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- PDB-3une: Mouse constitutive 20S proteasome -

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Basic information

Entry
Database: PDB / ID: 3une
TitleMouse constitutive 20S proteasome
Components
  • (Proteasome subunit alpha type- ...) x 7
  • (Proteasome subunit beta type- ...) x 7
KeywordsHYDROLASE / 20S proteasome comprises 28 subunits / Protease / Cytosol
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 / response to organonitrogen compound / Neutrophil degranulation / proteasome complex / proteolysis involved in protein catabolic process / sarcomere / ciliary basal body / proteasomal protein catabolic process / P-body / lipopolysaccharide binding / protein catabolic process / response to virus / response to organic cyclic compound / nuclear matrix / positive regulation of NF-kappaB transcription factor activity / peptidase activity / ubiquitin-dependent protein catabolic process / postsynapse / proteasome-mediated ubiquitin-dependent protein catabolic process / endopeptidase activity / response to oxidative stress / nuclear body / ribosome / intracellular membrane-bounded organelle / centrosome / synapse / ubiquitin protein ligase binding / mitochondrion / proteolysis / RNA binding / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
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
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-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: 3.2 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 1.2Sep 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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


Theoretical massNumber of molelcules
Total (without water)1,435,88856
Polymers1,435,88856
Non-polymers00
Water11,530640
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


Theoretical massNumber of molelcules
Total (without water)717,94428
Polymers717,94428
Non-polymers00
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


Theoretical massNumber of molelcules
Total (without water)717,94428
Polymers717,94428
Non-polymers00
Water50428
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)170.970, 201.300, 226.010
Angle α, β, γ (deg.)90.00, 108.07, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.998889, 0.037819, 0.028104), (0.040888, 0.992154, 0.118148), (-0.023415, 0.119166, -0.992598)31.6278, -3.75722, 49.05656
3given(0.997958, 0.061723, -0.016453), (-0.06269, 0.995797, -0.066776), (0.012262, 0.067671, 0.997632)-49.53659, 13.97071, -109.84821
4given(-0.999912, -0.010363, 0.008241), (-0.009947, 0.998752, 0.048934), (-0.008737, 0.048848, -0.998768)82.32807, -5.54937, 158.71318

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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)
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)
References: UniProt: Q9R1P0, proteasome endopeptidase complex
#3: Protein
Proteasome subunit alpha type-7 / / Proteasome subunit RC6-1


Mass: 27897.887 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
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)
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)
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)
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)
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)
References: UniProt: P70195, proteasome endopeptidase complex
#9: Protein
Proteasome subunit beta type-3 / PSMB3 / 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)
References: UniProt: Q9R1P1, proteasome endopeptidase complex
#10: Protein
Proteasome subunit beta type-2 / PSMB2 / 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)
References: UniProt: Q9R1P3, proteasome endopeptidase complex
#11: Protein
Proteasome subunit beta type-5 / PSMB5 / 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)
References: UniProt: O55234, proteasome endopeptidase complex
#12: Protein
Proteasome subunit beta type-1 / PSMB1 / 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)
References: UniProt: O09061, proteasome endopeptidase complex
#13: Protein
Proteasome subunit beta type-4 / PSMB4 / Proteasome beta chain / Low molecular mass protein 3 / Macropain beta chain / Multicatalytic ...Proteasome beta chain / Low molecular mass protein 3 / Macropain beta chain / Multicatalytic endopeptidase complex 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)
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)
References: UniProt: Q60692, proteasome endopeptidase complex

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Non-polymers , 1 types, 640 molecules

#15: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 640 / 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: 2.57 Å3/Da / Density % sol: 52.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: 0.2 M KAc, 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: May 23, 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: 3.2→30 Å / Num. all: 236232 / Num. obs: 235050 / % possible obs: 99.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 13.9
Reflection shellResolution: 3.2→3.3 Å / Rmerge(I) obs: 0.597 / Mean I/σ(I) obs: 2.4 / % possible all: 99.7

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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: pdb entry 1IRU

1iru


Resolution: 3.2→15 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.921 / SU B: 61.794 / SU ML: 0.458 / Cross valid method: THROUGHOUT / ESU R Free: 0.535 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.24636 11752 5 %RANDOM
Rwork0.22044 ---
obs0.22174 223279 98.14 %-
all-235031 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 78.682 Å2
Baniso -1Baniso -2Baniso -3
1--0.58 Å20 Å2-3.82 Å2
2--2.37 Å20 Å2
3----4.16 Å2
Refinement stepCycle: LAST / Resolution: 3.2→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms97316 0 0 640 97956
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0299076
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.7531.965133844
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.411512468
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.9623.8224364
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.391517400
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.05315684
X-RAY DIFFRACTIONr_chiral_restr0.0480.215024
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02174248
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_restr0.442399076
X-RAY DIFFRACTIONr_sphericity_free27.4255367
X-RAY DIFFRACTIONr_sphericity_bonded3.628597593
LS refinement shellResolution: 3.2→3.279 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.353 669 -
Rwork0.316 12771 -
obs--80.74 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.10830.16970.20241.086-0.02840.64090.0001-0.03150.1286-0.0849-0.10690.5388-0.1045-0.12550.10690.17040.0136-0.09920.3834-0.020.7874-48.558755.834737.9839
20.3383-0.03170.06890.41310.20150.4912-0.0485-0.07030.0699-0.01210.02330.16330.147-0.13230.02520.2839-0.1556-0.02230.3439-0.02970.6636-46.507224.314741.4507
30.6443-0.17060.75570.1003-0.23610.91410.2965-0.0845-0.1424-0.124-0.05050.16880.4131-0.0474-0.2460.5972-0.12950.03380.2366-0.01740.5843-28.17347.452861.8314
41.0744-0.2772-0.16180.4946-0.09720.4470.0632-0.2474-0.10950.1236-0.09880.21670.0950.12620.03560.472-0.08650.11340.3780.07410.3382-9.208420.108783.3811
51.16680.03170.18040.459-0.11980.1830.0607-0.41670.06230.10190.00260.1772-0.05890.1611-0.06330.3549-0.08180.14440.6028-0.12070.2674-3.826550.242690.9904
60.5391-0.00410.31040.5834-0.14840.8181-0.0235-0.25710.3170.123-0.08290.1649-0.09620.04660.10630.3163-0.07620.17940.3195-0.28110.6169-16.19775.980278.9148
70.6650.3757-0.00970.3011-0.20610.79120.04410.03350.2480.0809-0.03510.2185-0.1242-0.1532-0.00890.21330.05070.11970.2475-0.05760.8293-37.253278.542554.8489
80.2956-0.1425-0.17880.24850.20550.2430.0730.19550.15940.04710.00990.08590.1268-0.1303-0.08290.2961-0.0079-0.17470.44140.15860.6075-18.773162.136613.5114
91.3023-0.093-0.40030.1420.15670.25390.05150.27210.09540.1432-0.04370.05770.1532-0.153-0.00780.3517-0.1104-0.14050.4380.02020.4304-20.047934.02211.3323
100.5111-0.0227-0.13950.30160.03890.5026-0.15980.1034-0.07710.11220.04590.02210.1822-0.04430.11390.5045-0.0797-0.0340.1945-0.04250.4634-5.044410.608327.7333
111.53810.3574-0.28230.33310.17790.6018-0.0946-0.1057-0.13360.0367-0.02380.02410.14120.01590.11830.50990.002-0.02760.2560.09480.370217.153912.723552.2508
120.27990.0732-0.32630.4964-0.54130.89450.0427-0.17520.09920.0076-0.00060.03520.0770.1195-0.04210.3819-0.0078-0.03390.4609-0.04160.297128.684338.784964.8426
130.29790.0053-0.3360.1836-0.05430.86820.1226-0.23680.2702-0.0716-0.03360.14930.05080.1913-0.0890.3351-0.0990.06230.397-0.210.539122.178570.648857.3092
140.62490.1714-0.37531.2063-0.16940.95060.19830.04850.2319-0.0108-0.01180.16890.0043-0.0565-0.18650.24850.02-0.03370.2064-0.01080.67120.655182.917835.7554
150.412-0.21670.23481.1299-0.10830.3737-0.0281-0.05090.18480.03370.0375-0.24250.05460.1863-0.00930.26110.01610.00230.4527-0.11080.475482.795354.773315.7767
160.38980.0132-0.18450.5386-0.1010.2282-0.07690.0366-0.0659-0.02790.099-0.15150.08940.0727-0.02210.36690.11850.05140.366-0.08690.441679.497224.00269.1941
170.632-0.49380.52111.4708-0.21071.07980.1030.0434-0.1363-0.13670.0349-0.07540.30120.0063-0.13790.55810.06250.04770.297-0.16210.378460.518410.2727-12.9124
180.55420.0990.11280.6608-0.12450.09430.02840.2926-0.0784-0.1654-0.0156-0.08630.1015-0.0309-0.01290.5798-0.010.01440.5143-0.13230.188442.281526.0612-32.9965
190.19230.30280.21580.75720.51250.3718-0.00440.2261-0.018-0.21210.0864-0.0374-0.0760.0301-0.0820.51810.0380.00440.67020.11650.206737.803256.7952-37.0288
200.9693-0.07670.32480.2875-0.1880.91550.03590.16570.2695-0.16930.01180.0339-0.08360.056-0.04780.450.00230.09310.32110.18090.446550.898780.6287-22.1231
210.27520.26030.21881.393-0.10370.33670.04550.02090.1225-0.1019-0.0180.0179-0.02960.1228-0.02750.3336-0.0840.17450.3172-0.00660.544272.016979.70382.1219
220.34350.2482-0.06610.4625-0.18720.14120.0806-0.19920.1173-0.0343-0.0439-0.0240.06370.1029-0.03680.2985-0.0401-0.00960.4228-0.1070.45252.892659.41741.2174
230.63340.2573-0.28120.3951-0.44760.5740.0836-0.09470.029-0.0532-0.03020.06210.11560.1973-0.05340.3970.1046-0.00120.4057-0.03330.3653.332331.268340.1579
240.75440.2518-0.31120.16980.09920.6508-0.11580.1115-0.1229-0.05560.0487-0.0140.14760.00850.06710.54560.0302-0.02960.1978-0.05710.411937.566610.316121.3058
251.3206-0.1999-0.31370.3392-0.21570.3163-0.1310.2119-0.0803-0.15020.04390.00470.1387-0.08320.08710.5096-0.0959-0.07150.3763-0.15120.337515.512915.7781-2.8458
260.7138-0.2632-0.70080.32530.48880.954500.31060.0733-0.02820.0052-0.0638-0.0202-0.2214-0.00520.3717-0.0492-0.13990.5790.04030.28854.829643.5008-12.3519
270.9324-0.3226-0.62630.18470.14020.86670.0780.23890.3376-0.04690.0113-0.0274-0.0604-0.0968-0.08920.3950.0344-0.05470.33860.19580.497312.272674.118-1.2792
280.8766-0.09430.03480.58340.25820.66630.0555-0.06060.1895-0.050.04250.0201-0.0308-0.0111-0.0980.3613-0.05160.02280.2189-0.0320.557334.115383.143321.4791
290.41660.5634-0.18371.2629-0.18090.77690.05870.04770.1363-0.05880.04440.39490.0247-0.2707-0.10310.17430.0702-0.03250.59350.10520.50210.162751.7514144.6672
300.32630.0634-0.18570.7804-0.27310.6818-0.016-0.0245-0.088-0.00070.04020.2820.2413-0.1723-0.02420.3378-0.1508-0.05510.49340.02430.41714.123320.8008150.0198
310.64380.18260.26211.77560.00170.6870.1049-0.1215-0.09490.0737-0.06690.30160.38720.1452-0.03790.5724-0.0102-0.00890.4390.12770.288323.51816.4475171.259
321.23360.0330.39140.01370.01310.21490.0539-0.5023-0.06110.0741-0.0658-0.00710.13520.0560.0120.51880.0330.04210.83560.1840.099441.553121.539192.084
330.5377-0.33120.08150.682-0.10950.0661-0.0363-0.2725-0.10690.23890.14550.1155-0.11690.1232-0.10920.4452-0.09070.11340.9725-0.21140.120645.117752.4968197.697
340.81770.33190.66160.57210.14790.66770.0253-0.24160.24540.1615-0.02740.1413-0.1506-0.03730.00210.421-0.05360.28410.5736-0.36050.423631.332576.657183.8089
350.03080.06280.09680.17660.21540.95160.0119-0.03460.10550.00310.05910.2289-0.2499-0.1055-0.0710.29980.15860.21910.449-0.02270.646110.123476.2208159.7558
360.29690.1689-0.02660.71950.44120.41020.07260.14180.1105-0.0036-0.00550.1210.0513-0.1959-0.06710.30840.0965-0.11440.50730.10020.449129.661458.177119.6123
370.75910.0655-0.50940.30710.26140.77120.09590.12830.06560.08690.0593-0.04690.1686-0.2341-0.15520.4471-0.0327-0.13250.48160.01870.29329.978129.9302119.3297
381.38560.1442-0.57470.0254-0.0170.6893-0.1477-0.0828-0.12390.03170.0279-0.02650.2754-0.01410.11970.62060.043-0.10980.28620.04520.345546.26528.6066137.1256
391.54240.2019-0.57310.3324-0.00860.2859-0.1424-0.2942-0.12060.1273-0.04160.00480.03160.14550.1840.54580.1482-0.13260.55730.17560.273968.256913.5416161.3968
400.60080.2411-0.66530.3025-0.60971.33130.1465-0.43830.124-0.0643-0.04420.07820.03570.3103-0.10240.36410.0317-0.10140.9356-0.13250.150578.260940.9746172.2485
410.66740.0162-0.09190.23960.06940.79840.1552-0.37480.3244-0.0491-0.04720.08790.00290.1606-0.10810.3808-0.08140.05480.5534-0.3090.330169.979171.9644162.687
421.2221-0.4265-0.40740.65490.32871.02910.0933-0.0880.3583-0.08330.03190.12830.0407-0.0107-0.12520.32530.06280.06580.3188-0.11330.488147.799581.5522140.404
430.23830.02140.06241.045-0.17490.78240.1351-0.03980.10450.0958-0.0746-0.3185-0.02140.0757-0.06050.2480.0681-0.03550.6029-0.16690.4285131.321256.7656122.5043
440.0224-0.09640.06410.5276-0.24480.20410.0014-0.018-0.0108-0.08390.1079-0.17690.06150.0387-0.10940.29250.23030.02110.6053-0.10630.4666129.779925.4653117.726
451.0032-0.380.56020.3362-0.02920.66440.1884-0.0628-0.1954-0.05460.0132-0.16420.2367-0.0546-0.20160.55390.23920.03910.4365-0.12420.5126112.0429.421596.203
461.1742-0.1180.14470.1981-0.09810.0716-0.01360.2212-0.181-0.23350.0539-0.02520.06760.0307-0.04040.70070.15450.04510.5168-0.21350.204392.809622.739275.4534
471.18680.35610.11990.42430.03520.03-0.0430.3163-0.0177-0.18060.111-0.0587-0.0540.0551-0.0680.58110.04320.04620.6360.01210.15186.482652.799469.5059
480.4302-0.18280.42080.2273-0.20030.4404-0.09580.11660.1679-0.20660.0156-0.0692-0.07910.14080.08020.56140.00310.13130.42830.07620.352298.168978.293782.8738
490.0451-0.06910.01710.6371-0.07510.84720.0428-0.05980.1345-0.15710.0973-0.1178-0.12940.1132-0.14020.3223-0.02340.18970.4892-0.14190.4699119.493280.14106.9332
500.3045-0.0573-0.16020.9587-0.21940.17880.1569-0.42870.1067-0.0408-0.0648-0.10110.00180.3249-0.09210.2923-0.0448-0.09310.7563-0.23930.3223101.257561.4217147.3287
511.73690.4907-0.67230.2833-0.26740.34620.1399-0.54270.0015-0.181-0.1018-0.01270.14130.3287-0.03810.44240.1818-0.0610.7708-0.05020.2478103.260133.2708148.0765
521.12520.2258-0.83260.62520.29481.4722-0.2819-0.1488-0.1682-0.06890.2180.02130.23780.17360.06390.49230.2121-0.09130.33150.03850.322688.772410.3309130.6333
531.06460.0565-0.37370.4273-0.31740.3535-0.09570.085-0.1243-0.04120.069-0.04070.1437-0.04850.02680.67470.0719-0.12110.3376-0.11220.23866.62712.9758106.3116
540.37210.2739-0.16040.91070.40110.4497-0.08970.09540.0253-0.06750.11280.01020.0315-0.0228-0.02310.48920.0354-0.15340.49590.03760.198154.375439.185495.0452
550.6378-0.2041-0.35970.10780.30231.4640.15460.11810.3311-0.04-0.0021-0.04970.0204-0.0716-0.15250.45660.1008-0.02770.34940.11890.379359.991570.9682104.0562
560.79030.14560.23080.3765-0.07231.40.2068-0.13150.2774-0.03550.05840.0821-0.01120.0768-0.26520.3794-0.04320.10160.2922-0.12520.447381.248582.8135126.1074
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 233
2X-RAY DIFFRACTION1A301 - 312
3X-RAY DIFFRACTION2B2 - 249
4X-RAY DIFFRACTION2B301 - 311
5X-RAY DIFFRACTION3C2 - 240
6X-RAY DIFFRACTION3C301 - 307
7X-RAY DIFFRACTION4D9 - 241
8X-RAY DIFFRACTION4D301 - 305
9X-RAY DIFFRACTION5E4 - 241
10X-RAY DIFFRACTION5E301 - 308
11X-RAY DIFFRACTION6F1 - 244
12X-RAY DIFFRACTION6F301 - 311
13X-RAY DIFFRACTION7G2 - 245
14X-RAY DIFFRACTION7G301 - 311
15X-RAY DIFFRACTION8H1 - 220
16X-RAY DIFFRACTION8H301 - 317
17X-RAY DIFFRACTION9I1 - 204
18X-RAY DIFFRACTION9I301 - 312
19X-RAY DIFFRACTION10J1 - 196
20X-RAY DIFFRACTION10J301 - 313
21X-RAY DIFFRACTION11K1 - 201
22X-RAY DIFFRACTION11K301 - 311
23X-RAY DIFFRACTION12L1 - 213
24X-RAY DIFFRACTION12L301 - 318
25X-RAY DIFFRACTION13M1 - 216
26X-RAY DIFFRACTION13M301 - 315
27X-RAY DIFFRACTION14N1 - 202
28X-RAY DIFFRACTION14N301 - 313
29X-RAY DIFFRACTION15O1 - 233
30X-RAY DIFFRACTION15O301 - 318
31X-RAY DIFFRACTION16P2 - 249
32X-RAY DIFFRACTION16P301 - 324
33X-RAY DIFFRACTION17Q2 - 240
34X-RAY DIFFRACTION17Q301 - 312
35X-RAY DIFFRACTION18R9 - 241
36X-RAY DIFFRACTION18R301 - 312
37X-RAY DIFFRACTION19S4 - 241
38X-RAY DIFFRACTION19S301 - 319
39X-RAY DIFFRACTION20T1 - 244
40X-RAY DIFFRACTION20T301 - 313
41X-RAY DIFFRACTION21U2 - 245
42X-RAY DIFFRACTION21U301 - 321
43X-RAY DIFFRACTION22V1 - 220
44X-RAY DIFFRACTION22V301 - 319
45X-RAY DIFFRACTION23W1 - 204
46X-RAY DIFFRACTION23W301 - 321
47X-RAY DIFFRACTION24X1 - 196
48X-RAY DIFFRACTION24X301 - 308
49X-RAY DIFFRACTION25Y1 - 201
50X-RAY DIFFRACTION25Y301 - 308
51X-RAY DIFFRACTION26Z1 - 213
52X-RAY DIFFRACTION26Z301 - 316
53X-RAY DIFFRACTION27a1 - 216
54X-RAY DIFFRACTION27a301 - 316
55X-RAY DIFFRACTION28b1 - 202
56X-RAY DIFFRACTION28b301 - 320
57X-RAY DIFFRACTION29c1 - 233
58X-RAY DIFFRACTION29c301 - 315
59X-RAY DIFFRACTION30d2 - 249
60X-RAY DIFFRACTION30d301 - 309
61X-RAY DIFFRACTION31e2 - 240
62X-RAY DIFFRACTION31e301 - 303
63X-RAY DIFFRACTION32f9 - 241
64X-RAY DIFFRACTION32f301 - 303
65X-RAY DIFFRACTION33g4 - 241
66X-RAY DIFFRACTION33g301 - 307
67X-RAY DIFFRACTION34h1 - 244
68X-RAY DIFFRACTION34h301 - 307
69X-RAY DIFFRACTION35i2 - 245
70X-RAY DIFFRACTION35i301 - 310
71X-RAY DIFFRACTION36j1 - 220
72X-RAY DIFFRACTION36j301 - 313
73X-RAY DIFFRACTION37k1 - 204
74X-RAY DIFFRACTION37k301 - 311
75X-RAY DIFFRACTION38l1 - 196
76X-RAY DIFFRACTION38l301 - 308
77X-RAY DIFFRACTION39m1 - 201
78X-RAY DIFFRACTION39m301 - 311
79X-RAY DIFFRACTION40n1 - 213
80X-RAY DIFFRACTION40n301 - 313
81X-RAY DIFFRACTION41o1 - 216
82X-RAY DIFFRACTION41o301 - 311
83X-RAY DIFFRACTION42p1 - 202
84X-RAY DIFFRACTION42p301 - 306
85X-RAY DIFFRACTION43q1 - 233
86X-RAY DIFFRACTION43q301 - 303
87X-RAY DIFFRACTION44r2 - 249
88X-RAY DIFFRACTION44r301 - 310
89X-RAY DIFFRACTION45s2 - 240
90X-RAY DIFFRACTION45s301 - 307
91X-RAY DIFFRACTION46t9 - 241
92X-RAY DIFFRACTION46t301 - 306
93X-RAY DIFFRACTION47u4 - 241
94X-RAY DIFFRACTION47u301 - 307
95X-RAY DIFFRACTION48v1 - 244
96X-RAY DIFFRACTION48v301 - 311
97X-RAY DIFFRACTION49w2 - 245
98X-RAY DIFFRACTION49w301 - 310
99X-RAY DIFFRACTION50x1 - 220
100X-RAY DIFFRACTION50x301 - 306
101X-RAY DIFFRACTION51y1 - 204
102X-RAY DIFFRACTION51y301 - 310
103X-RAY DIFFRACTION52z1 - 196
104X-RAY DIFFRACTION52z301 - 306
105X-RAY DIFFRACTION5311 - 201
106X-RAY DIFFRACTION531301 - 312
107X-RAY DIFFRACTION5421 - 213
108X-RAY DIFFRACTION542301 - 317
109X-RAY DIFFRACTION5531 - 216
110X-RAY DIFFRACTION553301 - 310
111X-RAY DIFFRACTION5641 - 202
112X-RAY DIFFRACTION564301 - 307

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