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- PDB-4r17: Ligand-induced aziridine-formation at subunit beta5 of the yeast ... -

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Basic information

Entry
Database: PDB / ID: 4r17
TitleLigand-induced aziridine-formation at subunit beta5 of the yeast 20S proteasome
Components
  • (Proteasome subunit alpha type- ...) x 7
  • (Proteasome subunit beta type- ...) x 7
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Proteasome / Drug Development / Binding Analysis / Umpolung / Crosslink / HYDROLASE-HYDROLASE INHIBITOR complex
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
(2S,3S)-3-methylaziridine-2-carboxylic acid / 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 ...(2S,3S)-3-methylaziridine-2-carboxylic acid / 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 S288c (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsDubiella, C. / Cui, H. / Gersch, M. / Brouwer, A.J. / Sieber, S.A. / Krueger, A. / Liskamp, R. / Groll, M.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2014
Title: Selective inhibition of the immunoproteasome by ligand-induced crosslinking of the active site.
Authors: Dubiella, C. / Cui, H. / Gersch, M. / Brouwer, A.J. / Sieber, S.A. / Kruger, A. / Liskamp, R.M. / Groll, M.
History
DepositionAug 4, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 15, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 5, 2014Group: Database references
Revision 1.2Sep 20, 2023Group: 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 / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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: 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: 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)731,52041
Polymers731,05128
Non-polymers47013
Water62,5483472
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area118680 Å2
ΔGint-446 kcal/mol
Surface area214370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)134.720, 301.360, 144.740
Angle α, β, γ (deg.)90.00, 112.81, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.99945, -0.001572, 0.033137), (-0.004169, -0.985006, -0.172467), (0.032911, -0.17251, 0.984458)67.31203, -289.56424, -25.87582
DetailsAU contains one biological assembly.

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Components

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Proteasome subunit alpha type- ... , 7 types, 14 molecules AOBPCQDRESFTGU

#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 S288c (yeast) / Strain: ATCC 204508 / S288C
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 S288c (yeast) / Strain: ATCC 204508 / S288C
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 S288c (yeast) / Strain: ATCC 204508 / S288C
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 S288c (yeast) / Strain: ATCC 204508 / S288C
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 S288c (yeast) / Strain: ATCC 204508 / S288C
References: UniProt: P40302, proteasome endopeptidase complex
#6: Protein 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 S288c (yeast) / Strain: ATCC 204508 / S288C
References: UniProt: P21242, 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 S288c (yeast) / Strain: ATCC 204508 / S288C
References: UniProt: P21243, 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: 25114.459 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288C
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 S288c (yeast) / Strain: ATCC 204508 / S288C
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 S288c (yeast) / Strain: ATCC 204508 / S288C
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 S288c (yeast) / Strain: ATCC 204508 / S288C
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 S288c (yeast) / Strain: ATCC 204508 / S288C
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 S288c (yeast) / Strain: ATCC 204508 / S288C
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 S288c (yeast) / Strain: ATCC 204508 / S288C
References: UniProt: P38624, proteasome endopeptidase complex

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Non-polymers , 3 types, 3485 molecules

#15: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Mg
#16: Chemical ChemComp-3K4 / (2S,3S)-3-methylaziridine-2-carboxylic acid


Type: L-peptide linking / Mass: 101.104 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H7NO2
#17: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3472 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer details3K4 IS AZIRIDINE-THR. THE ACTIVE SITE NUCLEOPHILE THR1 IS MODIFIED IN CHAINS K AND Y BY FORMATION ...3K4 IS AZIRIDINE-THR. THE ACTIVE SITE NUCLEOPHILE THR1 IS MODIFIED IN CHAINS K AND Y BY FORMATION OF AN AZIRIDIN-RING TO BECOME 3K4. THIS REACTION IS INDUCED BY A PEPTIDIC SULFONYLFLUORIDE ACTING AS INHIBITOR BY INDUCING THE REACTION AT THE CATALYTIC SITE (CHAINS K AND Y ONLY).

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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 / pH: 6.8
Details: 20 MM MGAC2, 13% MPD, PH 6.8, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jun 8, 2013
RadiationMonochromator: LN2 COOLED FIXED-EXIT. SI(111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. obs: 608720 / % possible obs: 98.8 % / Observed criterion σ(I): 2 / Redundancy: 3.1 % / Rmerge(I) obs: 0.044 / Net I/σ(I): 18.3
Reflection shellResolution: 2.1→2.2 Å / Rmerge(I) obs: 0.568 / Mean I/σ(I) obs: 2.9 / % possible all: 99.4

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Processing

Software
NameClassification
XDSdata scaling
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1RYP

1ryp


Resolution: 2.1→15 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.961 / SU B: 9.449 / SU ML: 0.105 / Cross valid method: THROUGHOUT / ESU R: 0.285 / ESU R Free: 0.128 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.198 30436 5 %RANDOM
Rwork0.185 ---
obs0.186 578284 98.9 %-
all-608720 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 46.42 Å2
Baniso -1Baniso -2Baniso -3
1-1.89 Å20 Å2-0.5 Å2
2---3.72 Å20 Å2
3---1.51 Å2
Refinement stepCycle: LAST / Resolution: 2.1→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms49336 0 23 3472 52831
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.01950274
X-RAY DIFFRACTIONr_bond_other_d0.0010.0248048
X-RAY DIFFRACTIONr_angle_refined_deg1.0951.96368010
X-RAY DIFFRACTIONr_angle_other_deg0.7443110646
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.17456312
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.26524.4232252
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.436158756
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.33815284
X-RAY DIFFRACTIONr_chiral_restr0.0960.27662
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0257100
X-RAY DIFFRACTIONr_gen_planes_other0.0010.0211268
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_it1.2383.81125342
X-RAY DIFFRACTIONr_mcbond_other1.2383.81125341
X-RAY DIFFRACTIONr_mcangle_it1.2895.70131624
X-RAY DIFFRACTIONr_mcangle_other1.2895.70231625
X-RAY DIFFRACTIONr_scbond_it1.7714.23624932
X-RAY DIFFRACTIONr_scbond_other1.7714.23624932
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.5146.17336380
X-RAY DIFFRACTIONr_long_range_B_refined2.36631.01459291
X-RAY DIFFRACTIONr_long_range_B_other2.05630.71757749
X-RAY DIFFRACTIONr_rigid_bond_restr1.892398312
X-RAY DIFFRACTIONr_sphericity_free23.41751142
X-RAY DIFFRACTIONr_sphericity_bonded4.251599754
LS refinement shellResolution: 2.1→2.15 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 2216 -
Rwork0.307 42121 -
obs--99.43 %
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)
10.2256-0.02720.06080.14340.03810.0496-0.0130.00870.02090.01740.0224-0.0497-0.0153-0.0027-0.00940.0653-0.01870.01130.0341-0.02490.077466.1924-91.851646.1097
20.0685-0.02130.03560.02620.01080.1413-0.01310.00720.0158-0.0347-0.0043-0.0175-0.04380.02210.01750.0946-0.02180.03830.03630.01440.067358.727-87.459216.4647
30.13640.0770.08290.1516-0.00960.0923-0.03010.03660.0306-0.06510.02790.0218-0.02030.01740.00210.1138-0.00850.00460.03180.03650.068131.5416-87.24961.1635
40.0644-0.0308-0.04640.14980.06060.0755-0.0113-0.0130.0255-0.05010.0180.1156-0.0295-0.0007-0.00670.06320.0253-0.03310.02640.02490.14832.3453-90.28713.7783
50.05710.00520.05820.0835-0.01530.2615-0.0121-0.02970.04270.02470.02310.0867-0.0524-0.0597-0.0110.03330.03310.02670.04010.00450.1456-3.9455-94.870545.8134
60.15890.05020.03850.07540.08240.1077-0.0051-0.04410.05290.0391-0.02090.04850.0128-0.0160.0260.10580.00940.06280.0468-0.03410.074114.4917-95.498270.0039
70.01960.00560.02940.248-0.05380.1147-0.00460.01240.00010.0743-0.0033-0.0227-0.0208-0.00030.00780.1144-0.00270.00410.0321-0.02510.041446.9571-93.501471.2362
80.01590.01310.01780.14270.06080.04470.0164-0.00650.00690.0370.0085-0.09130.0076-0.0114-0.02490.06250.0006-0.00480.034-0.02240.079567.4815-129.197347.4543
90.0818-0.02390.01580.27560.04860.03360.00430.01890.0029-0.01330.0119-0.0788-0.02260.0008-0.01620.0433-0.00770.040.0497-0.0140.080468.175-126.816320.7867
100.1076-0.01580.02060.25480.01850.0125-0.00160.00350.0085-0.08360.0165-0.0026-0.01090.0048-0.01480.0928-0.01010.03220.04540.00710.038244.4014-126.3632-0.6982
110.03130.062-0.00330.37150.0570.11110.01380.00960.0132-0.07880.00710.0859-0.0170.0085-0.02090.06690.0112-0.04030.04020.02170.069610.6446-131.02822.4857
120.05440.00740.08010.20670.06850.16190.02260.0097-0.0121-0.0014-0.01110.10050.0072-0.0028-0.01150.0270.0111-0.00110.03720.02750.1276-4.6757-134.925928.3718
130.06530.00420.01970.27040.09170.0410.0109-0.01390.01360.0804-0.01970.06270.0191-0.00990.00880.0569-0.00530.05680.04720.00320.06687.5513-138.330960.2714
140.07330.0995-0.06070.35990.0320.11680.032-0.01320.010.0943-0.007-0.02910.0028-0.0039-0.0250.1022-0.0080.0070.0529-0.01590.01439.5952-134.183170.8391
150.2287-0.036-0.04550.16730.0480.1169-0.01580.0238-0.01230.03350.00380.060.0607-0.00660.0120.0851-0.032-0.01620.02060.02340.10672.6636-207.16736.7279
160.02480.01480.03880.13930.02690.102-0.0167-0.00010.008-0.0509-0.00810.00090.0178-0.03020.02480.0926-0.0188-0.0350.0256-0.0270.0879.218-206.16556.5462
170.18870.09950.0280.11520.01080.10210.01990.043-0.0475-0.07790.01830.03810.02840.0282-0.03820.16820.0048-0.05930.0231-0.04340.11636.3584-203.8881-9.3206
180.0525-0.03860.03950.39970.00810.03730.0202-0.00870.0076-0.0914-0.013-0.08150.02110.0038-0.00730.1050.03360.04290.0468-0.03630.165.7571-202.98813.2232
190.15410.0893-0.11150.136-0.06930.3167-0.00680.001-0.09270.03480.0486-0.12850.07090.0497-0.04180.05420.0465-0.04530.0425-0.05560.198172.7976-203.925435.2042
200.22550.137-0.10460.0986-0.08150.08480.0106-0.0607-0.11010.036-0.0268-0.0653-0.00020.01120.01620.14640.0184-0.07680.030.0350.112454.9004-207.655959.5008
210.00340.0152-0.01550.1169-0.08630.0975-0.00280.00290.00390.06540.00760.01090.0088-0.003-0.00470.1535-0.0078-0.01870.01720.0330.06722.4872-210.057761.093
220.05380.0308-0.01710.1002-0.00580.01030.0107-0.0196-0.0070.03-0.00950.08990.01410.0045-0.00110.0764-0.01590.00280.01750.01660.11671.5328-170.629944.5833
230.1547-0.03270.04790.2960.01340.03660.00040.017-0.007-0.0183-0.00210.07270.0251-0.00270.00160.0466-0.0131-0.03480.03420.0090.09340.2077-168.299317.9133
240.1441-0.0210.04830.3921-0.02320.02030.0132-0.0042-0.0311-0.09390.00470.01870.00520.0062-0.01790.09230.0032-0.0360.0395-0.01950.035623.4566-164.9479-3.9268
250.0110.01180.03150.3324-0.02850.12330.01090.0045-0.004-0.08930.023-0.04680.02740.0234-0.03390.08170.01080.03930.0486-0.02970.056757.285-160.8533-0.7171
260.0420.01370.01720.21740.00810.05070.01540.0089-0.0117-0.01310.0155-0.06160.00620.0244-0.03090.03530.0097-0.00070.0144-0.01850.037872.975-161.632325.147
270.04780.03510.030.3212-0.01260.02390.02820.0008-0.02710.0802-0.0163-0.07870.0094-0.0036-0.0120.06880.0128-0.04550.0415-0.00380.065361.7525-163.761957.3566
280.06560.10260.06830.3955-0.02210.14160.038-0.0034-0.01440.0886-0.00240.0130.0249-0.0064-0.03560.1142-0.0121-0.00520.04090.02610.023929.9867-169.772867.8156
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 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 - 233
14X-RAY DIFFRACTION14N1 - 196
15X-RAY DIFFRACTION15O2 - 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 - 233
28X-RAY DIFFRACTION28b1 - 196

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