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- PDB-4r18: Ligand-induced Lys33-Thr1 crosslinking at subunit beta5 of the ye... -

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Basic information

Entry
Database: PDB / ID: 4r18
TitleLigand-induced Lys33-Thr1 crosslinking at subunit beta5 of the yeast 20S proteasome
Components
  • (PROTEASOME SUBUNIT ALPHA TYPE- ...) x 7
  • (PROTEASOME SUBUNIT BETA TYPE- ...) x 7
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Proteasome / Drug Development / Binding Analysis / Umpolung / Crosslink / 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
ALPHA-AMINOBUTYRIC ACID / 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 ...ALPHA-AMINOBUTYRIC ACID / 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 S288c (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsDubiella, C. / Cui, H. / Gersch, M. / Brouwer, A.J. / Sieber, S.A. / Krueger, A. / Liskamp, R. / Groll, M.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2014
Title: Selective inhibition of the immunoproteasome by ligand-induced crosslinking of the active site.
Authors: Dubiella, C. / Cui, H. / Gersch, M. / Brouwer, A.J. / Sieber, S.A. / Kruger, A. / Liskamp, R.M. / Groll, M.
History
DepositionAug 4, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 15, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 5, 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.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 1.3Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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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: 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: 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)731,52441
Polymers731,05128
Non-polymers47413
Water31,3461740
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area119390 Å2
ΔGint-456 kcal/mol
Surface area216330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)136.580, 300.820, 146.290
Angle α, β, γ (deg.)90.00, 113.20, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.999758, 0.0006, 0.021988), (-0.004322, -0.985496, -0.169644), (0.021567, -0.169698, 0.98526)68.59579, -289.17142, -25.24635
DetailsAU contains one biological assembly.

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Components

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PROTEASOME SUBUNIT ALPHA TYPE- ... , 7 types, 14 molecules AOBPCQDRESFTGU

#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 S288c (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 S288c (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 S288c (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 S288c (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 S288c (yeast) / Strain: ATCC 204508 / S288C
References: UniProt: P40302, proteasome endopeptidase complex
#6: Protein 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 S288c (yeast) / Strain: ATCC 204508 / S288C
References: UniProt: P21242, 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 S288c (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 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (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 S288c (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 S288c (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 natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288C
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 S288c (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 S288c (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 S288c (yeast) / Strain: ATCC 204508 / S288C
References: UniProt: P38624, proteasome endopeptidase complex

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Non-polymers , 3 types, 1753 molecules

#15: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Mg
#16: Chemical ChemComp-ABA / ALPHA-AMINOBUTYRIC ACID / Α-Aminobutyric acid


Type: L-peptide linking / Mass: 103.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H9NO2
#17: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1740 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsTHE ACTIVE SITE NUCLEOPHILE THR1 IS MODIFIED IN CHAINS K AND Y BY FORMATION OF AN AZIRIDIN-RING. ...THE ACTIVE SITE NUCLEOPHILE THR1 IS MODIFIED IN CHAINS K AND Y BY FORMATION OF AN AZIRIDIN-RING. THIS REACTION IS INDUCED BY A PEPTIDIC SULFONYLFLUORIDE ACTING AS INHIBITOR BY INDUCING THE REACTION AT THE CATALYTIC SITE (CHAINS K AND Y ONLY). NEXT, THERE OCCURS AN INDUCED CROSSLINK (AFTER 24 H OF CRYSTAL INCUBATION), LYS33 OF CHAINS K AND Y, RESPECTIVELY, ATTACK THE AZIRIDIN FORMED AT THR1 HEREBY CAUSING RING OPENING AND ACTIVE SITE CROSSLINKING VIA FORMATION OF A SECONDARY AMINE TO FORM LIGAND ABA.

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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 5, 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: 2.4→30 Å / Num. obs: 408278 / % possible obs: 96.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.1 % / Rmerge(I) obs: 0.044 / Net I/σ(I): 17.3
Reflection shellResolution: 2.4→2.5 Å / Rmerge(I) obs: 0.417 / Mean I/σ(I) obs: 4 / % 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: 1RYP

1ryp


Resolution: 2.4→15 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.958 / SU B: 13.583 / SU ML: 0.134 / Cross valid method: THROUGHOUT / ESU R Free: 0.174 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19486 20414 5 %RANDOM
Rwork0.17718 ---
all0.181 408277 --
obs0.17806 387863 96.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 56.74 Å2
Baniso -1Baniso -2Baniso -3
1-3.41 Å2-0 Å2-0.67 Å2
2---4.79 Å2-0 Å2
3---1.22 Å2
Refinement stepCycle: LAST / Resolution: 2.4→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms49352 0 23 1740 51115
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.01950274
X-RAY DIFFRACTIONr_bond_other_d0.0010.0248046
X-RAY DIFFRACTIONr_angle_refined_deg0.9761.96368006
X-RAY DIFFRACTIONr_angle_other_deg0.7063110640
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.80156314
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.12124.4232252
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.178158758
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.17615284
X-RAY DIFFRACTIONr_chiral_restr0.0560.27660
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0257108
X-RAY DIFFRACTIONr_gen_planes_other0.0010.0211268
X-RAY DIFFRACTIONr_mcbond_it1.5764.74925346
X-RAY DIFFRACTIONr_mcbond_other1.5764.74925345
X-RAY DIFFRACTIONr_mcangle_it1.8487.10931630
X-RAY DIFFRACTIONr_mcangle_other1.8487.10931631
X-RAY DIFFRACTIONr_scbond_it1.935.25524928
X-RAY DIFFRACTIONr_scbond_other1.9295.25524928
X-RAY DIFFRACTIONr_scangle_other1.9567.67536376
X-RAY DIFFRACTIONr_long_range_B_refined2.61737.48555659
X-RAY DIFFRACTIONr_long_range_B_other2.50437.43955246
X-RAY DIFFRACTIONr_rigid_bond_restr1.47398320
X-RAY DIFFRACTIONr_sphericity_free25.2575785
X-RAY DIFFRACTIONr_sphericity_bonded8.08598386
LS refinement shellResolution: 2.4→2.461 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.324 1482 -
Rwork0.293 28155 -
obs--97.87 %
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)
10.1959-0.05140.08890.1387-0.04070.1612-0.00960.02280.01320.05470.0104-0.0358-0.0241-0.009-0.00080.0581-0.01320.0090.0455-0.02220.109666.6946-91.691146.3798
20.2118-0.0131-0.08320.16340.07850.3242-0.0076-0.01150.0152-0.0705-0.0017-0.013-0.05160.03870.00930.0664-0.02220.03570.04240.01240.09459.4592-87.440316.6291
30.20320.06370.08960.11820.01850.3508-0.02910.02510.0445-0.08770.02870.0125-0.05350.04570.00030.1094-0.008-0.00080.03620.03150.090332.1733-87.04381.2364
40.15280.0487-0.00790.26240.05640.2065-0.0126-0.02150.0348-0.06160.01070.1226-0.04440.00360.00190.06630.019-0.0380.02920.03310.1472.8169-89.950713.6904
50.07910.05410.08190.0720.01990.2296-0.0079-0.00540.0310.02460.00620.0888-0.0409-0.01830.00160.03490.03030.0450.04550.00530.1627-3.5861-94.361645.7581
60.06310.04090.05810.05830.03180.07190.0046-0.0230.02540.0556-0.0090.0388-0.0078-0.01840.00440.09550.01460.06580.0528-0.020.104914.7924-94.984170.0319
70.1078-0.01090.07820.1368-0.01720.1708-0.01180.02740.01230.0974-0.0001-0.0329-0.05-0.01140.01190.1251-0.00130.00930.0241-0.02120.074947.3265-93.285871.4347
80.02080.0121-0.00470.12440.02990.03590.02580.01120.0210.0426-0.0036-0.0623-0.0008-0.0047-0.02230.0580.0072-0.00760.0543-0.0150.108767.8929-129.098647.7254
90.107-0.0601-0.01090.47240.06320.2511-0.00410.02310.0252-0.00630.0187-0.0732-0.0106-0.0028-0.01460.027-0.00180.03520.0548-0.01250.100468.4749-126.777521.2019
100.12940.06690.05860.31360.0480.10160.00150.00370.0212-0.0880.00940.0162-0.0153-0.0049-0.01090.0945-0.00010.02590.05190.00320.060844.8463-126.2536-0.469
110.02880.08530.00190.29040.0170.1659-0.0079-0.00150.0147-0.07340.01970.0868-0.0070.0189-0.01180.07490.0088-0.04980.03910.02360.104311.0319-130.75492.5704
120.0719-0.04380.08860.21220.03910.2230.0326-0.0022-0.0002-0.0211-0.0080.09480.0273-0.0024-0.02460.02220.002200.04880.01420.1577-4.4836-134.478628.4289
130.0844-0.05050.0730.42120.02730.08560.0178-0.0030.01010.0871-0.01070.04920.01960.0001-0.00710.0547-0.00170.04860.05310.00340.09547.6957-137.890160.3881
140.20330.0067-0.06810.36660.0490.03790.01530.00640.00690.0934-0.0029-0.0040.0070.0007-0.01250.1037-0.00170.00970.0459-0.00950.054539.724-133.846270.9605
150.3322-0.0573-0.12480.1420.07780.1813-0.02080.03040.00380.0347-0.0010.04350.0711-0.01470.02190.0966-0.038-0.01870.02160.02040.11332.5912-206.774337.0281
160.1915-0.01330.04040.09210.02250.20450.0048-0.0041-0.0051-0.045-0.01920.01240.0344-0.03640.01440.1031-0.0192-0.04420.0277-0.01450.09799.2401-205.76456.8523
170.12980.0109-0.02340.2640.00520.17780.03490.0014-0.0329-0.1750.00290.07990.05570.0018-0.03790.19990.0018-0.06140.0191-0.02520.090236.6549-203.7797-8.9221
180.0843-0.01560.05040.3346-0.00090.14040.0019-0.04060.0246-0.1208-0.0001-0.07950.06140.0096-0.00180.12070.03260.03990.0394-0.02840.091266.0578-202.9633.6031
190.05970.0722-0.02980.1509-0.03720.18870.02310.0244-0.04210.04610.0458-0.09420.08320.0496-0.06890.08930.0637-0.05110.047-0.04270.13872.935-203.976535.7456
200.18620.1460.01920.11950.02960.17120.0548-0.0337-0.07570.0704-0.02-0.06760.07230.0084-0.03480.16280.0256-0.08340.02740.0240.107254.8228-207.546759.9717
210.0515-0.02-0.03440.191-0.09340.1757-0.01990.01440.00750.06650.01930.02270.0498-0.00350.00060.1513-0.0042-0.0160.01730.02270.074122.3299-209.678561.5123
220.0460.0075-0.0230.1209-0.00270.05330.0238-0.013-0.00290.0179-0.00750.09860.0348-0.0013-0.01630.0719-0.00690.00260.03080.02760.12531.5402-170.185144.7366
230.08580.04750.01290.3566-0.0210.1112-0.00470.01010.0026-0.04030.00880.08250.03890.0141-0.00410.0432-0.0118-0.04160.03660.01010.12240.5922-167.936918.1605
240.12510.0192-0.00750.40470.03430.02950.0159-0.0062-0.009-0.091-0.00060.0182-0.0010.0193-0.01530.10950.0015-0.03540.0389-0.00030.069323.9077-164.7334-3.6648
250.06540.07950.0430.4115-0.04080.06710.0087-0.0089-0.0056-0.08140.0097-0.02320.02410.0093-0.01840.08410.01120.0470.0554-0.02240.07457.7555-160.8015-0.3638
260.03180.01260.00530.18970.01290.03520.01740.00060.0008-0.01650.0223-0.07150.01270.0247-0.03970.02460.01560.01340.0467-0.02070.097336.076-145.67633.106
270.1394-0.0107-0.00740.40440.09680.05660.0175-0.0013-0.02010.0940.0072-0.04520.0276-0.0039-0.02470.08060.0139-0.03570.0433-0.00450.087461.9071-163.610757.7566
280.1552-0.03140.0820.2991-0.05190.06170.02210.00340.00010.0687-0.01120.00520.02380.0035-0.01090.1117-0.0040.0040.0410.01170.058230.0417-169.449468.0106
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 250
2X-RAY DIFFRACTION2B1 - 244
3X-RAY DIFFRACTION3C1 - 240
4X-RAY DIFFRACTION4D1 - 242
5X-RAY DIFFRACTION5E3 - 233
6X-RAY DIFFRACTION6F2 - 244
7X-RAY DIFFRACTION7G2 - 242
8X-RAY DIFFRACTION8H1 - 226
9X-RAY DIFFRACTION9I1 - 204
10X-RAY DIFFRACTION10J1 - 195
11X-RAY DIFFRACTION11K2 - 212
12X-RAY DIFFRACTION12L1 - 222
13X-RAY DIFFRACTION13M1 - 233
14X-RAY DIFFRACTION14N1 - 196
15X-RAY DIFFRACTION15O1 - 250
16X-RAY DIFFRACTION16P1 - 244
17X-RAY DIFFRACTION17Q1 - 240
18X-RAY DIFFRACTION18R1 - 242
19X-RAY DIFFRACTION19S3 - 233
20X-RAY DIFFRACTION20T2 - 244
21X-RAY DIFFRACTION21U2 - 242
22X-RAY DIFFRACTION22V1 - 226
23X-RAY DIFFRACTION23W1 - 204
24X-RAY DIFFRACTION24X1 - 195
25X-RAY DIFFRACTION25Y2 - 212
26X-RAY DIFFRACTION26A301 - 379
27X-RAY DIFFRACTION26B301 - 362
28X-RAY DIFFRACTION26C301 - 348
29X-RAY DIFFRACTION26D301 - 356
30X-RAY DIFFRACTION26E301 - 318
31X-RAY DIFFRACTION26F301 - 367
32X-RAY DIFFRACTION26G401 - 483
33X-RAY DIFFRACTION26H401 - 466
34X-RAY DIFFRACTION26I401 - 473
35X-RAY DIFFRACTION26J301 - 385
36X-RAY DIFFRACTION26K401 - 477
37X-RAY DIFFRACTION26L301 - 369
38X-RAY DIFFRACTION26M301 - 381
39X-RAY DIFFRACTION26N301 - 361
40X-RAY DIFFRACTION26O301 - 342
41X-RAY DIFFRACTION26P301 - 352
42X-RAY DIFFRACTION26Q301 - 331
43X-RAY DIFFRACTION26R301 - 350
44X-RAY DIFFRACTION26S301 - 324
45X-RAY DIFFRACTION26T301 - 362
46X-RAY DIFFRACTION26U301 - 362
47X-RAY DIFFRACTION26V401 - 458
48X-RAY DIFFRACTION26W301 - 368
49X-RAY DIFFRACTION26X201 - 266
50X-RAY DIFFRACTION26Y401 - 469
51X-RAY DIFFRACTION26Z401 - 481
52X-RAY DIFFRACTION26a301 - 384
53X-RAY DIFFRACTION26b201 - 266
54X-RAY DIFFRACTION27a1 - 233
55X-RAY DIFFRACTION28b1 - 196

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