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- PDB-5d0x: Yeast 20S proteasome beta5-T1S mutant in complex with Bortezomib -

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Basic information

Entry
Database: PDB / ID: 5d0x
TitleYeast 20S proteasome beta5-T1S mutant in complex with Bortezomib
Components
  • (Proteasome subunit alpha type- ...) x 6
  • (Proteasome subunit beta type- ...) x 7
  • Probable proteasome subunit alpha type-7
KeywordsHYDROLASE/HYDROLASE INHIBITOR / HYDROLASE-HYDROLASE INHIBITOR complex / Proteasome / Mutant / Inhibitor / 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 / Ubiquitin-Mediated Degradation of Phosphorylated Cdc25A / proteasomal ubiquitin-independent protein catabolic process / 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 / Ubiquitin-Mediated Degradation of Phosphorylated Cdc25A / proteasomal ubiquitin-independent protein catabolic process / 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 / Ub-specific processing proteases / proteasome endopeptidase complex / endopeptidase activator activity / 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
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 alpha5 / Proteasome subunit alpha6 / 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 alpha5 / Proteasome subunit alpha6 / 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 / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-BO2 / Probable proteasome subunit alpha type-7 / Proteasome subunit alpha type-1 / Proteasome subunit beta type-4 / Proteasome subunit alpha type-3 / Proteasome subunit alpha type-2 / Proteasome subunit beta type-6 / Proteasome subunit beta type-2 / Proteasome subunit beta type-3 / Proteasome subunit beta type-5 ...Chem-BO2 / 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
AuthorsHuber, E.M. / Groll, M.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationSFB1035/A2 Germany
CitationJournal: Nat Commun / Year: 2016
Title: A unified mechanism for proteolysis and autocatalytic activation in the 20S proteasome.
Authors: Huber, E.M. / Heinemeyer, W. / Li, X. / Arendt, C.S. / Hochstrasser, M. / Groll, M.
History
DepositionAug 3, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Mar 23, 2016Provider: repository / Type: Initial release
Revision 2.0Nov 7, 2018Group: Atomic model / Author supporting evidence ...Atomic model / Author supporting evidence / Data collection / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / entity / entity_src_gen / entity_src_nat / pdbx_audit_support / pdbx_nonpoly_scheme
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_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] / _entity.src_method / _pdbx_audit_support.funding_organization / _pdbx_nonpoly_scheme.auth_seq_num
Revision 2.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id
Revision 2.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)733,66446
Polymers731,02328
Non-polymers2,64218
Water9,980554
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)136.810, 300.230, 145.290
Angle α, β, γ (deg.)90.00, 113.10, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21O
12B
22P
13C
23Q
14D
24R
15E
25S
16F
26T
17G
27U
18H
28V
19I
29W
110J
210X
111K
211Y
112L
212Z
113M
213a
114N
214b

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A1 - 500
2111O1 - 500
1121B1 - 500
2121P1 - 500
1131C1 - 500
2131Q1 - 500
1141D1 - 500
2141R1 - 500
1151E1 - 500
2151S1 - 500
1161F1 - 500
2161T1 - 500
1171G1 - 500
2171U1 - 500
1181H1 - 500
2181V1 - 500
1191I1 - 500
2191W1 - 500
11101J1 - 500
21101X1 - 500
11111K1 - 500
21111Y1 - 500
11121L1 - 500
21121Z1 - 500
11131M1 - 500
21131a1 - 500
11141N1 - 500
21141b1 - 500

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

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.999616, -0.002062, 0.027623), (-0.002771, -0.984777, -0.173798), (0.027561, -0.173807, 0.984394)68.186729, -288.731659, -26.049049

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Components

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

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


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


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


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


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


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


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

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Protein , 1 types, 2 molecules FT

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


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

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

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


Mass: 25114.459 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P25043, proteasome endopeptidase complex
#9: Protein Proteasome subunit beta type-3 / Macropain subunit PUP3 / Multicatalytic endopeptidase complex subunit PUP3 / Proteasome component PUP3


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


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


Mass: 23311.223 Da / Num. of mol.: 2 / Mutation: T1S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Production host: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P30656, proteasome endopeptidase complex
#12: Protein Proteasome subunit beta type-6 / Multicatalytic endopeptidase complex subunit C5 / Proteasome component C5


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


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


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

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Non-polymers , 4 types, 572 molecules

#15: Chemical
ChemComp-MG / MAGNESIUM ION


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


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#17: Chemical
ChemComp-BO2 / N-[(1R)-1-(DIHYDROXYBORYL)-3-METHYLBUTYL]-N-(PYRAZIN-2-YLCARBONYL)-L-PHENYLALANINAMIDE / BORTEZOMIB


Mass: 384.237 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C19H25BN4O4 / Source: (synth.) synthetic construct (others) / Comment: medication*YM
#18: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 554 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

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

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Apr 12, 2014
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: 2.6→30 Å / Num. all: 329555 / Num. obs: 321316 / % possible obs: 97.5 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.063 / Net I/σ(I): 14.5
Reflection shellResolution: 2.6→2.7 Å / Rmerge(I) obs: 0.575 / Mean I/σ(I) obs: 2.7 / % possible all: 98.7

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
REFMACphasing
REFMAC5.7.0032refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1RYP

1ryp


Resolution: 2.6→15 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.939 / SU B: 22.801 / SU ML: 0.205 / Cross valid method: THROUGHOUT / ESU R Free: 0.242 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22362 16066 5 %RANDOM
Rwork0.20364 ---
obs0.20463 305250 97.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 64.531 Å2
Baniso -1Baniso -2Baniso -3
1-3.02 Å20 Å2-0.14 Å2
2---6.53 Å2-0 Å2
3---2.62 Å2
Refinement stepCycle: LAST / Resolution: 2.6→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms49374 0 180 554 50108
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.01950452
X-RAY DIFFRACTIONr_bond_other_d0.0020.0248190
X-RAY DIFFRACTIONr_angle_refined_deg0.8571.96768258
X-RAY DIFFRACTIONr_angle_other_deg0.6963.001110952
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.03956314
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.10124.4232252
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.956158752
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.49215284
X-RAY DIFFRACTIONr_chiral_restr0.0490.27684
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0257252
X-RAY DIFFRACTIONr_gen_planes_other0.0010.0211322
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_it1.9054.50425346
X-RAY DIFFRACTIONr_mcbond_other1.9054.50325345
X-RAY DIFFRACTIONr_mcangle_it2.4196.7431630
X-RAY DIFFRACTIONr_mcangle_other2.4196.7431631
X-RAY DIFFRACTIONr_scbond_it1.8624.92925106
X-RAY DIFFRACTIONr_scbond_other1.8624.92925106
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.1367.2336628
X-RAY DIFFRACTIONr_long_range_B_refined2.83335.21253889
X-RAY DIFFRACTIONr_long_range_B_other2.78835.19953828
X-RAY DIFFRACTIONr_rigid_bond_restr0.674398642
X-RAY DIFFRACTIONr_sphericity_free29.2115315
X-RAY DIFFRACTIONr_sphericity_bonded4.902597991
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A3099TIGHT POSITIONAL0.010.05
1A3249TIGHT POSITIONAL00.05
1A3439TIGHT POSITIONAL00.05
1A3618TIGHT POSITIONAL00.05
1A3001TIGHT POSITIONAL00.05
1A3795TIGHT THERMAL5.340.5
2B3756TIGHT THERMAL3.640.5
3C3729TIGHT THERMAL9.870.5
4D3578TIGHT THERMAL6.820.5
5E3509TIGHT THERMAL6.080.5
6F3749TIGHT THERMAL5.570.5
7G3770TIGHT THERMAL2.850.5
8H3455TIGHT THERMAL2.830.5
9I3119TIGHT THERMAL2.570.5
10J3099TIGHT THERMAL2.530.5
11K3249TIGHT THERMAL1.860.5
12L3439TIGHT THERMAL2.160.5
13M3618TIGHT THERMAL1.860.5
14N3001TIGHT THERMAL1.670.5
LS refinement shellResolution: 2.6→2.665 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.365 1164 -
Rwork0.338 22122 -
obs--98.79 %
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)
10.1609-0.01020.05930.0853-0.10580.1925-0.00990.0656-0.06570.07850.0095-0.0645-0.0754-0.04430.00040.183-0.05090.01510.1568-0.04940.258667.602-91.956146.1111
20.1515-0.0192-0.09730.04170.06150.1281-0.0384-0.0344-0.038-0.056-0.00550.0336-0.07410.03490.04390.2318-0.04020.08660.19340.04150.197260.2869-87.74516.4617
30.12920.1244-0.00460.14950.08640.4486-0.0473-0.01210.0347-0.07050.04830.0736-0.03960.1091-0.00090.2775-0.0004-0.00540.16220.08480.194132.9464-87.11711.1155
40.1497-0.0565-0.16610.11350.06150.18550.0043-0.08260.0083-0.10720.01250.1555-0.01360.1007-0.01670.1660.0565-0.09240.12150.08170.38163.629-89.793913.6821
50.01940.00130.05270.0408-0.00370.1937-0.02070.001-0.01210.0227-0.01030.1078-0.05060.02650.0310.09950.06420.12030.1140.00040.4229-2.6901-94.15445.7287
60.2670.09070.05070.15630.04730.01720.01180.05160.01080.1002-0.0360.05940.0341-0.00130.02410.2820.010.20160.1446-0.05330.195915.7513-94.767969.9449
70.14060.03290.00450.1357-0.09830.17740.05170.0958-0.00210.1626-0.0347-0.0328-0.046-0.0102-0.01710.3861-0.05490.01850.127-0.03050.123448.2935-93.263371.2515
80.02830.0398-0.02140.1532-0.0020.02630.05320.0384-0.01390.1134-0.0412-0.1045-0.024-0.0642-0.0120.17610.0137-0.05280.1966-0.020.242568.1567-129.455547.5586
90.05970.0318-0.07790.30390.03910.19640.06070.0257-0.0068-0.0305-0.0703-0.1391-0.0591-0.10010.00960.1164-0.00270.10640.2223-0.00440.267668.8659-127.387620.9515
100.13070.20380.13490.56140.27030.22230.0293-0.05510.0214-0.14830.02970.01850.00150.0121-0.0590.27760.00140.06580.21440.00940.125845.2597-126.3791-0.6044
110.18950.28270.00420.50540.02310.0634-0.0357-0.00820.0179-0.12570.070.146-0.00050.0943-0.03440.20070.0038-0.10540.20330.0440.231811.4091-130.56972.4202
120.1769-0.01230.18470.37770.08430.25310.04720.02990.00150.0013-0.06080.15530.03220.07490.01350.06170.01850.04520.1820.04220.3745-4.0774-134.040928.5867
130.0855-0.06020.07330.4688-0.10710.07350.05550.05190.0310.1328-0.03930.08830.01570.0484-0.01620.1922-0.00770.16940.18860.0040.23228.3127-137.644460.4487
140.24380.0224-0.17190.32110.09050.1630.07050.10280.01150.2022-0.0293-0.05280.0124-0.0578-0.04120.3482-0.0262-0.00290.181-0.02010.083240.3481-133.959570.7927
150.33920.045-0.19440.26210.15620.2668-0.03610.05570.05380.06620.00580.0590.08840.00450.03020.1786-0.0631-0.05530.11340.05770.312.0252-206.320336.8184
160.27420.17630.22830.1780.07130.2795-0.0393-0.05280.0448-0.0808-0.0378-0.00580.0326-0.0330.0770.2419-0.027-0.11850.1149-0.0670.25568.5612-205.19026.7192
170.21690.06370.17410.05720.04240.19550.0932-0.0307-0.022-0.0989-0.02570.05990.03110.0276-0.06750.45530.0621-0.15880.0761-0.10630.173835.8702-203.3023-9.1302
180.1293-0.06870.18450.1136-0.13150.30570.0161-0.09890.0843-0.1905-0.0597-0.08670.1494-0.09680.04360.35660.09920.13050.1461-0.05220.17865.3695-202.78523.3562
190.18290.1466-0.19590.1338-0.12610.27620.04670.0819-0.06670.06370.0623-0.1373-0.0015-0.0617-0.10890.09680.0758-0.15480.0739-0.08340.476572.3263-203.959335.3649
200.28960.1252-0.0040.0616-0.00350.05470.08990.0124-0.14310.0905-0.0391-0.1018-0.0628-0.0531-0.05080.2969-0.0096-0.23510.08260.09790.303354.3483-207.588459.6237
210.0376-0.022-0.01860.1253-0.09890.2389-0.00190.04790.00660.0886-0.00460.0317-0.00880.020.00660.3217-0.0246-0.06610.1070.07090.200721.9203-209.548161.2371
220.02130.01630.03450.20580.02520.0860.05210.0196-0.00750.0877-0.02690.14620.04460.0755-0.02520.1668-0.01820.0370.16970.05390.3061.6045-169.651744.7441
230.02180.0138-0.00080.2964-0.00320.07950.0385-0.02530.003-0.1077-0.0260.14240.03390.0987-0.01250.1438-0.0031-0.11240.15740.01770.32650.3587-167.035518.1329
240.11460.1072-0.01550.43830.00680.01590.0504-0.0847-0.0363-0.1834-0.02230.06-0.0090.0421-0.02810.31040.0094-0.09550.1644-0.02370.151523.5317-164.2406-3.7402
250.13860.14290.02550.4313-0.00420.0096-0.0003-0.0478-0.0139-0.11970.0268-0.02880.0058-0.0171-0.02650.23750.03150.11570.1923-0.06060.183357.4584-160.6343-0.649
260.0729-0.026-0.04220.5348-0.06850.08520.03560.0323-0.04090.0465-0.0644-0.1762-0.0183-0.07880.02880.0950.0333-0.00330.2002-0.03860.317373.4283-161.729825.4118
270.0436-0.0681-0.0270.39120.01160.02730.02640.0644-0.03050.1294-0.0371-0.0937-0.0124-0.06730.01060.2330.013-0.11680.16780.0020.225861.7047-163.726957.6245
280.07660.0660.03650.47080.04460.02620.07950.0775-0.00120.1572-0.04440.03560.03510.02-0.03510.3305-0.02650.02430.17390.04490.125629.8963-169.226967.8363
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 250
2X-RAY DIFFRACTION2B1 - 244
3X-RAY DIFFRACTION3C1 - 240
4X-RAY DIFFRACTION4D1 - 242
5X-RAY DIFFRACTION5E3 - 233
6X-RAY DIFFRACTION6F2 - 244
7X-RAY DIFFRACTION7G2 - 242
8X-RAY DIFFRACTION8H1 - 226
9X-RAY DIFFRACTION9I1 - 204
10X-RAY DIFFRACTION10J1 - 195
11X-RAY DIFFRACTION11K1 - 212
12X-RAY DIFFRACTION12L1 - 222
13X-RAY DIFFRACTION13M1 - 233
14X-RAY DIFFRACTION14N1 - 196
15X-RAY DIFFRACTION15O1 - 250
16X-RAY DIFFRACTION16P1 - 244
17X-RAY DIFFRACTION17Q1 - 240
18X-RAY DIFFRACTION18R1 - 242
19X-RAY DIFFRACTION19S3 - 233
20X-RAY DIFFRACTION20T2 - 244
21X-RAY DIFFRACTION21U2 - 242
22X-RAY DIFFRACTION22V1 - 226
23X-RAY DIFFRACTION23W1 - 204
24X-RAY DIFFRACTION24X1 - 195
25X-RAY DIFFRACTION25Y1 - 212
26X-RAY DIFFRACTION26Z1 - 222
27X-RAY DIFFRACTION27a1 - 233
28X-RAY DIFFRACTION28b1 - 196

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