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- PDB-9ft0: Yeast 20S proteasome in complex with epoxyketone inhibitor 42 -

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Basic information

Entry
Database: PDB / ID: 9ft0
TitleYeast 20S proteasome in complex with epoxyketone inhibitor 42
Components
  • (Proteasome subunit alpha type- ...) x 6
  • (Proteasome subunit beta type- ...) x 7
  • Probable proteasome subunit alpha type-7
KeywordsHYDROLASE / Proteasome / Inhibitor / Structure-based Drug Development / Binding Analysis
Function / homology
Function and homology information


proteasome core complex assembly / nuclear outer membrane-endoplasmic reticulum membrane network / Proteasome assembly / 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 ...proteasome core complex assembly / nuclear outer membrane-endoplasmic reticulum membrane network / Proteasome assembly / 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 / Ub-specific processing proteases / proteasome endopeptidase complex / proteasome core complex, beta-subunit complex / proteasome assembly / threonine-type endopeptidase activity / proteasome core complex, alpha-subunit complex / Neutrophil degranulation / proteasome complex / peroxisome / endopeptidase activity / proteasome-mediated ubiquitin-dependent protein catabolic process / mRNA binding / endoplasmic reticulum membrane / mitochondrion / nucleus / cytosol
Similarity search - Function
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 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 B-type subunit / Proteasome beta-type subunit profile. / : / Proteasome alpha-type subunit / Proteasome alpha-type subunit profile. / Proteasome subunit / Proteasome, subunit alpha/beta / Nucleophile aminohydrolases, N-terminal
Similarity search - Domain/homology
: / 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 ...: / 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)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsMaurits, E. / Huber, E.M. / Dekker, P.M. / Wang, X. / Heinemeyer, W. / Florea, B.I. / Groll, M. / Overkleeft, H.S.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)GR 1861/10-3 Germany
CitationJournal: to be published
Title: Structure-based design of peptide epoxyketones selectively targeting the three human immunoproteasome active sites
Authors: Maurits, E. / Huber, E.M. / Dekker, P.M. / Wang, X. / Heinemeyer, W. / Florea, B.I. / Groll, M. / Overkleeft, H.S.
History
DepositionJun 23, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 10, 2024Provider: repository / Type: Initial release
Revision 2.0Jul 17, 2024Group: Atomic model / Author supporting evidence ...Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations / Non-polymer description / Other / Polymer sequence / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / cell / chem_comp / chem_comp_atom / chem_comp_bond / entity / entity_name_com / entity_poly / entity_poly_seq / pdbx_entity_instance_feature / pdbx_entity_nonpoly / pdbx_entity_src_syn / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_refine_tls_group / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_ref / struct_ref_seq
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.occupancy / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.pdbx_label_seq_id / _atom_site_anisotrop.type_symbol / _cell.Z_PDB / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_entity_instance_feature.auth_comp_id / _pdbx_entity_instance_feature.comp_id / _pdbx_entity_src_syn.entity_id / _pdbx_refine_tls_group.beg_auth_seq_id / _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.value / _pdbx_struct_conn_angle.ptnr2_label_asym_id
Revision 2.1Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)734,79652
Polymers730,64628
Non-polymers4,14924
Water2,702150
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, AU contains one biological assembly
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area129480 Å2
ΔGint-538 kcal/mol
Surface area213310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.520, 299.480, 145.000
Angle α, β, γ (deg.)90.00, 112.90, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
33
44
55
66
77
88
99
1010
1111
1212
1313
1414
/ NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14

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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 (brewer's yeast) / References: UniProt: P23639
#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 (brewer's yeast) / References: UniProt: P23638
#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 (brewer's yeast) / References: UniProt: P40303
#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 (brewer's yeast) / References: UniProt: P32379
#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 (brewer's yeast) / References: UniProt: P40302
#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 (brewer's yeast) / References: UniProt: P21243

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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 (brewer's yeast) / References: UniProt: P21242

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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: 25013.355 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's 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 (brewer's yeast) / References: UniProt: P25451
#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 (brewer's yeast) / References: UniProt: P22141
#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: 23224.146 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's 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 (brewer's yeast) / References: UniProt: P23724
#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 (brewer's yeast) / References: UniProt: P30657
#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 (brewer's yeast)
References: UniProt: P38624, proteasome endopeptidase complex

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Non-polymers , 6 types, 174 molecules

#15: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Mg
#16: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#17: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#18: Chemical
ChemComp-A1IFL / (2S)-N-[(2S)-1-[[(1S)-2-cyclohexyl-1-[(2R,3S,6R,7S)-3-methanoyl-2,6-dimethyl-6,7-bis(oxidanyl)-1,4-oxazepan-7-yl]ethyl]amino]-3-(4-methoxyphenyl)-1-oxidanylidene-propan-2-yl]-2-(2-morpholin-4-ylethanoylamino)-4-oxidanyl-butanamide / epoxyketone inhibitor 42


Mass: 719.865 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C36H57N5O10 / Source: (synth.) synthetic construct (others) / Feature type: SUBJECT OF INVESTIGATION
#19: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#20: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 150 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 3.71 Å3/Da / Density % sol: 66.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.8 / Details: 20 mM MgAC2, 13% MPD, 0.1 M MES

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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: Oct 23, 2021
RadiationMonochromator: LN2 COOLED FIXED-EXIT. SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.75→30 Å / Num. obs: 264841 / % possible obs: 96.2 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.098 / Net I/σ(I): 7.4
Reflection shellResolution: 2.75→2.85 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.551 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 27405 / % possible all: 98.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.75→30 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.934 / SU B: 34.006 / SU ML: 0.277 / Cross valid method: THROUGHOUT / ESU R Free: 0.293 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23243 13235 5 %RANDOM
Rwork0.19044 ---
obs0.19253 251468 96.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 67.983 Å2
Baniso -1Baniso -2Baniso -3
1-0.94 Å20 Å2-0.54 Å2
2--0.77 Å2-0 Å2
3----0.92 Å2
Refinement stepCycle: 1 / Resolution: 2.75→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms49724 0 65 150 49939
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.01350690
X-RAY DIFFRACTIONr_bond_other_d0.0020.01548183
X-RAY DIFFRACTIONr_angle_refined_deg1.2341.64768586
X-RAY DIFFRACTIONr_angle_other_deg1.1291.591111065
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.86456340
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.55522.7822552
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.517158776
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.32315288
X-RAY DIFFRACTIONr_chiral_restr0.0350.26684
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0257588
X-RAY DIFFRACTIONr_gen_planes_other0.0010.0211404
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_it2.9516.2825444
X-RAY DIFFRACTIONr_mcbond_other2.9516.2825443
X-RAY DIFFRACTIONr_mcangle_it4.3029.41231756
X-RAY DIFFRACTIONr_mcangle_other4.3029.41231757
X-RAY DIFFRACTIONr_scbond_it2.5616.57225246
X-RAY DIFFRACTIONr_scbond_other2.5596.57125232
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.7779.74336813
X-RAY DIFFRACTIONr_long_range_B_refined5.81371.65252734
X-RAY DIFFRACTIONr_long_range_B_other5.80371.64952726
X-RAY DIFFRACTIONr_rigid_bond_restr0.439398873
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDNumberTypeRms dev position (Å)Weight position
10103136tight positional0.060.05
11113284tight positional0.010.05
12123429tight positional0.030.05
13133614tight positional00.05
14142941tight positional0.030.05
113789tight thermal12.970.5
223751tight thermal11.370.5
333740tight thermal15.780.5
443654tight thermal12.80.5
553545tight thermal12.570.5
663740tight thermal11.790.5
773784tight thermal11.50.5
883414tight thermal12.060.5
993115tight thermal11.140.5
10103136tight thermal9.650.5
11113284tight thermal10.270.5
12123429tight thermal11.120.5
13133614tight thermal10.190.5
14142941tight thermal8.870.5
LS refinement shellResolution: 2.75→2.821 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.375 993 -
Rwork0.315 18872 -
obs--98.34 %
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)
10.1487-0.04150.04440.0717-0.03470.1253-0.0063-0.00790.0061-0.00080.0039-0.0037-0.01270.00510.00240.1466-0.0026-0.02240.026-0.00330.138567.1917-91.974246.3143
20.15830.0132-0.06370.0370.03330.15410.00260.00350.0026-0.0086-0.0013-0.0007-0.00670.0165-0.00140.14310-0.02570.02770.00170.134859.9419-87.731116.5724
30.09560.03-0.03620.0688-0.00240.23650.0030.02570.0072-0.01310.0013-0.0156-0.0164-0.0032-0.00440.14520.0033-0.02250.01920.00670.136932.6345-87.01170.9881
40.13440.05380.00810.1429-0.04550.1329-0.00510.00090.0104-0.0011-0.0010.0142-0.003-0.00460.0060.13830.0045-0.02190.01720.00590.13293.8617-89.927114.2003
50.15670.02430.0660.05970.05890.1549-0.00820.00990.0095-0.00480.00920.01-0.0169-0.0316-0.0010.14270.0041-0.02120.0286-0.00030.136-2.6559-93.794745.751
60.12610.0287-0.10590.0289-0.01170.09670.00370.00570.00950.0132-0.00310.0121-0.0043-0.0105-0.00060.1504-0.0001-0.02950.028-0.0020.137215.5798-94.674370.033
70.08090.0303-0.00820.0438-0.02180.09050.0046-0.01240.0038-0.0003-0.00370.0079-0.00640.0065-0.00090.151-0.002-0.02240.0234-0.00440.140947.9512-93.163871.4381
80.03340.0206-0.00510.05370.02240.01770.0006-0.0259-0.00110.00440.0006-0.0142-0.00780.0147-0.00120.14440.0014-0.01960.02730.00050.129367.6337-129.943848.3599
90.1141-0.0278-0.03870.14760.0370.12760.0004-0.00550.00230.00210.0004-0.01-0.01370.0184-0.00080.147-0.0032-0.02530.0240.00210.136568.3244-127.306421.0121
100.16090.00270.02590.23020.08660.06740.00160.01120.0092-0.01470.0034-0.0075-0.0172-0.0121-0.0050.1448-0.001-0.02320.02550.00170.133644.7843-126.4725-0.8716
110.11810.04620.0520.11830.04630.03130.0050.02540.0029-0.0085-0.0008-0.0039-0.01290.0051-0.00420.15310.003-0.02230.030.00290.136911.0824-130.52852.5028
120.13310.042-0.00650.0647-0.02230.04920.01480.00540.01290.01110.00390.0107-0.01030.0117-0.01870.13960.0034-0.02670.02490.00030.1291-4.3561-133.949128.6288
130.0612-0.0326-0.00390.1637-0.04050.0757-0.0021-0.00480.00290.00910.00290.0141-0.0071-0.0024-0.00080.14640.0008-0.02570.02780.0010.13717.9388-137.513760.6119
140.2046-0.0208-0.01830.23010.02420.08650.0004-0.0181-0.00410.01790.00240.0006-0.0033-0.0025-0.00280.1442-0.003-0.02620.02880.00170.132139.952-133.826471.2443
150.09730.0174-0.05170.04280.0110.0897-0.0059-0.0006-0.0045-0.00040.00530.00630.0094-0.00510.00060.1462-0.0056-0.02550.02260.00160.13931.8319-206.018536.7529
160.2061-0.0020.03970.06520.00790.1103-0.00480.004-0.00840.0022-0.00180.00490.0011-0.01470.00660.1431-0.0008-0.02340.0219-0.00350.13338.2523-204.88086.5813
170.0811-0.04260.07320.0289-0.04430.17890.01980.0048-0.0357-0.0385-0.00380.02470.0221-0.004-0.0160.14270.0119-0.010.0155-0.02040.125635.3327-203.0808-9.4413
180.08410.0186-0.04550.0976-0.03330.1004-0.00210.0033-0.0141-0.0193-0.0075-0.00920.0057-0.00250.00970.1471-0.0005-0.02640.0018-0.00950.134364.3791-202.4673.6695
190.1874-0.0084-0.09110.0602-0.04350.084-0.0030.0058-0.0071-0.0043-0.0096-0.02980.01050.00540.01250.14510.0028-0.02450.0207-0.00570.135671.6446-204.052835.2352
200.12010.0791-0.0110.0549-0.00480.0151-0.0025-0.0086-0.02330.0090.001-0.01180.00960.00090.00150.1470.0045-0.0260.02520.00620.137753.9519-207.41459.5418
210.0914-0.0108-0.05270.0416-0.04340.1705-0.0091-0.0054-0.0080.00210.00720.00260.0116-0.00740.00190.1487-0.004-0.02720.01970.00180.1421.6815-209.342561.1825
220.0113-0.0010.0150.01110.00410.0254-0.004-0.01840.00480.02560.00140.02320.023-0.0260.00260.144-0.003-0.02940.03070.00050.1331.5587-169.041945.4861
230.21830.03950.02360.2117-0.00180.0615-0.00760.0030.0015-0.00220.00450.0190.0095-0.02580.00310.1470-0.02630.0270.00190.12870.1774-166.823218.0729
240.12760.0603-0.02050.06930.00210.0089-0.00180.0168-0.0049-0.01140.00270.01210.01090.0001-0.00090.14630.0009-0.02670.02980.0040.134523.2636-163.7707-4.0637
250.01180.0378-0.0110.1699-0.02470.0127-0.00260.004-0.0108-0.0065-0.0061-0.01750.0033-0.00880.00880.14650.0029-0.02750.0267-0.00080.143157.04-160.3568-0.581
260.04680.01870.00190.0772-0.03050.06790.0087-0.0122-0.0093-0.0075-0.0018-0.0020.00060.004-0.00690.14510.0016-0.02450.02220.00160.138773.0433-161.553325.4393
270.0949-0.024-0.03590.12810.04150.0429-0.0045-0.0166-0.00280.0021-0.0016-0.0119-0.00330.00570.00610.1446-0.0011-0.02420.02860.00330.136761.5084-163.601857.7864
280.163-0.0499-0.04360.19010.03750.11810.0032-0.0183-0.00490.0114-0.00520.00060.0040.01130.00210.1437-0.0031-0.02490.03150.00110.132329.7672-169.16968.1866
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 250
2X-RAY DIFFRACTION2B1 - 244
3X-RAY DIFFRACTION3C1 - 241
4X-RAY DIFFRACTION4D1 - 242
5X-RAY DIFFRACTION5E1 - 233
6X-RAY DIFFRACTION6F1 - 244
7X-RAY DIFFRACTION7G1 - 243
8X-RAY DIFFRACTION8H2 - 222
9X-RAY DIFFRACTION9I1 - 204
10X-RAY DIFFRACTION10J1 - 198
11X-RAY DIFFRACTION11K2 - 212
12X-RAY DIFFRACTION12L1 - 222
13X-RAY DIFFRACTION13M1 - 233
14X-RAY DIFFRACTION14N1 - 196
15X-RAY DIFFRACTION15O1 - 250
16X-RAY DIFFRACTION16P1 - 244
17X-RAY DIFFRACTION17Q1 - 241
18X-RAY DIFFRACTION18R1 - 242
19X-RAY DIFFRACTION19S1 - 233
20X-RAY DIFFRACTION20T1 - 244
21X-RAY DIFFRACTION21U1 - 243
22X-RAY DIFFRACTION22V2 - 222
23X-RAY DIFFRACTION23W1 - 204
24X-RAY DIFFRACTION24X1 - 198
25X-RAY DIFFRACTION25Y2 - 212
26X-RAY DIFFRACTION26Z1 - 222
27X-RAY DIFFRACTION27a1 - 233
28X-RAY DIFFRACTION28b1 - 196

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