220.0214-0.03270.0984-0.00530.0460.0002-0.0167-0.04690.3254-0.0188-0.0170.05530.04240.172729.4936-168.625367.5757
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 250
2X-RAY DIFFRACTION2B1 - 244
3X-RAY DIFFRACTION3C1 - 240
4X-RAY DIFFRACTION4D1 - 242
5X-RAY DIFFRACTION5E3 - 233
6X-RAY DIFFRACTION6F2 - 244
7X-RAY DIFFRACTION7G2 - 242
8X-RAY DIFFRACTION8H1 - 226
9X-RAY DIFFRACTION9I1 - 204
10X-RAY DIFFRACTION10J1 - 195
11X-RAY DIFFRACTION11K1 - 212
12X-RAY DIFFRACTION12L1 - 222
13X-RAY DIFFRACTION13M1 - 233
14X-RAY DIFFRACTION14N1 - 196
15X-RAY DIFFRACTION15O1 - 250
16X-RAY DIFFRACTION16P1 - 244
17X-RAY DIFFRACTION17Q1 - 240
18X-RAY DIFFRACTION18R1 - 242
19X-RAY DIFFRACTION19S3 - 233
20X-RAY DIFFRACTION20T2 - 244
21X-RAY DIFFRACTION21U2 - 242
22X-RAY DIFFRACTION22V1 - 226
23X-RAY DIFFRACTION23W1 - 204
24X-RAY DIFFRACTION24X1 - 195
25X-RAY DIFFRACTION25Y1 - 212
26X-RAY DIFFRACTION26Z1 - 222
27X-RAY DIFFRACTION27a1 - 233
28X-RAY DIFFRACTION28b1 - 196

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