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- PDB-3unb: Mouse constitutive 20S proteasome in complex with PR-957 -

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Basic information

Entry
Database: PDB / ID: 3unb
TitleMouse constitutive 20S proteasome in complex with PR-957
Components
  • (Proteasome subunit alpha type- ...) x 7
  • (Proteasome subunit beta type- ...) x 7
KeywordsHYDROLASE/HYDROLASE INHIBITOR / 20S proteasome comprises 28 subunits / each subunit adopts the fold of an antiparallel beta-sheet flanked by helices / Protease / Regulatory complexes / Covalent binding of PR-957 to all active sites / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


Regulation of ornithine decarboxylase (ODC) / Cross-presentation of soluble exogenous antigens (endosomes) / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Ubiquitin-dependent degradation of Cyclin D / AUF1 (hnRNP D0) binds and destabilizes mRNA / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / SCF(Skp2)-mediated degradation of p27/p21 / Assembly of the pre-replicative complex ...Regulation of ornithine decarboxylase (ODC) / Cross-presentation of soluble exogenous antigens (endosomes) / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Ubiquitin-dependent degradation of Cyclin D / AUF1 (hnRNP D0) binds and destabilizes mRNA / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / SCF(Skp2)-mediated degradation of p27/p21 / Assembly of the pre-replicative complex / CDK-mediated phosphorylation and removal of Cdc6 / Degradation of AXIN / Autodegradation of the E3 ubiquitin ligase COP1 / G2/M Checkpoints / Asymmetric localization of PCP proteins / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / Regulation of RUNX3 expression and activity / Regulation of RAS by GAPs / Regulation of PTEN stability and activity / Regulation of RUNX2 expression and activity / Degradation of GLI1 by the proteasome / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / Degradation of DVL / UCH proteinases / Orc1 removal from chromatin / Dectin-1 mediated noncanonical NF-kB signaling / NIK-->noncanonical NF-kB signaling / Hedgehog ligand biogenesis / TNFR2 non-canonical NF-kB pathway / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Hedgehog 'on' state / Degradation of beta-catenin by the destruction complex / Activation of NF-kappaB in B cells / The role of GTSE1 in G2/M progression after G2 checkpoint / FCERI mediated NF-kB activation / CLEC7A (Dectin-1) signaling / Interleukin-1 signaling / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Separation of Sister Chromatids / Downstream TCR signaling / KEAP1-NFE2L2 pathway / MAPK6/MAPK4 signaling / GLI3 is processed to GLI3R by the proteasome / ABC-family proteins mediated transport / Neddylation / Antigen processing: Ubiquitination & Proteasome degradation / Ub-specific processing proteases / proteasome core complex / immune system process / myofibril / NF-kappaB binding / proteasome endopeptidase complex / proteasome core complex, beta-subunit complex / proteasome core complex, alpha-subunit complex / threonine-type endopeptidase activity / skeletal muscle tissue development / negative regulation of inflammatory response to antigenic stimulus / : / Neutrophil degranulation / sarcomere / proteasome complex / ciliary basal body / proteolysis involved in protein catabolic process / lipopolysaccharide binding / P-body / protein catabolic process / response to virus / response to organic cyclic compound / nuclear matrix / peptidase activity / positive regulation of NF-kappaB transcription factor activity / postsynapse / proteasome-mediated ubiquitin-dependent protein catabolic process / endopeptidase activity / response to oxidative stress / nuclear body / ribosome / centrosome / ubiquitin protein ligase binding / synapse / mitochondrion / proteolysis / RNA binding / nucleoplasm / identical protein binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Proteasome subunit alpha 1 / 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 subunit alpha 1 / 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 / Proteasome subunit beta type-1 / Proteasome subunit beta type-5 / Proteasome subunit alpha type-3 / Proteasome subunit alpha type-2 / Proteasome subunit beta type-7 / Proteasome subunit beta type-4 / Proteasome subunit beta type-6 / Proteasome subunit alpha type-6 ...1,2,4-TRIDEOXY-4-METHYL-2-{[N-(MORPHOLIN-4-YLACETYL)-L-ALANYL-O-METHYL-L-TYROSYL]AMINO}-1-PHENYL-D-XYLITOL / Chem-04C / Proteasome subunit beta type-1 / Proteasome subunit beta type-5 / Proteasome subunit alpha type-3 / Proteasome subunit alpha type-2 / Proteasome subunit beta type-7 / Proteasome subunit beta type-4 / Proteasome subunit beta type-6 / Proteasome subunit alpha type-6 / Proteasome subunit alpha type-4 / Proteasome subunit beta type-3 / Proteasome subunit beta type-2 / Proteasome subunit alpha type-1 / Proteasome subunit alpha type-7 / Proteasome subunit alpha type-5
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsHuber, E. / Basler, M. / Schwab, R. / Heinemeyer, W. / Kirk, C. / Groettrup, M. / Groll, M.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2012
Title: Immuno- and constitutive proteasome crystal structures reveal differences in substrate and inhibitor specificity.
Authors: Huber, E.M. / Basler, M. / Schwab, R. / Heinemeyer, W. / Kirk, C.J. / Groettrup, M. / Groll, M.
History
DepositionNov 15, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 29, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 28, 2012Group: Database references
Revision 1.2Dec 12, 2012Group: Other
Revision 1.3Nov 13, 2013Group: Structure summary
Revision 1.4Nov 20, 2013Group: Structure summary
Revision 1.5Sep 13, 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 / 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 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_ref_seq_dif.details / _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-4
C: Proteasome subunit alpha type-7
D: Proteasome subunit alpha type-5
E: Proteasome subunit alpha type-1
F: Proteasome subunit alpha type-3
G: Proteasome subunit alpha type-6
H: Proteasome subunit beta type-7
I: Proteasome subunit beta type-3
J: Proteasome subunit beta type-2
K: Proteasome subunit beta type-5
L: Proteasome subunit beta type-1
M: Proteasome subunit beta type-4
N: Proteasome subunit beta type-6
O: Proteasome subunit alpha type-2
P: Proteasome subunit alpha type-4
Q: Proteasome subunit alpha type-7
R: Proteasome subunit alpha type-5
S: Proteasome subunit alpha type-1
T: Proteasome subunit alpha type-3
U: Proteasome subunit alpha type-6
V: Proteasome subunit beta type-7
W: Proteasome subunit beta type-3
X: Proteasome subunit beta type-2
Y: Proteasome subunit beta type-5
Z: Proteasome subunit beta type-1
a: Proteasome subunit beta type-4
b: Proteasome subunit beta type-6
c: Proteasome subunit alpha type-2
d: Proteasome subunit alpha type-4
e: Proteasome subunit alpha type-7
f: Proteasome subunit alpha type-5
g: Proteasome subunit alpha type-1
h: Proteasome subunit alpha type-3
i: Proteasome subunit alpha type-6
j: Proteasome subunit beta type-7
k: Proteasome subunit beta type-3
l: Proteasome subunit beta type-2
m: Proteasome subunit beta type-5
n: Proteasome subunit beta type-1
o: Proteasome subunit beta type-4
p: Proteasome subunit beta type-6
q: Proteasome subunit alpha type-2
r: Proteasome subunit alpha type-4
s: Proteasome subunit alpha type-7
t: Proteasome subunit alpha type-5
u: Proteasome subunit alpha type-1
v: Proteasome subunit alpha type-3
w: Proteasome subunit alpha type-6
x: Proteasome subunit beta type-7
y: Proteasome subunit beta type-3
z: Proteasome subunit beta type-2
1: Proteasome subunit beta type-5
2: Proteasome subunit beta type-1
3: Proteasome subunit beta type-4
4: Proteasome subunit beta type-6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,442,67268
Polymers1,435,65656
Non-polymers7,01612
Water26,6621480
1
A: Proteasome subunit alpha type-2
B: Proteasome subunit alpha type-4
C: Proteasome subunit alpha type-7
D: Proteasome subunit alpha type-5
E: Proteasome subunit alpha type-1
F: Proteasome subunit alpha type-3
G: Proteasome subunit alpha type-6
H: Proteasome subunit beta type-7
I: Proteasome subunit beta type-3
J: Proteasome subunit beta type-2
K: Proteasome subunit beta type-5
L: Proteasome subunit beta type-1
M: Proteasome subunit beta type-4
N: Proteasome subunit beta type-6
O: Proteasome subunit alpha type-2
P: Proteasome subunit alpha type-4
Q: Proteasome subunit alpha type-7
R: Proteasome subunit alpha type-5
S: Proteasome subunit alpha type-1
T: Proteasome subunit alpha type-3
U: Proteasome subunit alpha type-6
V: Proteasome subunit beta type-7
W: Proteasome subunit beta type-3
X: Proteasome subunit beta type-2
Y: Proteasome subunit beta type-5
Z: Proteasome subunit beta type-1
a: Proteasome subunit beta type-4
b: Proteasome subunit beta type-6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)721,33634
Polymers717,82828
Non-polymers3,5086
Water50428
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
c: Proteasome subunit alpha type-2
d: Proteasome subunit alpha type-4
e: Proteasome subunit alpha type-7
f: Proteasome subunit alpha type-5
g: Proteasome subunit alpha type-1
h: Proteasome subunit alpha type-3
i: Proteasome subunit alpha type-6
j: Proteasome subunit beta type-7
k: Proteasome subunit beta type-3
l: Proteasome subunit beta type-2
m: Proteasome subunit beta type-5
n: Proteasome subunit beta type-1
o: Proteasome subunit beta type-4
p: Proteasome subunit beta type-6
q: Proteasome subunit alpha type-2
r: Proteasome subunit alpha type-4
s: Proteasome subunit alpha type-7
t: Proteasome subunit alpha type-5
u: Proteasome subunit alpha type-1
v: Proteasome subunit alpha type-3
w: Proteasome subunit alpha type-6
x: Proteasome subunit beta type-7
y: Proteasome subunit beta type-3
z: Proteasome subunit beta type-2
1: Proteasome subunit beta type-5
2: Proteasome subunit beta type-1
3: Proteasome subunit beta type-4
4: Proteasome subunit beta type-6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)721,33634
Polymers717,82828
Non-polymers3,5086
Water50428
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)171.720, 198.590, 226.750
Angle α, β, γ (deg.)90.00, 106.59, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.997819, 0.065268, 0.009896), (0.066014, 0.986049, 0.152808), (0.000216, 0.153128, -0.988206)31.33581, -4.43493, 45.32309
3given(1, -0.000242, -0.000708), (0.000241, 0.999999, -0.001238), (0.000708, 0.001238, 0.999999)-53.35929, 0.17881, -108.78284
4given(-0.997786, 0.065734, 0.010155), (0.066514, 0.986102, 0.152243), (-6.0E-6, 0.152581, -0.988291)83.55444, -24.55868, 152.83635

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Components

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Proteasome subunit alpha type- ... , 7 types, 28 molecules AOcqBPdrCQesDRftESguFThvGUiw

#1: Protein
Proteasome subunit alpha type-2 / Macropain subunit C3 / Multicatalytic endopeptidase complex subunit C3 / Proteasome component C3


Mass: 25955.613 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Genus: 10090
References: UniProt: P49722, proteasome endopeptidase complex
#2: Protein
Proteasome subunit alpha type-4 / Macropain subunit C9 / Multicatalytic endopeptidase complex subunit C9 / Proteasome component C9 / ...Macropain subunit C9 / Multicatalytic endopeptidase complex subunit C9 / Proteasome component C9 / Proteasome subunit L


Mass: 29512.807 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Genus: 10090
References: UniProt: Q9R1P0, proteasome endopeptidase complex
#3: Protein
Proteasome subunit alpha type-7 / Proteasome subunit RC6-1


Mass: 27839.852 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Genus: 10090
References: UniProt: Q9Z2U0, proteasome endopeptidase complex
#4: Protein
Proteasome subunit alpha type-5 / Macropain zeta chain / Multicatalytic endopeptidase complex zeta chain / Proteasome zeta chain


Mass: 26435.977 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Genus: 10090
References: UniProt: Q9Z2U1, proteasome endopeptidase complex
#5: Protein
Proteasome subunit alpha type-1 / Macropain subunit C2 / Multicatalytic endopeptidase complex subunit C2 / Proteasome component C2 / ...Macropain subunit C2 / Multicatalytic endopeptidase complex subunit C2 / Proteasome component C2 / Proteasome nu chain


Mass: 29586.576 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Genus: 10090
References: UniProt: Q9R1P4, proteasome endopeptidase complex
#6: Protein
Proteasome subunit alpha type-3 / Macropain subunit C8 / Multicatalytic endopeptidase complex subunit C8 / Proteasome component C8 / ...Macropain subunit C8 / Multicatalytic endopeptidase complex subunit C8 / Proteasome component C8 / Proteasome subunit K


Mass: 28442.248 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Genus: 10090
References: UniProt: O70435, proteasome endopeptidase complex
#7: Protein
Proteasome subunit alpha type-6 / Macropain iota chain / Multicatalytic endopeptidase complex iota chain / Proteasome iota chain


Mass: 27405.434 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Genus: 10090
References: UniProt: Q9QUM9, proteasome endopeptidase complex

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Proteasome subunit beta type- ... , 7 types, 28 molecules HVjxIWkyJXlzKYm1LZn2Mao3Nbp4

#8: Protein
Proteasome subunit beta type-7 / Macropain chain Z / Multicatalytic endopeptidase complex chain Z / Proteasome subunit Z


Mass: 25280.010 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Genus: 10090
References: UniProt: P70195, proteasome endopeptidase complex
#9: Protein
Proteasome subunit beta type-3 / Proteasome chain 13 / Proteasome component C10-II / Proteasome theta chain


Mass: 22988.895 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Genus: 10090
References: UniProt: Q9R1P1, proteasome endopeptidase complex
#10: Protein
Proteasome subunit beta type-2 / Macropain subunit C7-I / Multicatalytic endopeptidase complex subunit C7-I / Proteasome component C7-I


Mass: 22935.377 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Genus: 10090
References: UniProt: Q9R1P3, proteasome endopeptidase complex
#11: Protein
Proteasome subunit beta type-5 / Macropain epsilon chain / Multicatalytic endopeptidase complex epsilon chain / Proteasome chain 6 / ...Macropain epsilon chain / Multicatalytic endopeptidase complex epsilon chain / Proteasome chain 6 / Proteasome epsilon chain / Proteasome subunit X


Mass: 22554.545 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Genus: 10090
References: UniProt: O55234, proteasome endopeptidase complex
#12: Protein
Proteasome subunit beta type-1 / Macropain subunit C5 / Multicatalytic endopeptidase complex subunit C5 / Proteasome component C5 / ...Macropain subunit C5 / Multicatalytic endopeptidase complex subunit C5 / Proteasome component C5 / Proteasome gamma chain


Mass: 23576.969 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Genus: 10090
References: UniProt: O09061, proteasome endopeptidase complex
#13: Protein
Proteasome subunit beta type-4 / Low molecular mass protein 3 / Macropain beta chain / Multicatalytic endopeptidase complex beta ...Low molecular mass protein 3 / Macropain beta chain / Multicatalytic endopeptidase complex beta chain / Proteasome beta chain / Proteasome chain 3


Mass: 24384.715 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Genus: 10090
References: UniProt: P99026, proteasome endopeptidase complex
#14: Protein
Proteasome subunit beta type-6 / Low molecular mass protein 19 / Macropain delta chain / Multicatalytic endopeptidase complex delta ...Low molecular mass protein 19 / Macropain delta chain / Multicatalytic endopeptidase complex delta chain / Proteasome delta chain / Proteasome subunit Y


Mass: 22014.920 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Genus: 10090
References: UniProt: Q60692, proteasome endopeptidase complex

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Non-polymers , 2 types, 1492 molecules

#15: 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.: 12 / 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
#16: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1480 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsTHE STARTING EPOXIDE RING OF AN EPOXOMICIN-LIKE INHIBITOR UNDERGOES RE-CYCLIZATION REACTION WITH ...THE STARTING EPOXIDE RING OF AN EPOXOMICIN-LIKE INHIBITOR UNDERGOES RE-CYCLIZATION REACTION WITH THE SIDE CHAIN OF N-TERMINAL RESIDUE THR-1 (CHAINS V,4,j,N,p,m,x,H,1,Y, b, AND k) AND THE FINAL PRODUCT 04C IS OBSERVED. SEE ALSO LINK RECORDS AND REMARK 630.

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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: 2.58 Å3/Da / Density % sol: 52.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: 0.2 M Sodium formate, 40% MPD , pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Aug 8, 2011
RadiationMonochromator: double-crystal fixed-exit 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: 321807 / Num. obs: 308934 / % possible obs: 96 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.081 / Net I/σ(I): 9.4
Reflection shellResolution: 2.9→3 Å / Rmerge(I) obs: 0.481 / Mean I/σ(I) obs: 2 / % possible all: 96.7

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Processing

Software
NameVersionClassification
XDSdata scaling
PHASERphasing
REFMAC5.6.0119refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1IRU

1iru


Resolution: 2.9→15 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.95 / SU B: 45.959 / SU ML: 0.36 / Cross valid method: THROUGHOUT / ESU R Free: 0.474 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.27259 15447 5 %RANDOM
Rwork0.22966 ---
obs0.23178 293487 96.03 %-
all-308934 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 67.88 Å2
Baniso -1Baniso -2Baniso -3
1--2.83 Å20 Å2-0.13 Å2
2---1.39 Å20 Å2
3---4.14 Å2
Refinement stepCycle: LAST / Resolution: 2.9→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms97252 0 504 1480 99236
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0299564
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.8851.967134532
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.55512444
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.16723.8224364
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.7571517388
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.95215684
X-RAY DIFFRACTIONr_chiral_restr0.0590.215156
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02174136
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr4.015399564
X-RAY DIFFRACTIONr_sphericity_free24.8685719
X-RAY DIFFRACTIONr_sphericity_bonded5.718598521
LS refinement shellResolution: 2.9→2.972 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.436 1096 -
Rwork0.411 20695 -
obs--96.55 %
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)
10.0595-0.0617-0.03350.3823-0.07550.15470.0031-0.01440.0093-0.0255-0.01570.0738-0.01810.00560.01260.1320.0298-0.00630.30560.00240.2814-47.9255.36737.467
20.1405-0.08210.10.46250.09190.163-0.0559-0.0516-0.1056-0.01610.04530.0695-0.0375-0.03430.01060.1568-0.05530.02680.2599-0.0010.3172-46.22724.18239.914
30.1245-0.00440.29110.04440.03680.7580.0764-0.0602-0.0439-0.08590.05310.01830.1017-0.0599-0.12950.2575-0.04490.00580.19150.11620.3239-28.0386.84359.842
40.10770.0821-0.03050.38250.02740.0223-0.0442-0.167-0.0658-0.11420.0030.08680.03020.06150.04120.2320.0230.04980.33370.1930.1881-9.30618.76181.895
50.0778-0.14280.02690.5453-0.04380.0196-0.0481-0.1442-0.03550.02010.06610.032-0.0538-0.0144-0.0180.1718-0.00580.04330.55590.07360.0217-3.49848.26290.269
60.5513-0.17650.3060.215-0.11920.176-0.0764-0.18280.1689-0.0293-0.0125-0.0227-0.008-0.08940.08890.21210.0360.06540.352-0.17360.1716-15.44774.16178.828
70.0208-0.03020.04560.20680.11690.3716-0.0249-0.05050.0189-0.01970.0855-0.0585-0.044-0.0731-0.06060.18290.06320.04350.2468-0.05440.3089-36.40577.42554.713
80.0886-0.0897-0.07440.28430.02960.13770.03710.01660.0579-0.0465-0.00240.06390.0436-0.064-0.03470.18010.0381-0.02830.2814-0.0010.2786-18.07761.88313.172
90.5799-0.0125-0.26020.34750.14630.2111-0.00970.09070.02160.07890.0037-0.020.0889-0.11170.0060.1834-0.0192-0.04740.258-0.04140.2609-19.55834.15310.192
100.4556-0.1019-0.16580.10110.19360.3938-0.1148-0.0497-0.08190.00360.02530.04640.04120.00580.08950.2773-0.0065-0.00260.11920.0080.3191-5.20810.36926.311
110.6610.2151-0.1810.4180.08380.2306-0.0411-0.1037-0.01340.0197-0.0236-0.03130.056-0.0080.06470.2760.0352-0.01080.16550.11690.238416.89311.05751.178
120.10450.1596-0.10650.3539-0.17240.2067-0.0205-0.09090.00770.0191-0.0048-0.01310.00690.01270.02530.20020.0429-0.0230.32910.01410.191229.0237.05564.337
130.59230.1121-0.24160.0739-0.16610.38640.1219-0.08490.1220.0159-0.02080.0420.02050.0431-0.10110.2519-0.0047-0.00090.2663-0.08180.187222.97968.78757.275
140.3558-0.0066-0.23080.0712-0.1450.59910.09270.0168-0.02520.00380.0186-0.021-0.0808-0.0916-0.11130.23040.04120.04060.1833-0.04250.28431.55481.76835.965
150.1817-0.01440.18330.59270.08030.21320.02990.0224-0.01040.03380.0281-0.02220.0270.0765-0.0580.12290.0642-0.00550.3275-0.1140.271783.03552.59516.104
160.1176-0.0030.10630.14330.0610.4582-0.0617-0.0203-0.00090.01470.0616-0.06650.0431-0.00010.00010.18840.12970.0210.2294-0.05170.281679.27822.3049.122
170.2866-0.05150.21990.46890.03530.19090.07660.006-0.11170.04430.021-0.07740.0197-0.0229-0.09770.27180.1101-0.01080.1578-0.09680.304560.2169.507-13.399
180.2621-0.05790.05410.1999-0.14580.10990.15440.086-0.0578-0.0106-0.09420.06420.01390.0606-0.06020.29480.0922-0.01920.2446-0.15870.19442.31425.886-33.24
190.39760.12010.3350.28710.09650.30160.04330.1147-0.049-0.03150.03130.01240.0530.0476-0.07470.27320.068-0.01620.3264-0.02730.135138.47456.491-36.89
200.1445-0.12990.10590.2730.06090.46920.00380.01780.127-0.0276-0.0128-0.0390.02440.00990.0090.19510.00750.04710.23140.03210.290352.05879.544-21.643
210.0517-0.08980.04780.321-0.05220.15230.02760.03690.03560.01720.03180.029-0.02760.1172-0.05940.1579-0.04530.07270.2508-0.04410.312373.02577.7152.631
220.1210.0972-0.03370.1583-0.02290.01180.0327-0.10050.01840.001-0.0115-0.08530.00680.0325-0.02120.2356-0.0083-0.02110.3178-0.04230.188853.46857.36141.267
230.1950.2102-0.10560.3848-0.1840.09030.048-0.045-0.0467-0.0678-0.0562-0.02810.04010.04510.00810.25640.10610.00670.31070.01650.170253.1529.42639.996
240.58280.3044-0.08350.1619-0.03420.43-0.0570.0469-0.0989-0.02860.0393-0.03170.0344-0.00840.01770.26580.0855-0.01430.1167-0.01230.322537.3359.39720.475
250.9069-0.0515-0.11840.0907-0.10050.153-0.01530.11780.0005-0.03210.00480.0230.0463-0.02520.01050.27670.0059-0.0440.1597-0.09150.275315.47515.357-3.895
260.02830.00490.00640.01610.00330.03950.00420.0195-0.0167-0.00770.0180.0324-0.00760.0125-0.02220.2720.0340.02310.2251-0.01770.121525.37145.16829.652
270.1222-0.1583-0.18740.23660.21860.6040.02120.00640.07320.00060.034-0.03690.0067-0.0126-0.05520.24780.04050.02410.2180.03520.221313.15173.599-1.096
280.3772-0.0863-0.40060.2960.01550.44970.0367-0.05210.0491-0.02010.00040.0185-0.01990.0631-0.03710.2211-0.00580.00920.1925-0.04780.282835.28881.70721.815
290.0644-0.1458-0.01780.36160.00210.1035-0.0002-0.01-0.027-0.0208-0.03110.0311-0.03120.01460.03120.11810.0283-0.02670.28510.00720.33665.56355.367146.185
300.0815-0.06720.03410.28050.03730.1164-0.0615-0.0432-0.1022-0.00730.04620.0148-0.0365-0.06490.01530.1447-0.05540.00660.24110.00760.3687.26124.169148.629
310.15620.00440.33640.05810.03680.76680.0636-0.0605-0.0325-0.10550.03570.01060.1076-0.0742-0.09920.2504-0.0378-0.01160.16420.11090.33325.4286.828168.582
320.1735-0.0291-0.14660.17020.01050.1516-0.0281-0.1505-0.0128-0.12520.02550.03460.05890.08290.00260.21050.00950.01710.29190.16970.260944.16818.759190.613
330.1121-0.11170.07360.460.01990.0934-0.0271-0.1457-0.04220.03020.05250.0208-0.0178-0.0453-0.02530.1528-0.00940.00480.51110.06880.083249.97648.261198.992
340.5024-0.25150.23950.1867-0.12550.1151-0.0679-0.17010.1512-0.0472-0.0005-0.0437-0.0198-0.08060.06840.19510.03070.03620.3225-0.18060.225638.05574.173187.524
350.03430.04220.10860.18310.00040.5668-0.0179-0.0209-0.0041-0.00140.0719-0.0338-0.0907-0.0576-0.0540.17090.06610.03580.2312-0.05820.318617.05677.436163.427
360.20140.0018-0.06450.2630.10660.10430.08340.01870.0015-0.0476-0.02330.0196-0.0126-0.0769-0.06010.16190.0495-0.05770.2431-0.00710.336535.37161.803121.993
370.35040.0358-0.25380.45910.22080.3223-0.01420.0763-0.03740.0534-0.00480.00210.0521-0.09040.0190.1585-0.0139-0.07060.236-0.04320.310933.92734.145118.912
380.472-0.1001-0.13210.28310.1650.3094-0.1028-0.0354-0.0872-0.0010.02910.01990.0345-0.01150.07380.2623-0.0113-0.0060.1080.02010.335748.28210.37135.014
390.72030.1159-0.19050.44840.05290.3318-0.034-0.11940.0089-0.0149-0.0221-0.01250.06320.01510.0560.26390.0341-0.02510.13420.11320.28670.35811.062159.878
400.115-0.0315-0.11560.2056-0.11270.3069-0.0362-0.09860.04720.01440.0190.02060.02610.03340.01710.20440.0382-0.03010.31120.01630.226582.49437.045173.089
410.52350.2063-0.27870.1073-0.20060.47260.1216-0.07190.11020.0353-0.02830.04340.00660.0315-0.09330.2256-0.0006-0.02370.2195-0.07540.282376.44968.788165.99
420.35030.1082-0.38930.0604-0.120.55920.08970.01250.03330.02180.045-0.0429-0.0484-0.0927-0.13470.21640.04810.01880.1745-0.04920.319655.02881.767144.692
430.1124-0.00020.14610.49940.02720.21830.04360.0167-0.00910.03890.0252-0.01230.04430.0923-0.06890.11590.0683-0.02780.3121-0.13060.3022136.51152.569124.849
440.0603-0.0036-0.04890.11660.10280.311-0.0791-0.0385-0.0165-0.01010.0896-0.03670.03030.0081-0.01050.18790.12820.0050.2181-0.06010.3122132.80122.323117.824
450.34-0.17530.23280.5459-0.04590.17340.0536-0.0118-0.09740.02930.0282-0.0910.0294-0.02-0.08180.25360.1076-0.01730.1306-0.1010.3193113.6719.50595.323
460.307-0.23040.11350.337-0.15510.07290.13550.0627-0.0675-0.0396-0.08950.06040.01840.0465-0.0460.30350.0915-0.02830.2314-0.1660.209795.79525.91275.487
470.33140.07430.23890.2850.05210.18450.04350.0953-0.0423-0.04740.02570.05150.0550.0679-0.06920.27040.06-0.02450.3233-0.03360.15891.95356.49371.814
480.1562-0.02090.18290.25940.15220.3904-0.00130.0180.0996-0.0395-0.0019-0.0280.00850.01540.00310.19120.00760.04820.2150.02730.3193105.5279.54987.092
490.0179-0.03190.03420.4554-0.00950.21210.03180.02620.01530.02040.00810.0136-0.0280.0893-0.03990.1664-0.04140.06570.2425-0.05010.3287126.48677.716111.325
500.16050.1539-0.05310.3483-0.04160.02710.0169-0.1080.0774-0.01680.0288-0.0650.03270.0564-0.04580.18510.0055-0.07710.2555-0.05950.318106.93257.354149.998
510.17480.2441-0.08680.5046-0.16630.07650.0577-0.0644-0.0373-0.049-0.07520.04570.05370.09490.01750.20620.1189-0.04360.25250.00820.2967106.62929.4148.759
520.56020.2108-0.21930.0838-0.09620.5778-0.05690.0383-0.0477-0.0190.0347-0.0040.05770.0270.02220.25090.0811-0.02530.1018-0.01350.351590.8199.405129.197
530.6328-0.2039-0.04150.1131-0.05230.12250.00570.09840.0071-0.0058-0.02330.03170.0372-0.01090.01760.28310.0027-0.06180.1531-0.08680.293768.95315.347104.855
540.12580.088-0.04750.31080.26310.4352-0.0136-0.00890.0388-0.08550.0368-0.019-0.0227-0.0305-0.02320.23670.0175-0.06030.2143-0.02120.287758.61943.74195.831
550.0857-0.1265-0.12610.23110.25380.42930.02470.01160.07750.0060.0266-0.04270.0127-0.0207-0.05130.21780.0461-0.00360.1730.02620.313166.63273.596107.648
560.259-0.0339-0.28430.3461-0.00240.37110.0423-0.04150.0343-0.0198-0.01620.0044-0.0290.0648-0.02610.215-0.0036-0.01630.1742-0.05080.32588.76581.709130.584
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 231
2X-RAY DIFFRACTION2B1 - 248
3X-RAY DIFFRACTION3C1 - 239
4X-RAY DIFFRACTION4D1 - 233
5X-RAY DIFFRACTION5E1 - 238
6X-RAY DIFFRACTION6F1 - 244
7X-RAY DIFFRACTION7G1 - 243
8X-RAY DIFFRACTION8H2 - 220
9X-RAY DIFFRACTION9I1 - 204
10X-RAY DIFFRACTION10J1 - 196
11X-RAY DIFFRACTION11K2 - 201
12X-RAY DIFFRACTION12L1 - 213
13X-RAY DIFFRACTION13M1 - 216
14X-RAY DIFFRACTION14N2 - 202
15X-RAY DIFFRACTION15O1 - 231
16X-RAY DIFFRACTION16P1 - 248
17X-RAY DIFFRACTION17Q1 - 239
18X-RAY DIFFRACTION18R1 - 233
19X-RAY DIFFRACTION19S1 - 238
20X-RAY DIFFRACTION20T1 - 244
21X-RAY DIFFRACTION21U1 - 243
22X-RAY DIFFRACTION22V2 - 220
23X-RAY DIFFRACTION23W1 - 204
24X-RAY DIFFRACTION24X1 - 196
25X-RAY DIFFRACTION25Y2 - 201
26X-RAY DIFFRACTION261401 - 427
27X-RAY DIFFRACTION262301 - 333
28X-RAY DIFFRACTION263301 - 337
29X-RAY DIFFRACTION264401 - 430
30X-RAY DIFFRACTION26A301 - 319
31X-RAY DIFFRACTION26B301 - 324
32X-RAY DIFFRACTION26C301 - 313
33X-RAY DIFFRACTION26D301 - 316
34X-RAY DIFFRACTION26E301 - 321
35X-RAY DIFFRACTION26F301 - 320
36X-RAY DIFFRACTION26G301 - 322
37X-RAY DIFFRACTION26H401 - 431
38X-RAY DIFFRACTION26I301 - 332
39X-RAY DIFFRACTION26J301 - 325
40X-RAY DIFFRACTION26K401 - 428
41X-RAY DIFFRACTION26L301 - 323
42X-RAY DIFFRACTION26M301 - 327
43X-RAY DIFFRACTION26N401 - 433
44X-RAY DIFFRACTION26O301 - 333
45X-RAY DIFFRACTION26P301 - 338
46X-RAY DIFFRACTION26Q301 - 316
47X-RAY DIFFRACTION26R301 - 319
48X-RAY DIFFRACTION26S301 - 325
49X-RAY DIFFRACTION26T301 - 325
50X-RAY DIFFRACTION26U301 - 337
51X-RAY DIFFRACTION26V401 - 435
52X-RAY DIFFRACTION26W301 - 337
53X-RAY DIFFRACTION26X301 - 333
54X-RAY DIFFRACTION26Y401 - 416
55X-RAY DIFFRACTION26Z301 - 332
56X-RAY DIFFRACTION26a301 - 333
57X-RAY DIFFRACTION26b401 - 440
58X-RAY DIFFRACTION26c301 - 321
59X-RAY DIFFRACTION26d301 - 319
60X-RAY DIFFRACTION26e301 - 314
61X-RAY DIFFRACTION26f301 - 313
62X-RAY DIFFRACTION26g301 - 315
63X-RAY DIFFRACTION26h301 - 319
64X-RAY DIFFRACTION26i301 - 329
65X-RAY DIFFRACTION26j401 - 425
66X-RAY DIFFRACTION26k301 - 330
67X-RAY DIFFRACTION26l301 - 322
68X-RAY DIFFRACTION26m401 - 420
69X-RAY DIFFRACTION26n301 - 329
70X-RAY DIFFRACTION26o301 - 327
71X-RAY DIFFRACTION26p401 - 432
72X-RAY DIFFRACTION26q301 - 326
73X-RAY DIFFRACTION26r301 - 334
74X-RAY DIFFRACTION26s301 - 319
75X-RAY DIFFRACTION26t301 - 317
76X-RAY DIFFRACTION26u301 - 327
77X-RAY DIFFRACTION26v301 - 331
78X-RAY DIFFRACTION26w301 - 327
79X-RAY DIFFRACTION26x401 - 434
80X-RAY DIFFRACTION26y301 - 332
81X-RAY DIFFRACTION26z301 - 338
82X-RAY DIFFRACTION27a1 - 216
83X-RAY DIFFRACTION28b2 - 202
84X-RAY DIFFRACTION29c1 - 231
85X-RAY DIFFRACTION30d1 - 248
86X-RAY DIFFRACTION31e1 - 239
87X-RAY DIFFRACTION32f1 - 233
88X-RAY DIFFRACTION33g1 - 238
89X-RAY DIFFRACTION34h1 - 244
90X-RAY DIFFRACTION35i1 - 243
91X-RAY DIFFRACTION36j2 - 220
92X-RAY DIFFRACTION37k1 - 204
93X-RAY DIFFRACTION38l1 - 196
94X-RAY DIFFRACTION39m2 - 201
95X-RAY DIFFRACTION40n1 - 213
96X-RAY DIFFRACTION41o1 - 216
97X-RAY DIFFRACTION42p2 - 202
98X-RAY DIFFRACTION43q1 - 231
99X-RAY DIFFRACTION44r1 - 248
100X-RAY DIFFRACTION45s1 - 239
101X-RAY DIFFRACTION46t1 - 233
102X-RAY DIFFRACTION47u1 - 238
103X-RAY DIFFRACTION48v1 - 244
104X-RAY DIFFRACTION49w1 - 243
105X-RAY DIFFRACTION50x2 - 220
106X-RAY DIFFRACTION51y1 - 204
107X-RAY DIFFRACTION52z1 - 196
108X-RAY DIFFRACTION5312 - 201
109X-RAY DIFFRACTION5421 - 213
110X-RAY DIFFRACTION5531 - 216
111X-RAY DIFFRACTION5642 - 202

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