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- PDB-4qvy: yCP beta5-A49T-mutant in complex with bortezomib -

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Basic information

Entry
Database: PDB / ID: 4qvy
TitleyCP beta5-A49T-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 / Cancer / Proteasome / Bortezomib / Drug Resistance / Binding Analysis / HYDROLASE-HYDROLASE INHIBITOR complex
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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.51 Å
AuthorsHuber, E.M. / Heinemeyer, W. / Groll, M.
CitationJournal: Structure / Year: 2015
Title: Bortezomib-Resistant Mutant Proteasomes: Structural and Biochemical Evaluation with Carfilzomib and ONX 0914.
Authors: Huber, E.M. / Heinemeyer, W. / Groll, M.
History
DepositionJul 16, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 4, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 18, 2015Group: 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_ref_seq_dif / 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.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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 20, 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)733,77747
Polymers731,11128
Non-polymers2,66619
Water7,674426
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area124520 Å2
ΔGint-489 kcal/mol
Surface area214800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.320, 300.900, 144.920
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(-0.999624, -0.002475, 0.027305), (-0.002284, -0.984935, -0.172909), (0.027321, -0.172906, 0.984559)67.43683, -289.29828, -26.07954

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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 / Mutation: A49T / 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 / 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 / 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 / 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 / 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 / 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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Protein , 1 types, 2 molecules FT

#6: Protein PROBABLE PROTEASOME SUBUNIT ALPHA TYPE-7 / Macropain subunit C1 / Multicatalytic endopeptidase complex subunit C1 / Proteasome component C1 / ...Macropain subunit C1 / Multicatalytic endopeptidase complex subunit C1 / Proteasome component C1 / Proteinase YSCE subunit 1


Mass: 31575.068 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c
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 (brewer's 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 (brewer's 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 (brewer's 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: 23355.275 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: PRE2, DOA3, PRG1, YPR103W, P8283.10 / Production host: SACCHAROMYCES CEREVISIAE (brewer's yeast)
References: UniProt: P30656, proteasome endopeptidase complex
#12: Protein PROTEASOME SUBUNIT BETA TYPE-6 / Multicatalytic endopeptidase complex subunit C5 / Proteasome component C5


Mass: 24883.928 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / 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 (brewer's 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 (brewer's yeast) / Strain: ATCC 204508 / S288c
References: UniProt: P38624, proteasome endopeptidase complex

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Non-polymers , 4 types, 445 molecules

#15: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 9 / 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 / Comment: medication*YM
#18: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 426 / 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, 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 / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: May 13, 2012
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→30 Å / Num. all: 366982 / Num. obs: 362946 / % possible obs: 98.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 16.4
Reflection shellResolution: 2.5→2.6 Å / Rmerge(I) obs: 0.421 / Mean I/σ(I) obs: 3.9 / % possible all: 92.3

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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: 2.51→15 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.947 / SU B: 19.95 / SU ML: 0.187 / Cross valid method: THROUGHOUT / ESU R Free: 0.213 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2189 18148 5 %RANDOM
Rwork0.1933 ---
all0.198 362946 --
obs0.19458 344798 99.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 62.692 Å2
Baniso -1Baniso -2Baniso -3
1-4.65 Å20 Å2-1.74 Å2
2---5.89 Å2-0 Å2
3---1.46 Å2
Refinement stepCycle: LAST / Resolution: 2.51→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms49370 0 181 426 49977
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.01950458
X-RAY DIFFRACTIONr_bond_other_d0.0020.0248198
X-RAY DIFFRACTIONr_angle_refined_deg0.8991.96768268
X-RAY DIFFRACTIONr_angle_other_deg0.7053.001110972
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.17356314
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.44724.4232252
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.411158754
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.34215284
X-RAY DIFFRACTIONr_chiral_restr0.050.27688
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0257252
X-RAY DIFFRACTIONr_gen_planes_other0.0010.0211322
X-RAY DIFFRACTIONr_mcbond_it2.1755.425346
X-RAY DIFFRACTIONr_mcbond_other2.1755.39925345
X-RAY DIFFRACTIONr_mcangle_it2.8738.08331630
X-RAY DIFFRACTIONr_mcangle_other2.8738.08331631
X-RAY DIFFRACTIONr_scbond_it2.1235.82225112
X-RAY DIFFRACTIONr_scbond_other2.1235.82225112
X-RAY DIFFRACTIONr_scangle_other2.5898.57236638
X-RAY DIFFRACTIONr_long_range_B_refined3.23942.13353875
X-RAY DIFFRACTIONr_long_range_B_other3.22542.12953839
X-RAY DIFFRACTIONr_rigid_bond_restr1.84398656
X-RAY DIFFRACTIONr_sphericity_free27.5365269
X-RAY DIFFRACTIONr_sphericity_bonded16.48597917
LS refinement shellResolution: 2.505→2.568 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.33 1263 -
Rwork0.309 24001 -
obs--96.74 %
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)
10.068-0.02250.04750.011-0.01610.0403-0.00210.0131-0.00470.00070.0005-0.0115-0.0197-0.00130.00160.084-0.01260.00660.0674-0.00310.114967.2563-92.136846.0876
20.0009-0.0022-0.00570.01250.03060.10020.0031-0.0011-0.0065-0.0103-0.0069-0.0007-0.00790.01690.00380.0862-0.01050.02020.06830.0060.107259.8251-87.928216.4332
30.03770.02090.00030.0205-0.01570.03950.0104-0.00170.0054-0.00410.00430.0173-0.00540.0213-0.01470.10910.00480.00160.06120.00380.100732.5228-87.36911.1374
40.0466-0.03220.04540.0283-0.02740.0477-0.0048-0.0039-0.0064-0.0074-0.00120.0262-0.0168-0.00590.0060.06040.0295-0.00230.03840.00820.11683.2296-90.059913.7055
50.0807-0.0120.04910.0059-0.00620.0309-0.0061-0.022-0.0160.0080.00580.0224-0.0044-0.00950.00020.01940.01680.02770.0699-0.0060.1093-3.0502-94.320145.8725
60.0219-0.0048-0.01930.0139-0.00980.04170.0031-0.0030.00260.02180.00880.0067-0.0018-0.0014-0.01190.10990.00260.02630.068-0.00650.101615.4731-94.988370.0418
70.00890.00610.0140.01380.02610.05760.01010.01280.00240.0194-0.0103-0.00130.01-0.01020.00030.1381-0.0079-0.00060.0543-0.00910.101247.9851-93.437171.2856
80.00550.0137-0.00130.0583-0.00220.00240.0151-0.0060.00080.0482-0.0079-0.0486-0.007-0.0082-0.00720.05690.0008-0.00670.057-0.00230.11367.8393-129.659647.6021
90.0084-0.0370.02090.38480.11780.329-0.00180.01240.0070.0008-0.0082-0.0217-0.03430.01320.010.0179-0.0070.03530.07950.00650.10668.4977-127.570520.9387
100.08830.07580.03240.07670.02610.01450.0055-0.00190.0024-0.0280.0054-0.00620.01090.0035-0.01090.10710.00230.01560.07080.00180.095244.8584-126.6114-0.6522
110.00320.00080.01270.11930.01240.09860.00790.0059-0.0007-0.03980.01030.0287-0.0156-0.0018-0.01820.0560.0067-0.00390.050.01230.091111.001-130.89022.5721
120.0425-0.00430.05750.08490.02980.13080.0021-0.02090.003-0.00450.00760.0369-0.01810.0104-0.00980.0130.00120.01810.07880.00720.1281-4.4534-134.357328.6943
130.0097-0.02590.00760.28680.00130.01090.0055-0.00510.0060.0396-0.010.017-0.0039-0.00810.00450.06060.00010.03230.0736-0.0010.10117.97-137.881660.5858
140.0681-0.0368-0.02490.09220.00390.01280.0136-0.0074-0.00390.0386-0.00380.0175-0.0029-0.0043-0.00980.1151-0.0068-0.00410.0648-0.0010.087740.04-134.17170.8928
150.05980.00710.00550.04130.04030.05110.00580.0090.007-0.0038-0.00190.00430.0259-0.0001-0.00380.0865-0.0173-0.01160.05870.01180.11761.7025-206.667236.955
160.00530.00240.00250.00160.00180.0023-0.01080.0044-0.0026-0.00670.00170.0065-0.00460.00340.00910.1041-0.003-0.02080.058-0.00350.11428.341-205.64566.8195
170.0095-0.00260.00910.0059-0.0070.0280.0124-0.0108-0.0032-0.02320.00280.00820.0120.013-0.01520.10910.0308-0.00340.0463-0.01420.099935.4935-203.7019-9.0068
180.0162-0.0320.00590.0784-0.0220.00940.0134-0.00310.0291-0.0574-0.0206-0.05250.02330.01460.00720.05810.0340.03030.0376-0.01770.101165.0289-203.12743.381
190.03020.009-0.00480.00770.00140.00770.0187-0.0012-0.0030.0093-0.0076-0.02560.0045-0.0079-0.01110.04750.0199-0.00920.0596-0.00560.130972.003-204.308335.5471
200.0488-0.00010.03930.0018-0.00130.03470.0248-0.0062-0.00960.0061-0.0171-0.00720.0147-0.0076-0.00780.10330.0037-0.02710.04340.00960.108254.0033-207.819859.8172
210.01540.0011-0.00590.0157-0.01530.0194-0.0026-0.0023-0.00410.00090.00120.0176-0.00430.00890.00140.1237-0.0076-0.00880.05960.00910.110721.5814-209.843661.4265
220.00850.01240.00550.02960.00090.01310.0158-0.01190.00250.0231-0.00340.03280.0217-0.0103-0.01240.0546-0.00850.01130.06290.00910.11011.2301-169.948444.9002
230.0021-0.01310.00350.2144-0.03030.00840.00610.008-0.005-0.0063-0.0040.02940.01760.0056-0.00210.0809-0.0002-0.01780.06690.00170.12170.0123-167.454618.2092
240.02840.0636-0.00770.1646-0.01810.0046-0.0010.0003-0.0053-0.04580.01030.0191-0.00380.0059-0.00930.10840.0044-0.01530.0663-0.00080.103223.186-164.6773-3.7692
250.0493-0.03110.07020.1344-0.0370.10590.01810.0126-0.0161-0.069-0.0067-0.02310.02580.0053-0.01140.04660.01210.03670.053-0.010.092757.0921-161.1172-0.5534
260.02720.0029-0.03720.1801-0.03980.09090.0113-0.0082-0.01190.0311-0.0165-0.05940.0047-0.00150.00520.04410.0080.00440.0754-0.00020.132673.0923-161.989325.4603
270.0167-0.0202-0.00420.1480.03440.010.00870.0133-0.01250.0555-0.0085-0.03720.0081-0.0039-0.00020.0869-0.0015-0.01020.06520.00520.107861.3764-163.962857.7316
280.0397-0.03690.02710.0549-0.02910.02080.01960.0003-0.00470.0242-0.0078-0.0090.0012-0.002-0.01180.1137-0.00530.00150.062800.094929.5464-169.45467.9825
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 250
2X-RAY DIFFRACTION1A301 - 312
3X-RAY DIFFRACTION2B1 - 244
4X-RAY DIFFRACTION2B301 - 314
5X-RAY DIFFRACTION3C1 - 240
6X-RAY DIFFRACTION3C301 - 312
7X-RAY DIFFRACTION4D1 - 242
8X-RAY DIFFRACTION4D301 - 307
9X-RAY DIFFRACTION5E3 - 233
10X-RAY DIFFRACTION5E301 - 306
11X-RAY DIFFRACTION6F2 - 244
12X-RAY DIFFRACTION6F301 - 315
13X-RAY DIFFRACTION7G2 - 242
14X-RAY DIFFRACTION7G301 - 302
15X-RAY DIFFRACTION7G401 - 418
16X-RAY DIFFRACTION8H1 - 226
17X-RAY DIFFRACTION8H301
18X-RAY DIFFRACTION8H401 - 431
19X-RAY DIFFRACTION9I1 - 204
20X-RAY DIFFRACTION9I301
21X-RAY DIFFRACTION9I401 - 413
22X-RAY DIFFRACTION10J1 - 195
23X-RAY DIFFRACTION10J201
24X-RAY DIFFRACTION10J301 - 313
25X-RAY DIFFRACTION11K1 - 212
26X-RAY DIFFRACTION11K301 - 303
27X-RAY DIFFRACTION11K401 - 419
28X-RAY DIFFRACTION12L1 - 222
29X-RAY DIFFRACTION12L301 - 324
30X-RAY DIFFRACTION13M1 - 233
31X-RAY DIFFRACTION13M301 - 324
32X-RAY DIFFRACTION14N1 - 196
33X-RAY DIFFRACTION14N201 - 203
34X-RAY DIFFRACTION14N301 - 313
35X-RAY DIFFRACTION15O1 - 250
36X-RAY DIFFRACTION15O301 - 315
37X-RAY DIFFRACTION16P1 - 244
38X-RAY DIFFRACTION16P301 - 312
39X-RAY DIFFRACTION17Q1 - 240
40X-RAY DIFFRACTION17Q301 - 306
41X-RAY DIFFRACTION18R1 - 242
42X-RAY DIFFRACTION18R301 - 307
43X-RAY DIFFRACTION19S3 - 233
44X-RAY DIFFRACTION19S301 - 305
45X-RAY DIFFRACTION20T2 - 244
46X-RAY DIFFRACTION20T301 - 313
47X-RAY DIFFRACTION21U2 - 242
48X-RAY DIFFRACTION21U301
49X-RAY DIFFRACTION21U401 - 415
50X-RAY DIFFRACTION22V1 - 226
51X-RAY DIFFRACTION22V301 - 302
52X-RAY DIFFRACTION22V401 - 423
53X-RAY DIFFRACTION23W1 - 204
54X-RAY DIFFRACTION23W301 - 307
55X-RAY DIFFRACTION24X1 - 195
56X-RAY DIFFRACTION24X201 - 219
57X-RAY DIFFRACTION25Y1 - 212
58X-RAY DIFFRACTION25Y301 - 302
59X-RAY DIFFRACTION25Y401 - 418
60X-RAY DIFFRACTION26Z1 - 222
61X-RAY DIFFRACTION26Z301
62X-RAY DIFFRACTION26Z401 - 415
63X-RAY DIFFRACTION27a1 - 233
64X-RAY DIFFRACTION27a301 - 330
65X-RAY DIFFRACTION28b1 - 196
66X-RAY DIFFRACTION28b201 - 202
67X-RAY DIFFRACTION28b301 - 320

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