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- PDB-4qwx: yCP in complex with the epoxyketone inhibitor ONX 0914 -

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Basic information

Entry
Database: PDB / ID: 4qwx
TitleyCP in complex with the epoxyketone inhibitor ONX 0914
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 / 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
1,2,4-TRIDEOXY-4-METHYL-2-{[N-(MORPHOLIN-4-YLACETYL)-L-ALANYL-O-METHYL-L-TYROSYL]AMINO}-1-PHENYL-D-XYLITOL / Chem-04C / 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 ...1,2,4-TRIDEOXY-4-METHYL-2-{[N-(MORPHOLIN-4-YLACETYL)-L-ALANYL-O-METHYL-L-TYROSYL]AMINO}-1-PHENYL-D-XYLITOL / Chem-04C / 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: 2.9 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 17, 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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_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
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)735,65150
Polymers731,05128
Non-polymers4,60022
Water3,711206
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area122190 Å2
ΔGint-466 kcal/mol
Surface area213310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.600, 300.050, 145.620
Angle α, β, γ (deg.)90.00, 112.77, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.99957, -0.001842, 0.029261), (-0.003238, -0.984985, -0.172607), (0.02914, -0.172627, 0.984556)67.7449, -288.25815, -25.75317

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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 (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 / 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 / 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 / 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 / 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 (brewer's yeast) / Strain: ATCC 204508 / S288c
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 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) / Strain (production host): 4932
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 / 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 (brewer's yeast) / Strain: ATCC 204508 / S288c
References: UniProt: P38624, proteasome endopeptidase complex

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Non-polymers , 6 types, 228 molecules

#15: Chemical
ChemComp-MG / MAGNESIUM ION


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


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#17: Chemical
ChemComp-04C / 1,2,4-trideoxy-4-methyl-2-{[N-(morpholin-4-ylacetyl)-L-alanyl-O-methyl-L-tyrosyl]amino}-1-phenyl-D-xylitol


Type: peptide-like, Peptide-like / Class: Inhibitor / Mass: 584.704 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C31H44N4O7
References: 1,2,4-TRIDEOXY-4-METHYL-2-{[N-(MORPHOLIN-4-YLACETYL)-L-ALANYL-O-METHYL-L-TYROSYL]AMINO}-1-PHENYL-D-XYLITOL
#18: Chemical
ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#19: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#20: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 206 / 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, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K, pH 6.8

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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: Sep 7, 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: 2.9→30 Å / Num. all: 236478 / Num. obs: 226546 / % possible obs: 95.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.087 / Net I/σ(I): 9.8
Reflection shellResolution: 2.9→3 Å / Rmerge(I) obs: 0.539 / Mean I/σ(I) obs: 2.1 / % possible all: 97.2

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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: 2.9→15 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.938 / SU B: 31.248 / SU ML: 0.249 / Cross valid method: THROUGHOUT / ESU R Free: 0.305 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21169 11328 5 %RANDOM
Rwork0.17166 ---
all0.177 226546 --
obs0.17366 215218 95.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 75.235 Å2
Baniso -1Baniso -2Baniso -3
1-2.43 Å20 Å20.07 Å2
2---9 Å2-0 Å2
3---4.83 Å2
Refinement stepCycle: LAST / Resolution: 2.9→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms49296 0 312 206 49814
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.01950526
X-RAY DIFFRACTIONr_bond_other_d0.0020.0248288
X-RAY DIFFRACTIONr_angle_refined_deg0.8921.9768372
X-RAY DIFFRACTIONr_angle_other_deg0.8023.003111204
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1556306
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.32424.4082246
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.416158736
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.24715284
X-RAY DIFFRACTIONr_chiral_restr0.0510.27690
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0257214
X-RAY DIFFRACTIONr_gen_planes_other0.0010.0211322
X-RAY DIFFRACTIONr_mcbond_it3.4336.81425314
X-RAY DIFFRACTIONr_mcbond_other3.4336.81425313
X-RAY DIFFRACTIONr_mcangle_it4.6410.20631590
X-RAY DIFFRACTIONr_mcangle_other4.6410.20731591
X-RAY DIFFRACTIONr_scbond_it3.3647.17925212
X-RAY DIFFRACTIONr_scbond_other3.3647.17925212
X-RAY DIFFRACTIONr_scangle_other4.35710.61536783
X-RAY DIFFRACTIONr_long_range_B_refined5.36152.95353843
X-RAY DIFFRACTIONr_long_range_B_other5.35852.95653824
X-RAY DIFFRACTIONr_rigid_bond_restr1.186398814
X-RAY DIFFRACTIONr_sphericity_free34.1475154
X-RAY DIFFRACTIONr_sphericity_bonded22.254597956
LS refinement shellResolution: 2.9→2.972 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.334 820 -
Rwork0.301 15575 -
obs--97.19 %
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)
10.003-0.0001-0.00130.00130.00040.0010.00470.0102-0.00650.002-0.0037-0.0087-0.0067-0.0032-0.00090.0753-0.012-0.01040.0507-0.00650.077567.092-91.63946.306
20.00710.01110.01180.03260.03830.0461-0.0116-0.0032-0.0125-0.01270.0020.0051-0.0150.01020.00960.075-0.01090.01510.05910.00770.068859.871-87.47616.637
30.02890.0296-0.01710.0318-0.01850.01180.0011-0.00290.0067-0.00580.00660.01410.01010.0024-0.00770.08450.00520.00110.05310.0110.068532.63-87.0511.19
40.03590.03240.01310.03990.01410.0088-0.0029-0.01390.0116-0.0096-0.00560.0417-0.00010.00650.00860.05940.0116-0.01280.04020.01550.09883.343-89.77813.669
50.00090.00080.00610.00720.00860.0546-0.0037-0.0019-0.00030.00680.00240.0262-0.00630.00710.00130.04610.01190.0350.03830.00550.1156-3.059-94.02445.676
60.0007-0.00020.00060.00090.00110.0026-0.0010.0046-0.00370.0084-0.00140.00650.01480.00390.00240.1009-0.00250.03560.0425-0.00360.066315.265-94.63369.998
70.0060.0004-0.00040.00360.0010.00110.00740.00980.00760.0189-0.0081-0.00140.0046-0.00590.00070.113-0.00750.0060.0402-0.01210.051347.767-92.99471.414
80.00590.01520.00730.07140.03090.02460.0133-0.0010.00240.0314-0.0141-0.0367-0.0058-0.01820.00080.0572-0.0028-0.01880.0514-0.00230.073467.55-129.66848.362
90.00220.0031-0.00450.0744-0.00920.01070.00860.00230.0023-0.0157-0.0099-0.0345-0.0163-0.01280.00130.063-0.00110.01130.0581-0.00130.080468.665-127.15521.049
100.03020.018-0.00040.04060.00030.00010.0032-0.0120.0189-0.0411-0.0005-0.0035-0.00090.001-0.00270.0855-0.0010.01380.05830.00250.045345.082-126.219-0.401
110.0021-0.01-0.00150.1338-0.00390.00250.0064-0.00360.0023-0.02920.00020.0372-0.00280.0068-0.00660.0630.0024-0.02070.0530.01020.068711.234-130.4692.634
120.02620.0420.02160.07450.02640.03850.005-0.00040.01440.00410.00330.0455-0.00640.0217-0.00830.0380.00570.00350.05060.00830.1067-4.238-133.94528.742
130.63750.1333-0.04130.04280.08450.62230.01520.0092-0.04370.0125-0.0051-0.01340.0909-0.0061-0.01010.0637-0.00350.01990.0414-0.00730.05497.92-137.50960.609
140.00820.0016-0.00150.05320.00340.00090.01910.00410.00160.0423-0.010.0096-0.00210.0022-0.0090.1115-0.00390.0030.0564-0.00690.037540.073-133.71870.818
150.02760.0251-0.010.06420.00730.0132-0.00470.01380.01170.01010.00370.01020.017-0.00160.0010.0658-0.0134-0.01360.04810.01450.08112.118-206.10436.989
160.02440.00160.01180.0017-0.00150.0098-0.00910.00190.001-0.00460.0007-0.00790.0062-0.00420.00840.0751-0.0034-0.02610.0477-0.00630.07518.5-204.9186.868
170.00510.0008-0.00170.00560.00270.00260.0066-0.0111-0.0008-0.0197-0.01070.0135-0.0166-0.00110.00410.10880.0184-0.02970.0371-0.01590.063735.803-202.831-9.078
180.0168-0.01650.00520.0236-0.00570.00260.0111-0.01180.0096-0.0322-0.0126-0.01420.0091-0.00360.00150.07310.01780.01830.0456-0.01110.067365.226-202.2443.41
190.00720.00920.00560.01350.00620.00980.01530.0018-0.02280.020.0086-0.03820.0045-0.0102-0.02390.04610.0161-0.03430.039-0.0230.138672.293-203.46835.172
200.00520.0025-0.00380.0016-0.00120.0040.01150.0055-0.01040.0112-0.0069-0.0093-0.009-0.0093-0.00470.0836-0.0023-0.04670.03060.00380.094954.53-207.20959.527
210.01230.006-0.01670.0169-0.02330.0429-0.00030.0129-0.00570.01740.00080.00550.0002-0.0022-0.00050.1019-0.0082-0.02090.03940.00960.063922.084-209.27261.34
220.00350.00730.00260.02250.00280.00370.011-0.00090.00360.0248-0.0040.03180.01130.0053-0.00690.0518-0.00190.00490.05270.01480.08821.827-169.02745.62
230.0190.03250.01460.0745-0.00570.06340.00140.00280.011-0.0120.00690.03660.00530.0098-0.00830.0548-0.0017-0.02430.04940.00850.10280.122-166.73918.268
240.01660.01120.00150.01960.00360.00120.0014-0.01-0.0001-0.03030.0020.006-0.00420.0037-0.00340.09420.0014-0.02490.0526-0.00120.057523.297-163.895-3.537
250.003-0.00320.00040.00350.00010.0020.0088-0.00510.0084-0.01140.0022-0.01080.0075-0.0003-0.0110.08210.00530.01340.0635-0.00810.057257.199-160.193-0.423
260.0039-0.014-0.00050.06950.00430.00330.00310.0026-0.00330.00720.0001-0.02760.0054-0.011-0.00320.04630.0059-0.00550.0595-0.00530.09773.158-161.26425.57
270.60150.07570.18360.0656-0.14890.66120.002-0.00370.0060.0317-0.0159-0.0071-0.1228-0.0250.01390.0718-0.0047-0.02850.04120.01720.04561.706-163.32957.785
280.02740.02850.00920.03160.00950.00340.02110.0073-0.01460.0405-0.0055-0.01040.01040.0006-0.01560.107-0.00560.00060.05480.00820.041229.791-168.89367.857
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 250
2X-RAY DIFFRACTION1A301 - 304
3X-RAY DIFFRACTION2B1 - 244
4X-RAY DIFFRACTION2B301 - 314
5X-RAY DIFFRACTION3C1 - 240
6X-RAY DIFFRACTION3C301 - 305
7X-RAY DIFFRACTION4D1 - 242
8X-RAY DIFFRACTION4D301 - 305
9X-RAY DIFFRACTION5E3 - 233
10X-RAY DIFFRACTION5E301 - 304
11X-RAY DIFFRACTION6F2 - 244
12X-RAY DIFFRACTION6F301 - 305
13X-RAY DIFFRACTION7G2 - 242
14X-RAY DIFFRACTION7G301 - 302
15X-RAY DIFFRACTION7G401 - 405
16X-RAY DIFFRACTION8H1 - 222
17X-RAY DIFFRACTION8H301 - 302
18X-RAY DIFFRACTION8H401 - 417
19X-RAY DIFFRACTION9I1 - 204
20X-RAY DIFFRACTION9I301
21X-RAY DIFFRACTION9I401 - 403
22X-RAY DIFFRACTION10J1 - 195
23X-RAY DIFFRACTION10J201 - 210
24X-RAY DIFFRACTION11K1 - 212
25X-RAY DIFFRACTION11K301 - 304
26X-RAY DIFFRACTION11K401 - 412
27X-RAY DIFFRACTION12L1 - 222
28X-RAY DIFFRACTION12L301 - 309
29X-RAY DIFFRACTION13M1 - 233
30X-RAY DIFFRACTION13M301 - 308
31X-RAY DIFFRACTION14N1 - 196
32X-RAY DIFFRACTION14N201 - 202
33X-RAY DIFFRACTION14N301 - 304
34X-RAY DIFFRACTION15O1 - 250
35X-RAY DIFFRACTION15O301 - 302
36X-RAY DIFFRACTION16P1 - 244
37X-RAY DIFFRACTION16P301 - 308
38X-RAY DIFFRACTION17Q1 - 240
39X-RAY DIFFRACTION17Q301 - 307
40X-RAY DIFFRACTION18R1 - 242
41X-RAY DIFFRACTION18R301 - 305
42X-RAY DIFFRACTION19S3 - 233
43X-RAY DIFFRACTION19S301 - 304
44X-RAY DIFFRACTION20T2 - 244
45X-RAY DIFFRACTION20T301 - 304
46X-RAY DIFFRACTION21U2 - 242
47X-RAY DIFFRACTION21U301
48X-RAY DIFFRACTION21U401 - 406
49X-RAY DIFFRACTION22V1 - 222
50X-RAY DIFFRACTION22V301 - 303
51X-RAY DIFFRACTION22V401 - 412
52X-RAY DIFFRACTION23W1 - 204
53X-RAY DIFFRACTION23W301 - 309
54X-RAY DIFFRACTION24X1 - 195
55X-RAY DIFFRACTION24X201
56X-RAY DIFFRACTION24X301 - 309
57X-RAY DIFFRACTION25Y1 - 212
58X-RAY DIFFRACTION25Y301 - 304
59X-RAY DIFFRACTION25Y401 - 408
60X-RAY DIFFRACTION26Z1 - 222
61X-RAY DIFFRACTION26Z301
62X-RAY DIFFRACTION26Z401 - 411
63X-RAY DIFFRACTION27a1 - 233
64X-RAY DIFFRACTION27a301 - 311
65X-RAY DIFFRACTION28b1 - 196
66X-RAY DIFFRACTION28b201
67X-RAY DIFFRACTION28b301 - 305

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