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- PDB-9ft1: Yeast 20S proteasome in complex with epoxyketone inhibitor 13 -

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Basic information

Entry
Database: PDB / ID: 9ft1
TitleYeast 20S proteasome in complex with epoxyketone inhibitor 13
Components
  • (Proteasome subunit alpha type- ...) x 6
  • (Proteasome subunit beta type- ...) x 7
  • Probable proteasome subunit alpha type-7
KeywordsHYDROLASE / Yeast 20S proteasome in complex with epoxyketone inhibitor 13
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
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 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
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: 2.6 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_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.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.id / _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_prop.value / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _struct_asym.entity_id
Revision 2.1Nov 13, 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)735,37344
Polymers730,64628
Non-polymers4,72716
Water6,828379
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 area123400 Å2
ΔGint-404 kcal/mol
Surface area211940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)136.000, 300.670, 144.540
Angle α, β, γ (deg.)90.00, 113.09, 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 , 4 types, 395 molecules

#15: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Mg
#16: Chemical
ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#17: Chemical
ChemComp-A1IFK / tert-butyl 4-[2-[[(2S)-1-[[(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]amino]-1-oxidanylidene-3-phenylmethoxy-propan-2-yl]amino]-2-oxidanylidene-ethyl]piperazine-1-carboxylate / epoxyketone inhibitor 13


Mass: 895.092 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C47H70N6O11 / Source: (synth.) synthetic construct (others) / Feature type: SUBJECT OF INVESTIGATION
#18: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 379 / 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: 3.72 Å3/Da / Density % sol: 66.9 %
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: Feb 16, 2020
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: 2.6→30 Å / Num. obs: 317828 / % possible obs: 97.4 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 16.4
Reflection shellResolution: 2.6→2.7 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.583 / Mean I/σ(I) obs: 3.1 / Num. unique obs: 34541 / % possible all: 99.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→30 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.945 / SU B: 27.877 / SU ML: 0.244 / Cross valid method: THROUGHOUT / ESU R Free: 0.241 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22199 15884 5 %RANDOM
Rwork0.18236 ---
obs0.18485 301792 97.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 62.047 Å2
Baniso -1Baniso -2Baniso -3
1--3.97 Å2-0 Å2-2.27 Å2
2--5.65 Å20 Å2
3---0.19 Å2
Refinement stepCycle: 1 / Resolution: 2.6→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms49532 0 67 379 49978
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.01350498
X-RAY DIFFRACTIONr_bond_other_d0.0070.01747110
X-RAY DIFFRACTIONr_angle_refined_deg1.3631.64868332
X-RAY DIFFRACTIONr_angle_other_deg1.3071.589109342
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1856306
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.67622.7912530
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.711158738
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.38315284
X-RAY DIFFRACTIONr_chiral_restr0.0490.26662
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0256600
X-RAY DIFFRACTIONr_gen_planes_other0.0020.0210404
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_it5.7665.45125314
X-RAY DIFFRACTIONr_mcbond_other5.7665.45125313
X-RAY DIFFRACTIONr_mcangle_it7.7568.19131590
X-RAY DIFFRACTIONr_mcangle_other7.7568.19131591
X-RAY DIFFRACTIONr_scbond_it6.145.88625184
X-RAY DIFFRACTIONr_scbond_other6.1385.88625182
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.1188.65836743
X-RAY DIFFRACTIONr_long_range_B_refined9.79663.04553132
X-RAY DIFFRACTIONr_long_range_B_other9.76663.02153100
X-RAY DIFFRACTIONr_rigid_bond_restr6.339397608
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
10103063tight positional0.010.05
11113283tight positional0.010.05
12123389tight positional0.010.05
13133564tight positional0.010.05
14142919tight positional0.010.05
113765tight thermal11.080.5
223714tight thermal11.330.5
333685tight thermal17.060.5
443540tight thermal120.5
553459tight thermal11.590.5
663693tight thermal13.090.5
773724tight thermal10.980.5
883406tight thermal9.210.5
993091tight thermal8.140.5
10103063tight thermal7.260.5
11113283tight thermal6.950.5
12123389tight thermal7.890.5
13133564tight thermal7.680.5
14142919tight thermal7.130.5
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.347 1188 -
Rwork0.281 22563 -
obs--99.18 %
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)
10.0143-0.01560.00490.04170.00910.0138-0.00530.00960.0060.00080.0007-0.00040.00090.00620.00460.1906-0.0007-0.00340.016-0.00050.165467.2709-92.382645.8143
20.0372-0.00050.03030-0.00050.0260.00280.00870.0044-0.00010-0.00060.00130.0035-0.00280.191-0.0017-0.00320.01460.00130.172260.1994-88.282216.124
30.02760.00460.02560.0148-0.00640.0336-0.00490.0083-0.00010.0027-0.0027-0.00240.00140.00640.00750.1861-0.0016-0.00240.01850.0020.168532.8362-87.77250.6945
40.02690.00470.02270.0407-0.00910.0235-0.0021-0.01190.0048-0.005-0.0022-0.0007-0.0002-0.01090.00430.19170.00160.00210.01170.00060.16643.6027-90.241413.1531
50.0165-0.00850.01830.03060.0020.0256-0.0064-0.0006-0.0034-0.00290.00640.003-0.00170.002400.19490.0013-0.00220.01360.00160.1656-3.0119-94.425545.1355
60.03940.0129-0.00690.06670.00030.00270.0057-0.0015-0.0065-0.0006-0.0070.01410.00370.00430.00130.1866-0.0016-0.0080.0159-0.00040.169415.4455-94.954669.4272
70.0020.0015-0.00220.073-0.00330.0056-0.001-0.0016-0.0118-0.00530.00220.0047-0.0041-0.0001-0.00130.1885-0.0015-0.00150.0172-0.00480.170947.9307-93.592270.7989
80.0033-0.0056-0.00090.0314-0.00520.0029-0.002-0.0054-0.0063-0.01560.00060.0091-0.00380.0050.00140.2031-0.0036-0.00150.0144-0.00180.175267.5535-130.446847.9261
90.01370.0110.01040.018-0.00520.0475-0.002-0.0005-0.0003-0.00530.00040.00820.0040.01430.00160.19160-0.00450.0143-0.00240.16668.6362-127.921220.7808
100.02580.03270.02020.0880.00970.02290.00190.00070.00310.0010.0022-0.0068-0.0014-0.0037-0.00410.18330.0028-0.00560.0165-0.00020.171345.0995-127.116-0.7697
110.00190.002-0.00420.10680.02760.0296-0.00410.0033-0.00080.00940.01440.00390.00330.0052-0.01040.18840.0018-0.00050.0165-0.00040.172111.2777-131.19232.5167
120.03460.0077-0.01320.01420.01660.0376-0.0001-0.00280.004-0.0008-0.00220.00260.00530.00490.00230.1905-0.0003-0.00280.01930.00090.1621-4.3261-134.451328.4048
130.0132-0.01240.01520.03820.00020.0314-0.0005-0.0023-0.0005-0.00290.00130.0045-0.00230.0054-0.00080.19010.0014-0.00440.01230.00060.17037.878-137.905660.2113
140.0434-0.00130.03090.07630.02310.03320.0028-0.0084-0.00260.0018-0.00130.00580.00810.0006-0.00150.1849-0.0015-0.0030.01520.0010.17139.8651-134.116670.834
150.0543-0.0057-0.03730.0185-0.00880.0351-0.00490.0052-0.0042-0.00290.00270.00120.0044-0.00320.00220.194-0.0023-0.00330.012-0.00040.16441.876-206.647336.9703
160.01920.0061-0.02990.0022-0.00970.0481-0.00230.00490.00050.0030.0016-0.0046-0.0052-0.0050.00070.1906-0.0008-0.00150.0088-0.00250.1718.2639-205.67726.8483
170.0453-0.01080.00120.02620.00140.0013-0.00380.00480.0002-0.009-0.0070.0035-0.0091-0.00040.01080.19260.00380.0020.0044-0.00830.163435.6354-203.7456-9.0111
180.012-0.004-0.03650.00410.01390.1128-0.0057-0.0038-0.0002-0.0078-0.0026-0.00450.00610.00870.00830.18930.0036-0.01040.01-0.00150.173865.0053-203.31873.4032
190.0079-0.0021-0.00090.07830.01070.0016-0.00170.00910.0024-0.00260.0006-0.0114-0.0007-0.00090.00110.19480.00360.00170.0116-0.00060.161472.1202-204.388435.3918
200.11520.02950.03340.05430.02570.05990.0133-0.0045-0.00560.0045-0.0076-0.01690.0047-0.0154-0.00580.193-0.00050.00130.00420.00090.16654.0819-207.965659.6406
210.0030.0110.00370.0796-0.00350.05270.00030.00430.00660.00210.0067-0.00490.0028-0.001-0.0070.18690.0003-0.00190.01390.00340.168621.6823-209.810361.2663
220.0023-0.00340.00140.03230.00080.00160.0008-0.00590.0021-0.02670.0056-0.00510.0031-0.0043-0.00640.2079-0.0018-0.00540.01580.00050.18021.7003-169.439945.3044
230.03160.00440.00040.0055-0.01340.03940.0021-0.00170.0038-0.00580.00360.00040.0013-0.0073-0.00570.1921-0.0021-0.00270.01290.00090.16710.1649-167.438218.0384
240.02270.0368-0.02480.0675-0.02540.0835-0.00040.0036-0.00190.0002-0.00060.00170.00250.00030.0010.18510.003-0.00270.016-0.00030.170423.3425-164.6469-3.7342
250.03850.01910.02690.09670.01040.0204-0.0030.00870.00030.01530.0109-0.0011-0.00350.0019-0.0080.18810.0004-0.00460.01510.00150.17157.2127-161.1275-0.3392
260.0024-0.00250.01230.0035-0.0150.0704-0.00090.0003-0.0057-0.0021-0.0001-0.0053-0.0073-0.00370.0010.19110.0006-0.00310.0139-0.00130.169573.2425-162.193925.4531
270.0235-0.0327-0.02690.05530.02290.0544-0.0008-0.00460.0003-0.00040.0052-0.00040.00310.002-0.00430.18930.0018-0.00140.0115-0.00090.167261.5711-164.054357.5926
280.02050.0009-0.03520.0771-0.01420.06330.0002-0.006-0.003-0.00170.0021-0.0006-0.00780.0091-0.00230.1841-0.0021-0.00430.0145-0.00140.170629.7763-169.581568.0165
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 DIFFRACTION8H2 - 222
9X-RAY DIFFRACTION9I1 - 204
10X-RAY DIFFRACTION10J1 - 195
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 - 240
18X-RAY DIFFRACTION18R1 - 242
19X-RAY DIFFRACTION19S3 - 233
20X-RAY DIFFRACTION20T2 - 244
21X-RAY DIFFRACTION21U2 - 242
22X-RAY DIFFRACTION22V2 - 222
23X-RAY DIFFRACTION23W1 - 204
24X-RAY DIFFRACTION24X1 - 195
25X-RAY DIFFRACTION25Y2 - 212
26X-RAY DIFFRACTION26Z1 - 222
27X-RAY DIFFRACTION27a1 - 233
28X-RAY DIFFRACTION28b1 - 196

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