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- PDB-9fst: Yeast 20S proteasome with human beta1i (1-51) in complex with epo... -

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Basic information

Entry
Database: PDB / ID: 9fst
TitleYeast 20S proteasome with human beta1i (1-51) in complex with epoxyketone inhibitor LU-001i
Components
  • (Proteasome subunit alpha type- ...) x 6
  • (Proteasome subunit beta type- ...) x 7
  • Probable proteasome subunit alpha type-7
KeywordsHYDROLASE / Proteasome / Mutant / Human Chimeric Subunit / Structure-based Drug Development / Inhibitor / Binding Analysis
Function / homology
Function and homology information


regulation of cysteine-type endopeptidase activity / spermatoproteasome complex / Regulation of ornithine decarboxylase (ODC) / proteasome core complex / Cross-presentation of soluble exogenous antigens (endosomes) / Somitogenesis / proteasome core complex assembly / nuclear outer membrane-endoplasmic reticulum membrane network / Cross-presentation of soluble exogenous antigens (endosomes) / TNFR2 non-canonical NF-kB pathway ...regulation of cysteine-type endopeptidase activity / spermatoproteasome complex / Regulation of ornithine decarboxylase (ODC) / proteasome core complex / Cross-presentation of soluble exogenous antigens (endosomes) / Somitogenesis / 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 / immune system process / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Regulation of PTEN stability and activity / KEAP1-NFE2L2 pathway / CDK-mediated phosphorylation and removal of Cdc6 / Neddylation / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / 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 / Ub-specific processing proteases / proteasome core complex, alpha-subunit complex / threonine-type endopeptidase activity / Neutrophil degranulation / proteasome complex / Regulation of activated PAK-2p34 by proteasome mediated degradation / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / SCF-beta-TrCP mediated degradation of Emi1 / Asymmetric localization of PCP proteins / NIK-->noncanonical NF-kB signaling / Ubiquitin-dependent degradation of Cyclin D / AUF1 (hnRNP D0) binds and destabilizes mRNA / TNFR2 non-canonical NF-kB pathway / Vpu mediated degradation of CD4 / Assembly of the pre-replicative complex / Degradation of DVL / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Dectin-1 mediated noncanonical NF-kB signaling / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Hh mutants are degraded by ERAD / Degradation of AXIN / Activation of NF-kappaB in B cells / Degradation of GLI1 by the proteasome / Hedgehog ligand biogenesis / Defective CFTR causes cystic fibrosis / Negative regulation of NOTCH4 signaling / G2/M Checkpoints / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / Autodegradation of the E3 ubiquitin ligase COP1 / Vif-mediated degradation of APOBEC3G / Hedgehog 'on' state / Regulation of RUNX3 expression and activity / Degradation of GLI2 by the proteasome / GLI3 is processed to GLI3R by the proteasome / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / MAPK6/MAPK4 signaling / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / ABC-family proteins mediated transport / Degradation of beta-catenin by the destruction complex / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / CDK-mediated phosphorylation and removal of Cdc6 / CLEC7A (Dectin-1) signaling / SCF(Skp2)-mediated degradation of p27/p21 / Regulation of expression of SLITs and ROBOs / FCERI mediated NF-kB activation / Interleukin-1 signaling / Regulation of PTEN stability and activity / Orc1 removal from chromatin / Regulation of RAS by GAPs / Separation of Sister Chromatids / Regulation of RUNX2 expression and activity / The role of GTSE1 in G2/M progression after G2 checkpoint / UCH proteinases / KEAP1-NFE2L2 pathway / Antigen processing: Ubiquitination & Proteasome degradation / Downstream TCR signaling / peroxisome / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Neddylation / ER-Phagosome pathway / proteasome-mediated ubiquitin-dependent protein catabolic process / endopeptidase activity / Ub-specific processing proteases / mRNA binding / endoplasmic reticulum membrane / mitochondrion / extracellular exosome / nucleoplasm / 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-9 ...: / 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-9 / 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 speciesHomo sapiens (human)
Saccharomyces cerevisiae (brewer's yeast)
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 21, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 17, 2024Provider: repository / Type: Initial release

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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-9,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-9,Proteasome subunit beta type-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)734,42849
Polymers730,35228
Non-polymers4,07621
Water4,882271
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 area121660 Å2
ΔGint-497 kcal/mol
Surface area213670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.370, 300.160, 143.970
Angle α, β, γ (deg.)90.00, 112.78, 90.00
Int Tables number4
Space group name H-MP1211

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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: 25114.459 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-9,Proteasome subunit beta type-1 / Low molecular mass protein 2 / Macropain chain 7 / Multicatalytic endopeptidase complex chain 7 / ...Low molecular mass protein 2 / Macropain chain 7 / Multicatalytic endopeptidase complex chain 7 / Proteasome chain 7 / Proteasome subunit beta-1i / Really interesting new gene 12 protein / Macropain subunit PRE3 / Multicatalytic endopeptidase complex subunit PRE3 / Proteasome component PRE3 / Proteinase YSCE subunit PRE3


Mass: 21268.834 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: PSMB9, LMP2, PSMB6i, RING12, PRE3, YJL001W, J1407 / Production host: Saccharomyces cerevisiae (brewer's yeast)
References: UniProt: P28065, UniProt: P38624, proteasome endopeptidase complex

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Non-polymers , 6 types, 292 molecules

#15: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#16: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#17: Chemical
ChemComp-A1IF8 / azanylidene-[2-[[(2S)-1-[(2S)-2-[[(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]-1-oxidanylidene-hexan-2-yl]carbamoyl]-4,4-bis(fluoranyl)pyrrolidin-1-yl]-1-oxidanylidene-propan-2-yl]amino]-2-oxidanylidene-ethyl]imino-azanium / epoxyketone inhibitor LU-001i


Mass: 715.809 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C32H53F2N8O8 / Feature type: SUBJECT OF INVESTIGATION
#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.: 1 / Source method: obtained synthetically / Formula: SO4
#20: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 271 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 3.69 Å3/Da / Density % sol: 66.64 %
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 21, 2023
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: 264849 / % possible obs: 96.7 % / Redundancy: 3 % / Rmerge(I) obs: 0.095 / Net I/σ(I): 7.5
Reflection shellResolution: 2.75→2.85 Å / Redundancy: 3 % / Rmerge(I) obs: 0.612 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 27384 / % possible all: 98.9

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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: 0.954 / Cor.coef. Fo:Fc free: 0.932 / SU B: 36.125 / SU ML: 0.307 / Cross valid method: THROUGHOUT / ESU R: 0.567 / ESU R Free: 0.308 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24466 13235 5 %RANDOM
Rwork0.20546 ---
obs0.20742 251463 96.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 72.513 Å2
Baniso -1Baniso -2Baniso -3
1-1.18 Å20 Å20.04 Å2
2---3.39 Å20 Å2
3---1.61 Å2
Refinement stepCycle: 1 / Resolution: 2.75→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms49427 0 65 271 49763
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.01350412
X-RAY DIFFRACTIONr_bond_other_d0.0020.01547908
X-RAY DIFFRACTIONr_angle_refined_deg1.4091.64668224
X-RAY DIFFRACTIONr_angle_other_deg1.21.59110448
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.34456305
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.12722.8322535
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.68158721
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.60415282
X-RAY DIFFRACTIONr_chiral_restr0.0540.26648
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0257231
X-RAY DIFFRACTIONr_gen_planes_other0.0020.0211297
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_it1.2473.57225304
X-RAY DIFFRACTIONr_mcbond_other1.2473.57225303
X-RAY DIFFRACTIONr_mcangle_it2.1965.3531581
X-RAY DIFFRACTIONr_mcangle_other2.1955.3531582
X-RAY DIFFRACTIONr_scbond_it1.1593.7525108
X-RAY DIFFRACTIONr_scbond_other1.1553.74825102
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.0445.55136638
X-RAY DIFFRACTIONr_long_range_B_refined4.4540.97653471
X-RAY DIFFRACTIONr_long_range_B_other4.44340.96153450
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.75→2.821 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.361 997 -
Rwork0.351 18935 -
obs--99.15 %
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)
10.8659-0.22420.20020.4919-0.01420.2827-0.05110.02610.03170.00170.0236-0.1639-0.0822-0.02210.02750.7522-0.0523-0.070.1448-0.03710.54667.2147-91.938145.7941
20.65160.2118-0.03980.3345-0.01440.4397-0.0903-0.02140.0452-0.1758-0.00450.0056-0.12070.12760.09490.8169-0.08540.00930.17950.05790.46359.7212-87.598416.248
30.46480.48030.04430.5202-0.07981.2068-0.0350.04530.0728-0.120.0330.049-0.00810.13940.0020.8754-0.0078-0.08460.11660.08070.465332.4523-87.21481.0175
40.71530.0554-0.01480.0744-0.11040.557-0.0642-0.01790.0489-0.03790.00450.1672-0.09650.05960.05970.76940.1016-0.23350.0590.08080.65233.2836-89.992213.6333
50.42620.15280.36810.2326-0.09210.7294-0.0964-0.08380.0699-0.05840.0120.154-0.1388-0.06590.08450.66730.1035-0.06130.1375-0.02620.6925-2.9218-94.387145.6878
60.93530.2514-0.31830.27870.07950.26680.0325-0.03530.11520.0827-0.07870.1236-0.02580.00650.04610.85590.04790.03940.1745-0.09860.456415.6528-95.028369.8235
70.2009-0.0299-0.00860.59230.01051.01070.06220.02890.02920.1513-0.0494-0.0798-0.0343-0.0571-0.01280.8645-0.0379-0.10050.1186-0.07610.451348.0817-93.359970.9736
80.2185-0.1271-0.12940.12640.08810.09310.0444-0.00180.0360.05560.0624-0.1627-0.0338-0.0101-0.10690.7439-0.0084-0.13740.173-0.06190.579268.1962-129.231447.3745
90.6266-0.14640.14010.7010.36070.30340.00120.0132-0.0182-0.11230.0354-0.1916-0.0665-0.0425-0.03670.7508-0.00850.02970.1694-0.02630.535968.5213-127.205820.6304
100.55660.00390.20050.66840.14310.11060.06150.03530.0821-0.2212-0.034-0.0436-0.0669-0.0009-0.02750.9123-0.00460.02040.20920.02390.354744.9407-126.363-0.8071
110.79290.48610.19310.6786-0.02770.29860.0571-0.00160.0158-0.1824-0.02790.1405-0.02950.0561-0.02920.77890.0493-0.21080.19910.02240.494911.1154-130.71892.4661
120.13270.16090.21170.22960.25690.38510.0761-0.0046-0.00590.0109-0.02580.12780.01180.0343-0.05020.690.0405-0.14730.17180.05420.7-4.3018-134.25328.5493
130.6017-0.1424-0.00821.3324-0.02460.01460.0372-0.05390.01380.1708-0.03040.1932-0.0180.0522-0.00680.7439-0.00190.01890.21750.00540.47987.8554-136.40160.2706
140.7353-0.1766-0.27770.84860.03610.59440.0210.02530.09270.2712-0.0086-0.0920.0708-0.0256-0.01250.8032-0.0061-0.11490.2475-0.02890.358640.2422-134.070870.4382
151.02590.0712-0.39850.3780.2680.5401-0.06270.07070.03590.0627-0.00360.0960.1904-0.02760.06630.7493-0.1363-0.20480.06620.09350.61192.2592-206.316936.4288
160.96010.12290.3040.54060.02190.3916-0.0603-0.015-0.0162-0.091-0.0008-0.00710.0395-0.11860.06120.7618-0.0269-0.20910.1202-0.08130.55638.6715-205.14826.3967
170.53540.24040.26770.4564-0.02310.66370.19630.0193-0.1254-0.2956-0.11160.2750.02730.0898-0.08471.01240.118-0.26840.0584-0.15310.549835.8899-203.0392-9.5006
180.8193-0.05720.26590.6054-0.00530.14490.0871-0.12-0.0006-0.3253-0.0962-0.15280.0756-0.05020.00910.92330.17410.06260.1137-0.13570.524465.2972-202.47753.0257
190.77090.1716-0.17460.5512-0.28140.22260.01820.0399-0.07030.0430.0631-0.2570.10930.0062-0.08120.66320.1443-0.22370.0441-0.13630.831972.3688-203.67934.9577
200.89990.2990.24960.1170.02820.50010.1254-0.0646-0.26490.0738-0.0392-0.16520.0753-0.0578-0.08620.84230.026-0.34110.04320.1280.646554.446-207.391959.2147
210.4021-0.07450.03320.60820.00990.72680.0601-0.0119-0.0180.0775-0.00870.08960.05770.0634-0.05150.8651-0.0506-0.19320.03480.11530.529622.1166-209.487160.7647
220.03310.02190.05030.12190.06660.09060.0637-0.0279-0.08320.0744-0.00410.15290.0738-0.0557-0.05950.7154-0.0639-0.12710.18160.09580.61291.4111-169.858244.5866
230.83450.06710.22070.69050.00580.44290.04680.0288-0.0497-0.04570.01270.23590.02770.0683-0.05950.7075-0.0327-0.20680.1324-0.01190.58470.3921-167.105917.9348
240.5289-0.0749-0.00970.2661-0.03010.01820.07050.0467-0.1719-0.2101-0.03740.04120.0310.0461-0.0330.91170.0451-0.15910.1605-0.04750.394923.3673-164.0757-3.9625
250.4862-0.04270.1230.3164-0.00030.09320.02340.0361-0.0445-0.23250.0525-0.06660.01040.0046-0.0760.83020.0640.0360.226-0.07460.45457.2851-160.3616-0.7618
260.02860.0888-0.10860.2828-0.32550.56470.0251-0.0044-0.04270.0594-0.0265-0.18430.001-0.08370.00140.62820.0713-0.02220.237-0.06530.653273.3822-161.45125.1516
270.42510.09320.00180.62780.02940.1542-0.04010.0018-0.07940.13110.0323-0.1525-0.0056-0.0370.00780.7440.035-0.20880.16930.00180.543861.9693-164.453557.1968
280.827-0.0460.20110.670.28640.2780.00330.0278-0.08180.2378-0.08460.0769-0.0065-0.01210.08130.8344-0.0378-0.0780.18890.0680.387530.0054-169.144767.4394
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 DIFFRACTION11K2 - 212
12X-RAY DIFFRACTION12L1 - 222
13X-RAY DIFFRACTION13M1 - 225
14X-RAY DIFFRACTION14N2 - 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 DIFFRACTION25Y2 - 212
26X-RAY DIFFRACTION26Z1 - 222
27X-RAY DIFFRACTION27a1 - 228
28X-RAY DIFFRACTION28b2 - 196

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