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- PDB-4qw7: yCP beta5-M45T mutant in complex with carfilzomib -

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Basic information

Entry
Database: PDB / ID: 4qw7
TitleyCP beta5-M45T mutant in complex with carfilzomib
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 / Cross-presentation of soluble exogenous antigens (endosomes) / TNFR2 non-canonical NF-kB pathway / proteasomal ubiquitin-independent protein catabolic process / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Regulation of PTEN stability and activity / CDK-mediated phosphorylation and removal of Cdc6 / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / KEAP1-NFE2L2 pathway ...proteasome core complex assembly / nuclear outer membrane-endoplasmic reticulum membrane network / Cross-presentation of soluble exogenous antigens (endosomes) / TNFR2 non-canonical NF-kB pathway / proteasomal ubiquitin-independent protein catabolic process / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Regulation of PTEN stability and activity / CDK-mediated phosphorylation and removal of Cdc6 / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / KEAP1-NFE2L2 pathway / Neddylation / Orc1 removal from chromatin / MAPK6/MAPK4 signaling / proteasome storage granule / Antigen processing: Ubiquitination & Proteasome degradation / endopeptidase activator activity / proteasome assembly / proteasome endopeptidase complex / proteasome core complex, beta-subunit complex / proteasome core complex, alpha-subunit complex / Ub-specific processing proteases / threonine-type endopeptidase activity / Neutrophil degranulation / proteasome complex / peroxisome / proteasome-mediated ubiquitin-dependent protein catabolic process / endopeptidase activity / mRNA binding / endoplasmic reticulum membrane / mitochondrion / nucleus / cytosol
Similarity search - Function
Aminohydrolase, N-terminal nucleophile (Ntn) domain / Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 / Proteasome beta subunit, C-terminal / Proteasome beta subunits C terminal / Proteasome subunit beta 4 / Proteasome subunit beta 2 / Proteasome beta 3 subunit / Proteasome subunit alpha6 / Proteasome subunit alpha5 / Proteasome beta-type subunits signature. ...Aminohydrolase, N-terminal nucleophile (Ntn) domain / Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 / Proteasome beta subunit, C-terminal / Proteasome beta subunits C terminal / Proteasome subunit beta 4 / Proteasome subunit beta 2 / Proteasome beta 3 subunit / Proteasome subunit alpha6 / Proteasome subunit alpha5 / Proteasome beta-type subunits signature. / Peptidase T1A, proteasome beta-subunit / Proteasome beta-type subunit, conserved site / Proteasome subunit A N-terminal signature / Proteasome alpha-type subunits signature. / Proteasome alpha-subunit, N-terminal domain / Proteasome subunit A N-terminal signature Add an annotation / : / Proteasome alpha-type subunit / Proteasome alpha-type subunit profile. / Proteasome B-type subunit / Proteasome beta-type subunit profile. / Proteasome subunit / Proteasome, subunit alpha/beta / Nucleophile aminohydrolases, N-terminal / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
CARFILZOMIB, bound form / Chem-3BV / 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 ...CARFILZOMIB, bound form / Chem-3BV / 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: 2.7 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 6, 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)736,42749
Polymers730,99128
Non-polymers5,43721
Water10,377576
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)136.630, 300.130, 145.260
Angle α, β, γ (deg.)90.00, 113.11, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.999733, -0.000559, 0.023104), (-0.003504, -0.984488, -0.175416), (0.022844, -0.17545, 0.984223)68.08339, -288.52271, -26.25675

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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: M45T / 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: 23295.158 Da / Num. of mol.: 2
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 , 5 types, 597 molecules

#15: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 7 / 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-3BV / N-{(2S)-2-[(morpholin-4-ylacetyl)amino]-4-phenylbutanoyl}-L-leucyl-N-[(2R,3S,4S)-1,3-dihydroxy-2,6-dimethylheptan-4-yl]-L-phenylalaninamide / CARFILZOMIB, bound form


Type: peptide-like, Peptide-like / Class: Inhibitor / Mass: 723.942 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C40H61N5O7 / References: CARFILZOMIB, bound form / Comment: medication, anticancer, inhibitor*YM
#18: Chemical
ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#19: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 576 / 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: Aug 14, 2013
RadiationMonochromator: LN2 COOLED FIXED-EXIT. SI(111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→30 Å / Num. all: 293794 / Num. obs: 284293 / % possible obs: 96.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.086 / Net I/σ(I): 11.5
Reflection shellResolution: 2.7→2.8 Å / Rmerge(I) obs: 0.472 / Mean I/σ(I) obs: 3.3 / % possible all: 97.8

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Processing

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

1ryp


Resolution: 2.7→15 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.928 / SU B: 24.956 / SU ML: 0.22 / Cross valid method: THROUGHOUT / ESU R Free: 0.271 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22618 14215 5 %RANDOM
Rwork0.20495 ---
obs0.20602 270078 96.88 %-
all-285293 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 58.492 Å2
Baniso -1Baniso -2Baniso -3
1-2.58 Å20 Å2-0.71 Å2
2---5.57 Å20 Å2
3---2.42 Å2
Refinement stepCycle: LAST / Resolution: 2.7→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms49293 0 371 576 50240
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.01950583
X-RAY DIFFRACTIONr_bond_other_d0.0030.0248384
X-RAY DIFFRACTIONr_angle_refined_deg0.8731.97168448
X-RAY DIFFRACTIONr_angle_other_deg0.7723.003111430
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.00956306
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.82924.4082246
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.91158732
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.64615284
X-RAY DIFFRACTIONr_chiral_restr0.0490.27710
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0257216
X-RAY DIFFRACTIONr_gen_planes_other0.0010.0211340
X-RAY DIFFRACTIONr_mcbond_it2.1944.61925313
X-RAY DIFFRACTIONr_mcbond_other2.1944.61925312
X-RAY DIFFRACTIONr_mcangle_it2.8996.91231588
X-RAY DIFFRACTIONr_mcangle_other2.8996.91231589
X-RAY DIFFRACTIONr_scbond_it2.0845.00125270
X-RAY DIFFRACTIONr_scbond_other2.0845.00125270
X-RAY DIFFRACTIONr_scangle_other2.5467.34736861
X-RAY DIFFRACTIONr_long_range_B_refined3.30136.03254427
X-RAY DIFFRACTIONr_long_range_B_other3.28636.03154369
X-RAY DIFFRACTIONr_rigid_bond_restr1.155398967
X-RAY DIFFRACTIONr_sphericity_free27.6665328
X-RAY DIFFRACTIONr_sphericity_bonded18.109598304
LS refinement shellResolution: 2.7→2.768 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.356 1027 -
Rwork0.312 19509 -
obs--97.91 %
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)
10.01140.00180.00240.00150.00210.0050.00560.0043-0.0041-0.0052-0.0033-0.0108-0.0163-0.0117-0.00230.1225-0.0088-0.00750.1077-0.00180.148867.1623-91.937646.1613
20.0032-0.0014-0.00030.00740.00180.0006-0.0053-0.001-0.0188-0.0199-0.00390.0173-0.0070.00180.00930.1389-0.01040.0210.10810.00550.124959.922-87.750316.5059
30.00490.00760.00150.01720.0060.0043-0.0064-0.0083-0.0068-0.01310.0091-0.00570.00990.0119-0.00270.1767-0.0092-0.00930.10450.0040.146132.6944-87.23821.2007
40.0060.00180.00140.00750.00250.001-0.006-0.01870.0097-0.0072-0.00040.0321-0.0066-0.00140.00640.1582-0.0042-0.02190.07090.00920.13873.4682-89.891113.6937
50.04040.0428-0.02970.0487-0.03230.02210.0023-0.00050.0035-0.0050.00230.02550.0050.0033-0.00470.14350.0064-0.00450.0924-0.00990.1475-2.8895-94.164245.6637
60.00080.00080.00050.00350.00130.00180.0071-0.00170.00060.0125-0.01170.01590.01130.00690.00450.14830.00430.02540.1004-0.01730.095415.4613-94.785669.8718
70.00590.0012-0.00190.00610.00020.00070.01410.0190.00020.0311-0.012-0.002-0.0029-0.0076-0.00210.1788-0.0046-0.0110.0942-0.01940.12747.8772-93.244571.2145
80.00110.00140.00010.01470.00360.00430.01080.00250.00040.0197-0.0051-0.04120.005-0.0184-0.00570.12790.0102-0.00650.0921-0.00860.148267.523-130.019348.1669
90.00020.00090.00040.0139-0.00230.0053-0.0011-0.0023-0.0024-0.02480.0065-0.0091-0.0032-0.0226-0.00550.13760.00380.02190.1048-0.0050.135668.5461-127.386721.0379
100.0035-0.00230.00250.0361-0.01340.0060.012-0.00880.0155-0.0334-0.01310.01430.0139-0.00330.00110.1791-0.00340.01120.11180.00060.132445.0352-126.4411-0.4549
110.0045-0.0018-0.0070.00180.00380.01190.0072-0.01150.015-0.00340.01070.0015-0.01810.0251-0.01790.16020.0013-0.02930.10180.01290.139411.2689-130.74462.8495
120.0016-0.0004-0.00170.00120.00150.01150.01150.00170.0036-0.00820.00040.0106-0.01770.0286-0.01190.17020.0087-0.01750.10010.0070.1517-4.172-134.011728.7192
130.0010.00030.00150.03460.00540.00980.01060.00380.00420.0085-0.0042-0.00190.00940.0282-0.00640.164-0.0027-0.00890.10120.00350.14318.0519-137.648860.4693
140.0111-0.0198-0.0130.04940.03420.02540.01130.011-0.01140.011-0.0099-0.00670.010.006-0.00140.16980.0049-0.0190.10010.00430.139940.1606-134.036170.4394
150.02940.0043-0.00390.0016-0.00150.0053-0.0010.0110.0086-0.0130.0018-0.00170.01460.0167-0.00080.1844-0.0031-0.01030.09860.00580.1471.833-206.24136.7759
160.01620.0130.0230.01090.01850.0347-0.0076-0.0034-0.00180.0012-0.0019-0.006-0.00530.00350.00950.17890.001-0.0150.09810.00120.14178.369-205.11046.725
170.0125-0.00610.01530.0058-0.01390.03890.0265-0.0054-0.02440.00260.00940.0254-0.01220.023-0.03590.17880.015-0.00630.066-0.03250.124635.6308-203.1169-9.0071
180.0134-0.006-0.00680.0231-0.02270.06360.0125-0.01290.0105-0.0442-0.0256-0.011-0.00470.01570.01310.14330.03330.01360.0455-0.02680.106764.9986-202.63343.4618
190.00310.0022-0.00090.00540.00450.00780.01880.01130.0010.0210.0048-0.02130.0093-0.0134-0.02360.14920.0281-0.0080.0881-0.02080.167271.8895-203.900335.3809
200.01040.0022-0.00020.00190.00070.01110.027-0.0048-0.01130.0079-0.0156-0.0158-0.0065-0.0257-0.01140.1544-0.0047-0.04320.06220.0050.144153.9463-207.516559.5946
210.00290.0001-0.00090.00060.00010.0039-0.00180.0149-0.0013-0.0088-0.00130.0042-0.00850.0020.00310.18680.0052-0.01170.09420.01160.138521.617-209.464161.1858
220.0010.00030.00080.00020.0010.00770.0125-0.00260.00170.00450.0020.00140.01940.0191-0.01460.1785-0.014-0.0110.09950.00450.14751.6528-169.120145.3644
230.01590.04580.01160.1370.03660.0112-0.0004-0.00720.0079-0.00320.00060.02160.00690.0105-0.00020.1872-0.0031-0.00940.1110.00360.14590.1458-166.982818.1677
240.00410.01140.00390.07090.02510.01030.0089-0.0091-0.0123-0.0178-0.00370.0002-0.00470.0082-0.00520.1784-0.0002-0.01870.10550.0010.125423.2671-164.136-3.621
250.00150.00010.00230.00110.00080.00440.0111-0.0065-0.0040.00220.006-0.00950.0147-0.0079-0.01710.18510.00360.01250.1028-0.01380.132957.1398-160.4459-0.1664
260.00180.00270.00230.01430.00380.00480.0109-0.0062-0.00460.0061-0.0025-0.04510.0043-0.0193-0.00840.15150.01630.01410.1016-0.01130.154272.9867-161.701125.616
270.1296-0.04440.05230.0604-0.01320.0301-0.0073-0.0004-0.01210.0109-0.0031-0.0249-0.0166-0.02450.01040.15620.0077-0.00360.09570.00310.142961.3285-163.660857.7085
280.00240.00210.00010.00830.00350.00410.01910.0039-0.00240.0034-0.0041-0.0105-0-0.0145-0.0150.17540.0014-0.00950.11240.00070.142729.4048-169.014867.4923
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 250
2X-RAY DIFFRACTION1A301 - 325
3X-RAY DIFFRACTION2B1 - 244
4X-RAY DIFFRACTION2B301 - 318
5X-RAY DIFFRACTION3C1 - 240
6X-RAY DIFFRACTION3C301 - 313
7X-RAY DIFFRACTION4D1 - 242
8X-RAY DIFFRACTION4D301 - 307
9X-RAY DIFFRACTION5E3 - 233
10X-RAY DIFFRACTION5E301 - 310
11X-RAY DIFFRACTION6F2 - 244
12X-RAY DIFFRACTION6F301 - 312
13X-RAY DIFFRACTION7G2 - 242
14X-RAY DIFFRACTION7G301 - 302
15X-RAY DIFFRACTION7G401 - 427
16X-RAY DIFFRACTION8H1 - 222
17X-RAY DIFFRACTION8H301 - 302
18X-RAY DIFFRACTION8H401 - 434
19X-RAY DIFFRACTION9I1 - 204
20X-RAY DIFFRACTION9I301
21X-RAY DIFFRACTION9I401 - 430
22X-RAY DIFFRACTION10J1 - 195
23X-RAY DIFFRACTION10J201
24X-RAY DIFFRACTION10J301 - 322
25X-RAY DIFFRACTION11K1 - 212
26X-RAY DIFFRACTION11K301 - 302
27X-RAY DIFFRACTION11K401 - 424
28X-RAY DIFFRACTION12L1 - 222
29X-RAY DIFFRACTION12L301 - 325
30X-RAY DIFFRACTION13M1 - 233
31X-RAY DIFFRACTION13M301 - 328
32X-RAY DIFFRACTION14N1 - 196
33X-RAY DIFFRACTION14N201 - 203
34X-RAY DIFFRACTION14N301 - 324
35X-RAY DIFFRACTION15O1 - 250
36X-RAY DIFFRACTION15O301 - 311
37X-RAY DIFFRACTION16P1 - 244
38X-RAY DIFFRACTION16P301 - 313
39X-RAY DIFFRACTION17Q1 - 240
40X-RAY DIFFRACTION17Q301 - 311
41X-RAY DIFFRACTION18R1 - 242
42X-RAY DIFFRACTION18R301 - 309
43X-RAY DIFFRACTION19S3 - 233
44X-RAY DIFFRACTION19S301 - 309
45X-RAY DIFFRACTION20T2 - 244
46X-RAY DIFFRACTION20T301 - 314
47X-RAY DIFFRACTION21U2 - 242
48X-RAY DIFFRACTION21U301
49X-RAY DIFFRACTION21U401 - 431
50X-RAY DIFFRACTION22V1 - 222
51X-RAY DIFFRACTION22V301 - 303
52X-RAY DIFFRACTION22V401 - 422
53X-RAY DIFFRACTION23W1 - 204
54X-RAY DIFFRACTION23W301 - 321
55X-RAY DIFFRACTION24X1 - 195
56X-RAY DIFFRACTION24X201 - 227
57X-RAY DIFFRACTION25Y1 - 212
58X-RAY DIFFRACTION25Y301 - 303
59X-RAY DIFFRACTION25Y401 - 424
60X-RAY DIFFRACTION26Z1 - 222
61X-RAY DIFFRACTION26Z301
62X-RAY DIFFRACTION26Z401 - 424
63X-RAY DIFFRACTION27a1 - 233
64X-RAY DIFFRACTION27a301 - 336
65X-RAY DIFFRACTION28b1 - 196
66X-RAY DIFFRACTION28b201 - 202
67X-RAY DIFFRACTION28b301 - 325

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