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- PDB-4ya5: Yeast 20S proteasome beta2-H114D mutant in complex with Ac-PAE-ep -

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Basic information

Entry
Database: PDB / ID: 4ya5
TitleYeast 20S proteasome beta2-H114D mutant in complex with Ac-PAE-ep
Components
  • (Proteasome subunit alpha type- ...) x 6
  • (Proteasome subunit beta type- ...) x 7
  • Ac-PAE-ep
  • 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 / Cross-presentation of soluble exogenous antigens (endosomes) / TNFR2 non-canonical NF-kB pathway / proteasomal ubiquitin-independent protein catabolic process / Ub-specific processing proteases / proteasome storage granule / endopeptidase activator activity / proteasome assembly / proteasome endopeptidase complex ...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 / Ub-specific processing proteases / proteasome storage granule / endopeptidase activator activity / proteasome assembly / proteasome endopeptidase complex / proteasome core complex, beta-subunit complex / proteasome core complex, alpha-subunit complex / threonine-type endopeptidase activity / Neutrophil degranulation / proteasome complex / proteasomal protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / endopeptidase activity / mRNA binding / endoplasmic reticulum membrane / mitochondrion / nucleus / cytosol / cytoplasm
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
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 ...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: 2.5 Å
AuthorsHuber, E.M. / Groll, M.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research FoundationGR1861/10-1 Germany
German Research FoundationSFB1035/A2 Germany
CitationJournal: J.Am.Chem.Soc. / Year: 2015
Title: Systematic Analyses of Substrate Preferences of 20S Proteasomes Using Peptidic Epoxyketone Inhibitors.
Authors: Huber, E.M. / de Bruin, G. / Heinemeyer, W. / Paniagua Soriano, G. / Overkleeft, H.S. / Groll, M.
History
DepositionFeb 17, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jun 17, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 1, 2015Group: Database references
Revision 2.0Jan 17, 2018Group: Atomic model / Author supporting evidence ...Atomic model / Author supporting evidence / Derived calculations / Experimental preparation
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / exptl_crystal_grow / pdbx_audit_support / pdbx_struct_conn_angle / struct_conn / struct_site
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_seq_id / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_seq_id / _exptl_crystal_grow.temp / _pdbx_audit_support.funding_organization / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_site.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_seq_id
Revision 2.1Oct 24, 2018Group: Data collection / Source and taxonomy / Structure summary
Category: entity / entity_src_gen / entity_src_nat / Item: _entity.src_method
Revision 3.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_conn_type
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _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_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_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_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
Revision 3.1Jan 10, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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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
c: Ac-PAE-ep
d: Ac-PAE-ep
hetero molecules


Theoretical massNumber of molelcules
Total (without water)731,94938
Polymers731,74430
Non-polymers2068
Water17,348963
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)136.710, 301.320, 145.930
Angle α, β, γ (deg.)90.00, 113.18, 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 - 300
2111O1 - 300
1121B1 - 300
2121P1 - 300
1131C1 - 300
2131Q1 - 300
1141D1 - 300
2141R1 - 300
1151E1 - 300
2151S1 - 300
1161F1 - 300
2161T1 - 300
1171G1 - 300
2171U1 - 300
1181H1 - 300
2181V1 - 300
1191I1 - 300
2191W1 - 300
11101J1 - 300
21101X1 - 300
11111K1 - 300
21111Y1 - 300
11121L1 - 300
21121Z1 - 300
11131M1 - 300
21131a1 - 300
11141N1 - 300
21141b1 - 300

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(-0.99968, -0.000203, 0.025308), (-0.004192, -0.984825, -0.173501), (0.02496, -0.173551, 0.984508)68.54884, -289.89563, -26.07136

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

#8: Protein Proteasome subunit beta type-2 / PSMB2 / 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: 25091.400 Da / Num. of mol.: 2 / Mutation: His114Asn
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: P25043, proteasome endopeptidase complex
#9: Protein Proteasome subunit beta type-3 / PSMB3 / 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 / PSMB4 / 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 / PSMB5 / 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 (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 / PSMB1 / 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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Protein / Protein/peptide , 2 types, 4 molecules FTcd

#15: Protein/peptide Ac-PAE-ep


Mass: 369.456 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#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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Non-polymers , 3 types, 971 molecules

#16: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Mg
#17: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#18: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 963 / Source method: isolated from a natural source / Formula: H2O

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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: 2.5→50 Å / Num. all: 339556 / Num. obs: 339556 / % possible obs: 95.8 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 14.1
Reflection shellResolution: 2.5→2.6 Å / Rmerge(I) obs: 0.557 / % possible all: 94.1

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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: 2.5→15 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.911 / SU B: 22.935 / SU ML: 0.218 / Cross valid method: THROUGHOUT / ESU R Free: 0.24 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24174 17872 5 %RANDOM
Rwork0.22608 ---
obs0.22687 339556 95.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 53.604 Å2
Baniso -1Baniso -2Baniso -3
1-2.26 Å20 Å20.01 Å2
2---4.64 Å20 Å2
3---1.73 Å2
Refinement stepCycle: LAST / Resolution: 2.5→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms49372 0 64 963 50399
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.01950328
X-RAY DIFFRACTIONr_bond_other_d0.0010.0248096
X-RAY DIFFRACTIONr_angle_refined_deg0.9061.96568094
X-RAY DIFFRACTIONr_angle_other_deg0.7343110758
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1656314
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.65924.4322252
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.742158756
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.68915284
X-RAY DIFFRACTIONr_chiral_restr0.0520.27672
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0257144
X-RAY DIFFRACTIONr_gen_planes_other0.0010.0211264
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_it1.5283.77125346
X-RAY DIFFRACTIONr_mcbond_other1.5283.77125345
X-RAY DIFFRACTIONr_mcangle_it1.9125.64231630
X-RAY DIFFRACTIONr_mcangle_other1.9125.64231631
X-RAY DIFFRACTIONr_scbond_it1.5964.15124982
X-RAY DIFFRACTIONr_scbond_other1.5964.15124982
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.796.0836464
X-RAY DIFFRACTIONr_long_range_B_refined2.51229.42253773
X-RAY DIFFRACTIONr_long_range_B_other2.4429.453636
X-RAY DIFFRACTIONr_rigid_bond_restr1.002398424
X-RAY DIFFRACTIONr_sphericity_free30.1955431
X-RAY DIFFRACTIONr_sphericity_bonded4.467598064
Refine LS restraints NCS

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

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
10O3099tight positional00.05
11O3201tight positional00.05
12O3439tight positional00.05
13O3618tight positional00.05
14O3003tight positional00.05
1O3795tight thermal5.070.5
2P3756tight thermal3.520.5
3Q3729tight thermal6.90.5
4R3578tight thermal3.180.5
5S3509tight thermal4.680.5
6T3749tight thermal5.650.5
7U3770tight thermal3.040.5
8V3397tight thermal2.930.5
9W3119tight thermal2.210.5
10X3099tight thermal1.790.5
11Y3201tight thermal1.660.5
12Z3439tight thermal1.910.5
13a3618tight thermal1.940.5
14b3003tight thermal1.820.5
LS refinement shellResolution: 2.5→2.563 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.374 1279 -
Rwork0.378 24293 -
obs--95.44 %
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)
10.3855-0.09450.08540.2717-0.03580.0949-0.00380.0244-0.01970.03650.0405-0.107-0.074-0.0337-0.03670.1394-0.04080.02540.1381-0.04630.197367.0268-92.10946.3166
20.35870.0243-0.15360.20440.25730.4211-0.0585-0.0060.0056-0.09450.04050.0066-0.08260.04790.0180.1667-0.03660.07090.12360.03920.141259.728-87.801416.5812
30.25310.2541-0.08060.2857-0.13760.7226-0.0535-0.00580.0359-0.11460.02860.04-0.0760.08220.02490.2185-0.0213-0.0030.10290.07630.139832.454-87.39361.2344
40.20760.0213-0.19090.16530.0860.3686-0.0167-0.07650.0072-0.09580.04160.1743-0.05380.0992-0.0250.12430.0167-0.09490.07570.06470.31013.1188-90.334113.7657
50.27190.14550.22660.10190.0450.6094-0.0102-0.00640.07530.008-0.00060.1034-0.0392-0.02940.01080.04880.05750.0710.09020.02160.323-3.2054-94.918445.8165
60.55650.1070.10290.0881-0.01440.0805-0.0364-0.06790.08540.0709-0.00330.0770.0208-0.01470.03970.19690.020.14130.1242-0.07160.17115.2101-95.526170.0701
70.02740.01390.00340.357-0.05070.2566-0.01180.04270.00340.18160.0099-0.04-0.0565-0.05120.00190.2663-0.01210.00590.1161-0.04860.097647.7213-93.688971.4344
80.0671-0.0295-0.01190.15250.08610.17630.03280.01710.03820.09450.0124-0.12040.0333-0.0799-0.04530.1371-0.0108-0.02430.1389-0.04180.182768.1103-129.546847.6949
90.2260.0829-0.0040.53040.06260.340.01350.02030.008-0.11240.0127-0.1174-0.0542-0.02-0.02620.0945-0.00210.08880.1616-0.03210.168368.8184-127.2521.0045
100.06790.01640.03970.56050.04120.02680.0021-0.06660.0093-0.16650.00490.04220.0021-0.0338-0.0070.2503-0.0090.05550.15160.01520.068945.0572-126.7009-0.5309
110.15850.2584-0.01020.5720.10970.2375-0.032-0.02940.0218-0.14650.04330.1568-0.01260.0956-0.01130.1540.014-0.13610.10020.04480.201211.2207-131.13652.6065
120.1042-0.12020.04340.3335-0.0780.02810.0185-0.0133-0.00550.0015-0.00210.2050.00070.0211-0.01640.05260.0091-0.02030.12760.04160.3189-4.1095-134.955428.3964
130.0827-0.10640.0860.721-0.09170.10180.01890.02910.05350.1315-0.04880.11540.00870.03810.02990.1522-0.01230.10880.1379-0.00380.17248.1186-138.452160.3146
140.4471-0.0365-0.18730.49850.06810.13050.0570.04070.01020.10460.00480.01670.00470.003-0.06180.2521-0.02510.00610.1299-0.02450.067440.1914-134.505270.8214
150.1832-0.1835-0.06480.70440.28890.1647-0.0350.05770.10240.0896-0.00930.10370.1126-0.00390.04430.1972-0.0672-0.04220.08730.04870.21822.5035-207.34636.9104
160.26760.12970.2350.3482-0.05760.3179-0.0605-0.03910.0321-0.07290.0029-0.0086-0.0033-0.06120.05760.212-0.0349-0.09410.0893-0.05910.18939.0493-206.30816.7364
170.41370.2324-0.08060.2847-0.15960.38860.0953-0.0089-0.0395-0.19-0.01740.11170.09890.036-0.07790.38360.0311-0.18340.0331-0.06470.171636.3468-204.2448-9.1031
180.1821-0.02750.16290.0882-0.04960.1967-0.0011-0.11480.0499-0.1489-0.0106-0.1080.0911-0.05510.01170.29960.07120.1260.1171-0.06010.204365.8155-203.46723.4518
190.20480.1551-0.09760.1205-0.06610.10260.02660.0511-0.07620.03660.0587-0.07280.03760.0211-0.08530.12370.1086-0.10320.1006-0.10940.310772.7721-204.384835.5
200.85520.30160.06510.11120.04910.18910.0843-0.0659-0.15450.0544-0.022-0.07370.0746-0.0298-0.06240.30860.0259-0.17410.05610.04640.1754.8145-208.051259.8135
210.0197-0.00960.02970.03880.05090.5117-0.00410.03420.01530.054-0.00290.03380.06480.03480.0070.3077-0.0277-0.0240.07330.0650.122722.3456-210.29661.386
220.03620.00440.07680.1874-0.04050.21830.04860.0009-0.01580.083-0.01350.17070.04340.0516-0.03510.1247-0.04860.01450.09860.05670.231.5734-170.737944.7459
230.1695-0.02350.04650.4597-0.11770.04410.0150.01520.0102-0.10770.00470.14050.02870.0245-0.01970.1308-0.0169-0.11670.13070.01180.24490.3567-168.365618.0538
240.2751-0.09950.02950.99010.03850.00810.0096-0.0718-0.0517-0.15880.01390.031-0.00120.0036-0.02350.2556-0.0073-0.09810.1377-0.01290.109123.7116-165.14-3.7421
250.09030.16530.02430.768-0.0610.0710.0189-0.0149-0.0014-0.16890.0479-0.04680.02460.0252-0.06680.21660.01780.10030.1436-0.06720.150857.5838-161.2929-0.4566
260.14540.1338-0.0740.7693-0.08380.06130.0185-0.0133-0.0362-0.0569-0.0076-0.15120.0157-0.009-0.0110.09840.03790.01690.1691-0.06230.235873.3999-161.977925.3042
270.0596-0.07620.01730.58690.07840.14280.06190.0422-0.03950.1318-0.0167-0.12210.0356-0.0372-0.04520.18390.0264-0.09470.1387-0.01210.16461.8237-164.067457.5554
280.3169-0.20920.07510.7754-0.17290.17350.03830.04220.00130.1370.01980.06920.03870.0323-0.05810.2538-0.02990.0060.12150.04630.058929.9504-169.836867.8629
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-10 - 9999
2X-RAY DIFFRACTION2B-10 - 9999
3X-RAY DIFFRACTION3C-10 - 9999
4X-RAY DIFFRACTION4D-10 - 9999
5X-RAY DIFFRACTION5E-10 - 9999
6X-RAY DIFFRACTION6F-10 - 9999
7X-RAY DIFFRACTION7G-10 - 9999
8X-RAY DIFFRACTION8H-10 - 9999
9X-RAY DIFFRACTION9I-10 - 9999
10X-RAY DIFFRACTION10J-10 - 9999
11X-RAY DIFFRACTION11K-10 - 9999
12X-RAY DIFFRACTION12L-10 - 9999
13X-RAY DIFFRACTION13M-10 - 9999
14X-RAY DIFFRACTION14N-10 - 9999
15X-RAY DIFFRACTION15O-10 - 9999
16X-RAY DIFFRACTION16P-10 - 9999
17X-RAY DIFFRACTION17Q-10 - 9999
18X-RAY DIFFRACTION18R-10 - 9999
19X-RAY DIFFRACTION19S-10 - 9999
20X-RAY DIFFRACTION20T-10 - 9999
21X-RAY DIFFRACTION21U-10 - 9999
22X-RAY DIFFRACTION22V-10 - 9999
23X-RAY DIFFRACTION23W-10 - 9999
24X-RAY DIFFRACTION24X-10 - 9999
25X-RAY DIFFRACTION25Y-10 - 9999
26X-RAY DIFFRACTION26Z-10 - 9999
27X-RAY DIFFRACTION27a-10 - 9999
28X-RAY DIFFRACTION28b-10 - 9999

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