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- PDB-4qby: yCP in complex with BOC-ALA-ALA-ALA-CHO -

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Basic information

Entry
Database: PDB / ID: 4qby
TitleyCP in complex with BOC-ALA-ALA-ALA-CHO
Components
  • (Proteasome subunit alpha type- ...) x 6
  • (Proteasome subunit beta type- ...) x 7
  • BOC-ALA-ALA-ALA-CHO
  • Probable proteasome subunit alpha type-7
Keywordshydrolase/hydrolase inhibitor / 20S Proteasome / Peptide Aldehyde / Allosteric Regulation / PCA Analysis / Immunoproteasome / 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 / proteasome storage granule / endopeptidase activator activity / proteasome assembly / proteasome endopeptidase complex / Ub-specific processing proteases ...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 / proteasome storage granule / endopeptidase activator activity / proteasome assembly / proteasome endopeptidase complex / Ub-specific processing proteases / 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
BOC-ALA-ALA-ALA-CHO / 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 ...BOC-ALA-ALA-ALA-CHO / 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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsArciniega, M. / Beck, P. / Lange, O. / Groll, M. / Huber, R.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Differential global structural changes in the core particle of yeast and mouse proteasome induced by ligand binding.
Authors: Arciniega, M. / Beck, P. / Lange, O.F. / Groll, M. / Huber, R.
History
DepositionMay 9, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 18, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 16, 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.pdbx_value_order / _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
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / struct_conn
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 / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr2_label_atom_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: 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
1: BOC-ALA-ALA-ALA-CHO
Z: Proteasome subunit beta type-6
2: BOC-ALA-ALA-ALA-CHO
a: Proteasome subunit beta type-7
3: BOC-ALA-ALA-ALA-CHO
b: Proteasome subunit beta type-1
4: BOC-ALA-ALA-ALA-CHO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)732,58843
Polymers732,32032
Non-polymers26711
Water3,243180
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)134.990, 300.130, 144.800
Angle α, β, γ (deg.)90.00, 112.51, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.99944, -0.003073, 0.033333), (-0.002667, -0.985301, -0.170809), (0.033368, -0.170802, 0.98474)67.27092, -289.04437, -25.78635
DetailsAU contains one biological assembly.

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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 / Fragment: alpha subunit / Mutation: wild type / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's 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 / Fragment: alpha subunit / Mutation: wild type / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's 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 / Fragment: alpha subunit / Mutation: wild type / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's 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 / Fragment: alpha subunit / Mutation: wild type / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's 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 / Fragment: alpha subunit / Mutation: wild type / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c
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 / Fragment: alpha subunit / Mutation: wild type / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's 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 / 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: 25114.459 Da / Num. of mol.: 2 / Fragment: beta subunit / Mutation: wild type / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c
References: UniProt: P25043, proteasome endopeptidase complex
#9: Protein Proteasome subunit beta type-3 / PSMB3


Mass: 22627.842 Da / Num. of mol.: 2 / Fragment: alpha subunit / Mutation: wild type / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c
References: UniProt: P25451, proteasome endopeptidase complex
#10: Protein Proteasome subunit beta type-4 / PSMB4 / Macropain subunit PUP3 / Multicatalytic endopeptidase complex subunit PUP3 / Proteasome component PUP3


Mass: 22545.676 Da / Num. of mol.: 2 / Fragment: beta subunit / Mutation: wild type / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c
References: UniProt: P22141, proteasome endopeptidase complex
#11: Protein Proteasome subunit beta type-5 / PSMB5 / 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: 23325.248 Da / Num. of mol.: 2 / Fragment: beta subunit / Mutation: wild type / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c
References: UniProt: P30656, proteasome endopeptidase complex
#12: Protein Proteasome subunit beta type-6 / / 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: 24883.928 Da / Num. of mol.: 2 / Fragment: beta subunit / Mutation: wild type / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c
References: UniProt: P23724, proteasome endopeptidase complex
#13: Protein Proteasome subunit beta type-7 / / Multicatalytic endopeptidase complex subunit C5 / Proteasome component C5


Mass: 27200.893 Da / Num. of mol.: 2 / Fragment: beta subunit / Mutation: wild type / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c
References: UniProt: P30657, proteasome endopeptidase complex
#14: Protein Proteasome subunit beta type-1 / PSMB1 / 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: 21517.186 Da / Num. of mol.: 2 / Fragment: beta subunit / Mutation: wild type / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c
References: UniProt: P38624, proteasome endopeptidase complex

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Protein / Protein/peptide , 2 types, 6 molecules FT1234

#15: Protein/peptide
BOC-ALA-ALA-ALA-CHO / 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


Type: Peptide-like / Class: Inhibitor / Mass: 317.381 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast) / References: BOC-ALA-ALA-ALA-CHO
#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 / Fragment: alpha subunit / Mutation: wild type / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c
References: UniProt: P21242, proteasome endopeptidase complex

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Non-polymers , 2 types, 191 molecules

#16: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Mg
#17: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 180 / 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: 3.7 Å3/Da / Density % sol: 66.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 20 mM MgAc2, 100 mM MES, 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 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Nov 30, 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: 3→20 Å / Num. all: 211987 / Num. obs: 194983 / % possible obs: 92 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 10.4
Reflection shellResolution: 3→3.1 Å / Rmerge(I) obs: 0.541 / Mean I/σ(I) obs: 2.3 / % possible all: 88.4

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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: 3→15 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.939 / SU B: 32.174 / SU ML: 0.246 / Cross valid method: THROUGHOUT / σ(I): 2 / ESU R Free: 0.336 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20675 9750 5 %RANDOM
Rwork0.17846 ---
obs0.17988 185233 92.09 %-
all-194983 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 68.738 Å2
Baniso -1Baniso -2Baniso -3
1-4.97 Å2-0 Å2-1.43 Å2
2---7.17 Å2-0 Å2
3---2.08 Å2
Refinement stepCycle: LAST / Resolution: 3→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms49454 0 11 180 49645
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.01950362
X-RAY DIFFRACTIONr_bond_other_d0.0010.0248152
X-RAY DIFFRACTIONr_angle_refined_deg1.1021.96568138
X-RAY DIFFRACTIONr_angle_other_deg0.7473.001110862
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4556314
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.2924.4232252
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.587158754
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3515284
X-RAY DIFFRACTIONr_chiral_restr0.0620.27682
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0257168
X-RAY DIFFRACTIONr_gen_planes_other0.0010.0211280
X-RAY DIFFRACTIONr_mcbond_it2.7996.08325346
X-RAY DIFFRACTIONr_mcbond_other2.7996.08325345
X-RAY DIFFRACTIONr_mcangle_it3.4199.10931630
X-RAY DIFFRACTIONr_mcangle_other3.4189.10931631
X-RAY DIFFRACTIONr_scbond_it2.8516.43425016
X-RAY DIFFRACTIONr_scbond_other2.856.43425016
X-RAY DIFFRACTIONr_scangle_other3.1529.50736508
X-RAY DIFFRACTIONr_long_range_B_refined3.83447.67854467
X-RAY DIFFRACTIONr_long_range_B_other3.82947.6854455
X-RAY DIFFRACTIONr_rigid_bond_restr2.173398514
X-RAY DIFFRACTIONr_sphericity_free32.9815139
X-RAY DIFFRACTIONr_sphericity_bonded6.813597668
LS refinement shellResolution: 3→3.075 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.347 664 -
Rwork0.296 12608 -
obs--88.5 %
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)
10.024-0.00710.01410.0059-0.00560.0155-0.0190.00070.0238-0.00050.0079-0.0248-0.0141-0.01890.01110.0498-0.02120.01390.078-0.01810.116766.988-91.9346.109
20.04540.01550.05580.04320.08740.1928-0.03730.0083-0.0081-0.020.01490.0206-0.0620.04610.02240.0737-0.02880.04650.08130.03160.084759.595-87.72716.524
30.1360.1679-0.01940.21990.01530.2231-0.01460.01330.0172-0.04110.03720.0289-0.02130.0407-0.02260.0892-0.0009-0.00350.05630.04020.05132.307-87.281.161
40.0780.0017-0.07520.00820.02560.1926-0.0309-0.00240.0336-0.0161-0.00170.0293-0.0642-0.01360.03270.08130.0346-0.03650.04880.0450.13153.076-90.06713.709
50.0122-0.01320.0510.0151-0.04340.3658-0.0204-0.0105-0.02980.02130.00860.0425-0.0719-0.05690.01170.03460.02970.05330.06530.00640.1966-3.219-94.32345.779
60.3090.0230.09660.07050.0570.08480.0227-0.04150.0350.04-0.02950.0437-0.0023-0.02720.00690.11350.00480.08590.0726-0.03040.08115.302-94.94369.981
70.0439-0.07820.06660.2634-0.1040.13050.01570.00930.02020.0503-0.0558-0.0153-0.01510.00240.04010.1218-0.0160.01270.0569-0.02120.021247.807-93.34971.271
80.00970.0240.00560.124-0.0070.02620.0180.005-0.02480.0550.0019-0.1071-0.01750.0011-0.020.0616-0.0032-0.01570.0772-0.02070.136867.767-129.35947.498
90.04120.0748-0.01370.2838-0.03430.00530.01540.02450.0128-0.0275-0.0209-0.06280.0003-0.00720.00550.03560.00250.05470.110.00090.085868.519-127.34720.916
100.14130.07750.2030.06540.1270.3118-0.0072-0.01570.008-0.04820.0032-0.0223-0.03360.010.0040.09050.00210.05870.07350.01210.041544.767-126.43-0.533
110.14530.1252-0.12330.1146-0.10980.10660.00990.02990.0369-0.00730.03390.05760.0014-0.0272-0.04380.04280.0116-0.05680.08230.0220.108910.955-130.7572.659
120.0066-0.0259-0.01490.16660.12280.10080.00140.0035-0.0223-0.0056-0.01330.0645-0.0043-0.01130.01190.01210.00910.00130.08510.03830.1425-4.413-134.35428.663
130.0336-0.04250.00640.2470.03580.01340.0036-0.0156-0.01320.0938-0.00670.07770.0135-0.01010.00310.0782-0.00510.07090.0820.00730.07867.901-137.79760.486
140.0819-0.1321-0.11750.27040.17140.23130.01240.00290.00020.0696-0.0145-0.0003-0.010.03550.00210.1313-0.02210.00350.0688-0.01510.004239.957-133.89271.033
150.0931-0.0067-0.0440.04460.07680.1925-0.0124-0.01280.01050.00030.01050.01880.0607-0.02320.00190.0715-0.0416-0.01070.05470.02860.11092.152-206.49537.122
160.1517-0.0173-0.05630.0990.00060.0248-0.055-0.01740.0134-0.07190.04420.00510.0214-0.00790.01080.0963-0.0235-0.03940.0795-0.02550.088.527-205.4416.983
170.09050.09640.06620.12890.05770.230.01970.01280.0081-0.04890.02450.01650.0316-0.0101-0.04410.1320.0148-0.02930.0502-0.0430.077135.607-203.496-8.878
180.17570.05290.13180.04690.00760.2039-0.0002-0.02670.0166-0.057-0.0165-0.03970.05170.03330.01680.11120.040.07060.0608-0.02750.106165.159-202.7663.38
190.03850.0119-0.06190.0229-0.0590.20880.00570.00040.0015-0.0158-0.0087-0.03110.05410.05060.0030.05010.0532-0.0280.0649-0.05080.191772.347-203.89435.37
200.19110.0448-0.02670.0293-0.02270.12410.0396-0.04-0.08610.0404-0.0159-0.05040.0279-0.0137-0.02370.14240.0166-0.0970.03950.03050.11754.492-207.42159.719
210.01730.00310.00650.203-0.01620.10420.02930.0038-0.02290.01860.00920.0231-0.02190.0043-0.03840.1087-0.0138-0.02110.04620.0220.065322.11-209.53661.45
220.06540.08730.0140.20060.02480.00350.0184-0.0015-0.00010.0542-0.01860.08970.0072-0.00240.00020.0372-0.0090.0220.07740.02750.11651.555-169.85344.896
230.1214-0.06-0.04320.4115-0.01350.01920.00490.0402-0.0023-0.10820.00420.10720.0091-0.01-0.00910.0346-0.0033-0.04610.08770.01090.08710.056-167.28718.327
240.0048-0.02480.01360.1741-0.09580.06140.0009-0.0138-0.0012-0.07860.03370.01970.0279-0.0343-0.03460.10680.012-0.02090.07080.00730.057523.196-164.458-3.572
250.2110.17670.12530.19640.07340.1193-0.00440.0492-0.0351-0.05140.0488-0.0660.01760.0199-0.04440.07760.00770.06680.0919-0.02870.103857.111-160.704-0.52
260.0856-0.0775-0.09670.3635-0.06660.20580.0076-0.00450.0283-0.0161-0.0031-0.11350.01060.0239-0.00450.01940.02170.01920.0927-0.02910.124973.185-161.56825.327
270.03880.01040.01960.1546-0.04650.02770.0030.0196-0.02980.0486-0.0057-0.0551-0.0160.01330.00270.06490.0184-0.03890.0689-0.00710.075261.773-163.61257.538
280.0336-0.01640.0710.1914-0.17320.26040.00830.0016-0.00180.07230.0060.0042-0.0152-0.0212-0.01430.1097-0.01870.01350.06070.0280.022530.013-169.37668.129
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 250
2X-RAY DIFFRACTION1A301 - 307
3X-RAY DIFFRACTION2B1 - 244
4X-RAY DIFFRACTION2B301 - 306
5X-RAY DIFFRACTION3C1 - 240
6X-RAY DIFFRACTION3C301 - 305
7X-RAY DIFFRACTION4D1 - 242
8X-RAY DIFFRACTION4D301 - 305
9X-RAY DIFFRACTION5E3 - 233
10X-RAY DIFFRACTION5E301 - 305
11X-RAY DIFFRACTION6F2 - 244
12X-RAY DIFFRACTION6F301 - 306
13X-RAY DIFFRACTION7G2 - 242
14X-RAY DIFFRACTION7G301
15X-RAY DIFFRACTION7G401 - 410
16X-RAY DIFFRACTION8H1 - 226
17X-RAY DIFFRACTION8H301
18X-RAY DIFFRACTION8H401 - 408
19X-RAY DIFFRACTION9I1 - 204
20X-RAY DIFFRACTION9I301 - 302
21X-RAY DIFFRACTION9I401 - 404
22X-RAY DIFFRACTION10J1 - 195
23X-RAY DIFFRACTION10J201
24X-RAY DIFFRACTION10J301 - 308
25X-RAY DIFFRACTION11K1 - 212
26X-RAY DIFFRACTION11K301 - 302
27X-RAY DIFFRACTION11K401 - 403
28X-RAY DIFFRACTION12L1 - 222
29X-RAY DIFFRACTION12L301 - 307
30X-RAY DIFFRACTION13M1 - 233
31X-RAY DIFFRACTION13M301 - 310
32X-RAY DIFFRACTION14N1 - 196
33X-RAY DIFFRACTION14N201
34X-RAY DIFFRACTION14N301 - 306
35X-RAY DIFFRACTION15O1 - 250
36X-RAY DIFFRACTION15O301 - 305
37X-RAY DIFFRACTION16P1 - 244
38X-RAY DIFFRACTION16P301 - 308
39X-RAY DIFFRACTION17Q1 - 240
40X-RAY DIFFRACTION17Q301 - 306
41X-RAY DIFFRACTION18R1 - 242
42X-RAY DIFFRACTION18R301 - 303
43X-RAY DIFFRACTION19S3 - 233
44X-RAY DIFFRACTION19S301
45X-RAY DIFFRACTION20T2 - 244
46X-RAY DIFFRACTION20T301 - 307
47X-RAY DIFFRACTION21U2 - 242
48X-RAY DIFFRACTION21U301 - 305
49X-RAY DIFFRACTION22V1 - 226
50X-RAY DIFFRACTION22V301
51X-RAY DIFFRACTION22V401 - 411
52X-RAY DIFFRACTION23W1 - 204
53X-RAY DIFFRACTION23W301 - 303
54X-RAY DIFFRACTION24X1 - 195
55X-RAY DIFFRACTION24X201 - 207
56X-RAY DIFFRACTION25Y1 - 212
57X-RAY DIFFRACTION25Y301
58X-RAY DIFFRACTION25Y401 - 405
59X-RAY DIFFRACTION26Z1 - 222
60X-RAY DIFFRACTION26Z301
61X-RAY DIFFRACTION26Z401 - 404
62X-RAY DIFFRACTION27a1 - 233
63X-RAY DIFFRACTION27a301 - 316
64X-RAY DIFFRACTION28b1 - 196
65X-RAY DIFFRACTION28b201 - 205

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