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- PDB-4ddg: Crystal structure of human OTUB1/UbcH5b~Ub/Ub -

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Basic information

Entry
Database: PDB / ID: 4ddg
TitleCrystal structure of human OTUB1/UbcH5b~Ub/Ub
Components
  • Polyubiquitin-C
  • Ubiquitin-conjugating enzyme E2 D2, Ubiquitin thioesterase OTUB1
KeywordsHYDROLASE/LIGASE / inhibition / HYDROLASE-LIGASE complex
Function / homology
Function and homology information


negative regulation of double-strand break repair / ubiquitin-protein transferase inhibitor activity / deNEDDylase activity / protein K48-linked deubiquitination / (E3-independent) E2 ubiquitin-conjugating enzyme / E2 ubiquitin-conjugating enzyme / ubiquitin conjugating enzyme activity / protein deubiquitination / protein K48-linked ubiquitination / protein autoubiquitination ...negative regulation of double-strand break repair / ubiquitin-protein transferase inhibitor activity / deNEDDylase activity / protein K48-linked deubiquitination / (E3-independent) E2 ubiquitin-conjugating enzyme / E2 ubiquitin-conjugating enzyme / ubiquitin conjugating enzyme activity / protein deubiquitination / protein K48-linked ubiquitination / protein autoubiquitination / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / Prevention of phagosomal-lysosomal fusion / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Endosomal Sorting Complex Required For Transport (ESCRT) / Membrane binding and targetting of GAG proteins / Negative regulation of FLT3 / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / positive regulation of TORC1 signaling / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / Constitutive Signaling by NOTCH1 HD Domain Mutants / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / NOTCH2 Activation and Transmission of Signal to the Nucleus / TICAM1,TRAF6-dependent induction of TAK1 complex / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / Downregulation of ERBB4 signaling / Regulation of FZD by ubiquitination / APC-Cdc20 mediated degradation of Nek2A / p75NTR recruits signalling complexes / InlA-mediated entry of Listeria monocytogenes into host cells / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / TRAF6-mediated induction of TAK1 complex within TLR4 complex / Regulation of pyruvate metabolism / NF-kB is activated and signals survival / Regulation of innate immune responses to cytosolic DNA / Pexophagy / Downregulation of ERBB2:ERBB3 signaling / NRIF signals cell death from the nucleus / VLDLR internalisation and degradation / Regulation of PTEN localization / Regulation of BACH1 activity / Activated NOTCH1 Transmits Signal to the Nucleus / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / MAP3K8 (TPL2)-dependent MAPK1/3 activation / Translesion synthesis by REV1 / TICAM1, RIP1-mediated IKK complex recruitment / InlB-mediated entry of Listeria monocytogenes into host cell / Translesion synthesis by POLK / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Downregulation of TGF-beta receptor signaling / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / Josephin domain DUBs / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / IKK complex recruitment mediated by RIP1 / Regulation of activated PAK-2p34 by proteasome mediated degradation / ubiquitin binding / PINK1-PRKN Mediated Mitophagy / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / TNFR1-induced NF-kappa-B signaling pathway / Autodegradation of Cdh1 by Cdh1:APC/C / TCF dependent signaling in response to WNT / APC/C:Cdc20 mediated degradation of Securin / Regulation of NF-kappa B signaling / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Asymmetric localization of PCP proteins / activated TAK1 mediates p38 MAPK activation / Ubiquitin-dependent degradation of Cyclin D / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / TNFR2 non-canonical NF-kB pathway / AUF1 (hnRNP D0) binds and destabilizes mRNA / Regulation of signaling by CBL / Negative regulators of DDX58/IFIH1 signaling / NOTCH3 Activation and Transmission of Signal to the Nucleus / Deactivation of the beta-catenin transactivating complex / Vpu mediated degradation of CD4 / Assembly of the pre-replicative complex / Ubiquitin-Mediated Degradation of Phosphorylated Cdc25A / Negative regulation of FGFR3 signaling / Degradation of DVL / Fanconi Anemia Pathway / Peroxisomal protein import / Dectin-1 mediated noncanonical NF-kB signaling / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Negative regulation of FGFR2 signaling / Stabilization of p53 / Negative regulation of FGFR4 signaling / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Negative regulation of FGFR1 signaling / Degradation of AXIN
Similarity search - Function
Ubiquitin thioesterase Otubain / Peptidase C65 Otubain, subdomain 2 / Peptidase C65 Otubain, subdomain 1 / Peptidase C65, otubain / Peptidase C65, otubain, subdomain 2 / Peptidase C65, otubain, subdomain 1 / Peptidase C65 Otubain / 3 helical TM bundles of succinate and fumarate reductases / OTU domain / OTU domain profile. ...Ubiquitin thioesterase Otubain / Peptidase C65 Otubain, subdomain 2 / Peptidase C65 Otubain, subdomain 1 / Peptidase C65, otubain / Peptidase C65, otubain, subdomain 2 / Peptidase C65, otubain, subdomain 1 / Peptidase C65 Otubain / 3 helical TM bundles of succinate and fumarate reductases / OTU domain / OTU domain profile. / Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme/RWD-like / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Papain-like cysteine peptidase superfamily / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Phosphorylase Kinase; domain 1 / Roll / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Polyubiquitin-C / Ubiquitin-conjugating enzyme E2 D2 / Ubiquitin thioesterase OTUB1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2987 Å
AuthorsJuang, Y.C. / Sanches, M. / Sicheri, F.
CitationJournal: Mol.Cell / Year: 2012
Title: OTUB1 Co-opts Lys48-Linked Ubiquitin Recognition to Suppress E2 Enzyme Function.
Authors: Juang, Y.C. / Landry, M.C. / Sanches, M. / Vittal, V. / Leung, C.C. / Ceccarelli, D.F. / Mateo, A.R. / Pruneda, J.N. / Mao, D.Y. / Szilard, R.K. / Orlicky, S. / Munro, M. / Brzovic, P.S. / ...Authors: Juang, Y.C. / Landry, M.C. / Sanches, M. / Vittal, V. / Leung, C.C. / Ceccarelli, D.F. / Mateo, A.R. / Pruneda, J.N. / Mao, D.Y. / Szilard, R.K. / Orlicky, S. / Munro, M. / Brzovic, P.S. / Klevit, R.E. / Sicheri, F. / Durocher, D.
History
DepositionJan 18, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 22, 2012Provider: repository / Type: Initial release
Revision 1.1May 23, 2012Group: Other
Revision 1.2Aug 2, 2017Group: Source and taxonomy / Category: entity_src_gen
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software
Revision 1.4Sep 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 / struct_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details
Revision 1.5Nov 27, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ubiquitin-conjugating enzyme E2 D2, Ubiquitin thioesterase OTUB1
B: Ubiquitin-conjugating enzyme E2 D2, Ubiquitin thioesterase OTUB1
C: Ubiquitin-conjugating enzyme E2 D2, Ubiquitin thioesterase OTUB1
D: Polyubiquitin-C
E: Polyubiquitin-C
F: Polyubiquitin-C
G: Polyubiquitin-C
H: Polyubiquitin-C
I: Polyubiquitin-C
J: Ubiquitin-conjugating enzyme E2 D2, Ubiquitin thioesterase OTUB1
K: Ubiquitin-conjugating enzyme E2 D2, Ubiquitin thioesterase OTUB1
L: Ubiquitin-conjugating enzyme E2 D2, Ubiquitin thioesterase OTUB1
M: Polyubiquitin-C
N: Polyubiquitin-C
O: Polyubiquitin-C
P: Polyubiquitin-C
Q: Polyubiquitin-C
R: Polyubiquitin-C


Theoretical massNumber of molelcules
Total (without water)377,61718
Polymers377,61718
Non-polymers00
Water00
1
A: Ubiquitin-conjugating enzyme E2 D2, Ubiquitin thioesterase OTUB1
B: Ubiquitin-conjugating enzyme E2 D2, Ubiquitin thioesterase OTUB1
C: Ubiquitin-conjugating enzyme E2 D2, Ubiquitin thioesterase OTUB1
D: Polyubiquitin-C
E: Polyubiquitin-C
F: Polyubiquitin-C
G: Polyubiquitin-C
H: Polyubiquitin-C
I: Polyubiquitin-C


Theoretical massNumber of molelcules
Total (without water)188,8099
Polymers188,8099
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13330 Å2
ΔGint-69 kcal/mol
Surface area63270 Å2
MethodPISA
2
J: Ubiquitin-conjugating enzyme E2 D2, Ubiquitin thioesterase OTUB1
K: Ubiquitin-conjugating enzyme E2 D2, Ubiquitin thioesterase OTUB1
L: Ubiquitin-conjugating enzyme E2 D2, Ubiquitin thioesterase OTUB1
M: Polyubiquitin-C
N: Polyubiquitin-C
O: Polyubiquitin-C
P: Polyubiquitin-C
Q: Polyubiquitin-C
R: Polyubiquitin-C


Theoretical massNumber of molelcules
Total (without water)188,8099
Polymers188,8099
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13140 Å2
ΔGint-66 kcal/mol
Surface area63600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)134.566, 104.928, 148.479
Angle α, β, γ (deg.)90.00, 104.19, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11G
21H
31I
41Q
51P
61R
12A
22B
32C
42J
52K
62L
13A
23B
33C
43J
53K
63L
14D
24E
34F
44N
54M
64O

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETGLYGLYchain 'G'GG1 - 761 - 76
21METMETGLYGLYchain 'H'HH1 - 761 - 76
31METMETGLYGLYchain 'I'II1 - 761 - 76
41METMETGLYGLYchain 'Q'QQ1 - 761 - 76
51METMETGLYGLYchain 'P'PP1 - 761 - 76
61METMETGLYGLYchain 'R'RR1 - 761 - 76
12ALAALAALAALAchain 'A' and (resseq 1:150 ) and (not element H) and (not element D)AA02
22ALAALAALAALAchain 'B' and (resseq 1:150 ) and (not element H) and (not element D)BB02
32ALAALAALAALAchain 'C' and (resseq 1:150 ) and (not element H) and (not element D)CC02
42ALAALAALAALAchain 'J' and (resseq 1:150 ) and (not element H) and (not element D)JJ02
52ALAALAALAALAchain 'K' and (resseq 1:150 ) and (not element H) and (not element D)KK02
62ALAALAALAALAchain 'L' and (resseq 1:150 ) and (not element H) and (not element D)LL02
13ALAALAALAALAchain 'A' and (resseq 1025:1271 ) and (not element H) and (not element D)AA02
23ALAALAALAALAchain 'B' and (resseq 1025:1271 ) and (not element H) and (not element D)BB02
33ALAALAALAALAchain 'C' and (resseq 1025:1271 ) and (not element H) and (not element D)CC02
43ALAALAALAALAchain 'J' and (resseq 1025:1271 ) and (not element H) and (not element D)JJ02
53ALAALAALAALAchain 'K' and (resseq 1025:1271 ) and (not element H) and (not element D)KK02
63ALAALAALAALAchain 'L' and (resseq 1025:1271 ) and (not element H) and (not element D)LL02
14METMETGLYGLYchain 'D'DD1 - 761 - 76
24METMETGLYGLYchain 'E'EE1 - 761 - 76
34METMETGLYGLYchain 'F'FF1 - 761 - 76
44METMETGLYGLYchain 'N'NN1 - 761 - 76
54METMETGLYGLYchain 'M'MM1 - 761 - 76
64METMETGLYGLYchain 'O'OO1 - 761 - 76

NCS ensembles :
ID
1
2
3
4
DetailsThe biological complex defined by the author consists of: Complex 1: chain H, chain E, residues 1 to 147 of chain C, and residues 1025-1271 of Chain B; Complex 2: chain G, chain D, residues 1 to 147 of chain B, and residues 1025-1271 of Chain A; Complex 3: chain I, chain F, residues 1 to 147 of chain A, and residues 1025-1271 of Chain C; Complex 4: chain Q, chain N, residues 1 to 147 of chain L, and residues 1025-1271 of Chain K; Complex 5: chain P, chain M, residues 1 to 147 of chain K, and residues 1025-1271 of Chain J; Complex 6: chain R, chain O, residues 1 to 147 of chain J, and residues 1025-1271 of Chain L

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Components

#1: Protein
Ubiquitin-conjugating enzyme E2 D2, Ubiquitin thioesterase OTUB1 / Ubiquitin carrier protein D2 / Ubiquitin-conjugating enzyme E2(17)KB 2 / Ubiquitin-conjugating ...Ubiquitin carrier protein D2 / Ubiquitin-conjugating enzyme E2(17)KB 2 / Ubiquitin-conjugating enzyme E2-17 kDa 2 / Ubiquitin-protein ligase D2 / Deubiquitinating enzyme OTUB1 / OTU domain-containing ubiquitin aldehyde-binding protein 1 / Otubain-1 / hOTU1 / Ubiquitin-specific-processing protease OTUB1


Mass: 45782.543 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: E2, HSPC263, OTB1, OTU1, OTUB1, UBC4, UBC5B, UBCH4, UBCH5B, UBE2D2
Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: P62837, UniProt: Q96FW1, ubiquitin-protein ligase, ubiquitinyl hydrolase 1
#2: Protein
Polyubiquitin-C / Ubiquitin


Mass: 8576.831 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBC / Production host: Escherichia coli (E. coli) / References: UniProt: P0CG48
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.69 Å3/Da / Density % sol: 54.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 25% PEG1500, 0.1 M SPG, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 198.25 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Dec 12, 2011
RadiationMonochromator: ACCEL/BRUKER double crystal monochromator (DCM)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 3.2987→49.29 Å / Num. all: 60666 / Num. obs: 60387 / % possible obs: 99.54 %
Reflection shellResolution: 3.2987→3.5 Å / % possible all: 97.6

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Processing

Software
NameVersionClassification
MxDCdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2ESK AND 2ZFY

2esk

2zfy


Resolution: 3.2987→49.121 Å / SU ML: 0.4 / σ(F): 1.99 / Phase error: 33.26 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2802 3053 5.06 %
Rwork0.2332 --
obs0.2356 60385 99.54 %
all-60402 -
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 110.304 Å2 / ksol: 0.311 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--4.7794 Å20 Å2-2.5662 Å2
2--3.1302 Å2-0 Å2
3---1.6492 Å2
Refinement stepCycle: LAST / Resolution: 3.2987→49.121 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms26568 0 0 0 26568
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00427126
X-RAY DIFFRACTIONf_angle_d0.93836660
X-RAY DIFFRACTIONf_dihedral_angle_d16.51110326
X-RAY DIFFRACTIONf_chiral_restr0.074032
X-RAY DIFFRACTIONf_plane_restr0.0054782
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11G601X-RAY DIFFRACTIONPOSITIONAL0.001
12H601X-RAY DIFFRACTIONPOSITIONAL0.001
13I601X-RAY DIFFRACTIONPOSITIONAL0.001
14Q601X-RAY DIFFRACTIONPOSITIONAL0.001
15P601X-RAY DIFFRACTIONPOSITIONAL0.001
16R601X-RAY DIFFRACTIONPOSITIONAL0.001
21A1191X-RAY DIFFRACTIONPOSITIONAL0.003
22B1191X-RAY DIFFRACTIONPOSITIONAL0.003
23C1191X-RAY DIFFRACTIONPOSITIONAL0.003
24J1191X-RAY DIFFRACTIONPOSITIONAL0.002
25K1191X-RAY DIFFRACTIONPOSITIONAL0.002
26L1191X-RAY DIFFRACTIONPOSITIONAL0.003
31A2026X-RAY DIFFRACTIONPOSITIONAL0.002
32B2026X-RAY DIFFRACTIONPOSITIONAL0.002
33C2026X-RAY DIFFRACTIONPOSITIONAL0.002
34J2026X-RAY DIFFRACTIONPOSITIONAL0.001
35K2026X-RAY DIFFRACTIONPOSITIONAL0.002
36L2026X-RAY DIFFRACTIONPOSITIONAL0.002
41D601X-RAY DIFFRACTIONPOSITIONAL0.001
42E601X-RAY DIFFRACTIONPOSITIONAL0.001
43F601X-RAY DIFFRACTIONPOSITIONAL0.001
44N601X-RAY DIFFRACTIONPOSITIONAL0.001
45M601X-RAY DIFFRACTIONPOSITIONAL0.001
46O601X-RAY DIFFRACTIONPOSITIONAL0.001
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2987-3.35020.39611360.37652567X-RAY DIFFRACTION99
3.3502-3.40520.42591450.37182578X-RAY DIFFRACTION100
3.4052-3.46390.41291280.36972597X-RAY DIFFRACTION99
3.4639-3.52680.41141240.32822601X-RAY DIFFRACTION100
3.5268-3.59460.3751390.32472582X-RAY DIFFRACTION100
3.5946-3.6680.40921260.32162610X-RAY DIFFRACTION100
3.668-3.74770.34551450.2932621X-RAY DIFFRACTION100
3.7477-3.83490.35671430.27482588X-RAY DIFFRACTION100
3.8349-3.93070.33761410.28182564X-RAY DIFFRACTION99
3.9307-4.0370.30171540.24652607X-RAY DIFFRACTION100
4.037-4.15570.27741350.2452619X-RAY DIFFRACTION100
4.1557-4.28980.3141380.22612564X-RAY DIFFRACTION100
4.2898-4.4430.26981300.21222635X-RAY DIFFRACTION100
4.443-4.62070.25261250.20752641X-RAY DIFFRACTION100
4.6207-4.83090.27471410.19862591X-RAY DIFFRACTION100
4.8309-5.08530.25761450.21162598X-RAY DIFFRACTION100
5.0853-5.40360.27331380.21832610X-RAY DIFFRACTION100
5.4036-5.82020.27141400.24162654X-RAY DIFFRACTION100
5.8202-6.40470.32061470.25072627X-RAY DIFFRACTION100
6.4047-7.32890.26881710.20212607X-RAY DIFFRACTION100
7.3289-9.22360.19911330.17382659X-RAY DIFFRACTION100
9.2236-49.12680.16841290.17722612X-RAY DIFFRACTION95
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)
14.0807-0.54620.32554.9080.94393.3389-0.419-0.8663-0.26640.54220.5825-0.4760.47961.8712-0.20260.94190.14920.16581.63360.00610.4728-58.9105-14.46029.1567
20.4574-0.38890.25190.6582-0.41360.2849-1.0755-0.82521.45521.0662-0.0036-0.6423-1.5783-0.1924-0.48981.93240.3414-1.60011.0264-0.23341.8534-22.93399.875417.1484
33.078-0.57960.47055.10690.15214.0853-0.2898-0.10990.28450.5541-0.2047-0.23870.18620.1770.5010.1894-0.0208-0.05780.30640.02510.2552-36.0794-9.0058-9.4012
42.3740.0549-0.31741.5529-0.53223.31430.05980.2840.8090.37170.4770.5065-0.964-0.5032-0.28430.42010.12920.13670.41430.30350.7802-54.331913.8772-42.3539
53.3648-0.077-0.98243.19540.32383.83010.2069-0.2358-0.2104-0.27640.08820.02130.37180.2477-0.03520.4495-0.03270.40840.32320.34310.1768-70.490441.049720.0663
63.4590.66620.28952.146-0.39613.1508-0.43520.3382-0.5676-0.03130.1473-0.1456-0.12640.00080.29780.37690.01080.10250.32280.02320.0702-45.202355.8861-10.6272
72.9494-1.18230.69372.0690.7833.731-1.1612-0.06340.97710.2854-0.8336-1.6717-1.25011.02781.11791.12410.0984-0.47241.5070.82552.3957-1.9547-6.997321.3419
84.13830.65121.72962.7618-0.10123.957-0.12680.4125-0.9753-0.3865-0.1439-0.61250.52771.46680.3010.24640.00240.12070.77110.16950.5682-56.1234-3.5318-63.2212
91.16080.1223-0.55182.11241.93583.71890.09780.9546-1.1516-0.242-0.0184-0.97431.18291.03090.28481.08330.2070.42931.5423-0.4931.3303-31.184635.142-21.2524
103.45971.2149-0.65222.2868-0.05460.1409-0.7744-1.9095-0.59161.03450.246-0.2977-0.7385-1.50420.07581.19770.7024-0.09692.435-0.16441.0369-31.3618-12.909626.6998
111.69240.4790.43953.6849-0.14954.8960.1682-0.40190.3535-0.0156-0.26450.04040.7237-0.3778-0.01910.12590.0235-0.15480.7978-0.09380.3539-98.122247.760941.5723
125.20070.402-2.00172.57060.9272.9649-0.5086-0.1912-1.7469-0.0422-0.26820.59530.8081-0.29660.43230.3589-0.21970.2470.5334-0.16810.924-92.0553-15.475-6.5831
133.590.93150.74163.8721-0.35532.15680.00850.0968-0.1019-0.0482-0.23110.05520.01-0.57210.19690.44710.11710.07011.39320.26911.10179.8367-13.3747-80.2532
142.55070.24750.98594.7121-0.28893.7965-0.3027-0.10470.4058-0.1071-0.0958-0.4224-0.77950.05520.36950.41780.0522-0.1560.66580.07190.5706-13.0959-8.5163-61.5791
152.2311-0.6458-0.60114.19690.02213.0654-0.14860.17420.4181-0.3245-0.0793-0.2555-0.710.4860.22040.7401-0.1225-0.33610.45660.11840.5977-26.940410.6581-87.4801
161.18210.60020.36481.1696-0.37972.0293-0.4755-0.53481.26910.2594-0.0378-0.7963-0.56070.8415-2.2680.20540.0083-0.8521.3101-0.74131.99974.872813.396-27.3988
172.96240.3984-1.2623.4864-1.5033.667-0.09640.20170.4343-0.4078-0.09790.16910.1852-0.54540.09820.4329-0.10120.08711.3269-0.40341.266421.52541.502-93.1211
182.9861-0.42220.27132.97040.17752.4779-0.438-0.3978-0.39930.22890.317-0.3195-0.33120.27660.0830.3013-0.01860.00320.4407-0.1350.1486-4.0556.3017-61.992
194.47890.6505-0.68031.6485-1.08443.2077-0.8028-0.54620.13120.1359-0.12530.47740.5436-0.57210.83721.1272-0.1738-0.19820.7074-0.23810.8545-47.1965-7.0626-92.1962
201.83570.430.43480.9924-0.21242.3652-0.1334-0.452-0.89320.0405-0.5350.2396-0.0706-1.2376-0.29570.47760.1036-0.36641.6826-0.4341.53236.9972-4.6255-7.2317
211.94950.093-0.07823.0763-1.28244.24980.098-1.6565-1.49530.5155-0.18930.79281.4231-0.48870.10021.0656-0.03510.42371.49180.49721.3305-18.051435.1583-52.1277
224.7753-0.60571.23683.24710.0322.73220.3415-0.5625-1.1439-0.509-0.1719-0.13260.04381.1875-0.09630.67570.00250.00150.8090.23990.8103-17.7606-11.2334-97.5855
231.0545-0.52680.73342.06160.7664.5475-0.15280.74910.7884-0.1670.19410.28220.4024-0.40810.07180.3084-0.3418-0.3720.91250.31040.758649.308347.2202-114.8069
244.81750.7614-1.87754.0405-0.89933.2463-0.6080.1884-1.83030.10670.0333-0.35320.4703-0.28670.47160.50160.0060.1770.57360.04140.902842.9515-14.7086-64.1468
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq -1:147)
2X-RAY DIFFRACTION2chain 'A' and (resseq 1025:1271)
3X-RAY DIFFRACTION3chain 'B' and (resseq -1:147)
4X-RAY DIFFRACTION4chain 'B' and (resseq 1025:1271)
5X-RAY DIFFRACTION5chain 'C' and (resseq -1:147)
6X-RAY DIFFRACTION6chain 'C' and (resseq 1025:1271)
7X-RAY DIFFRACTION7chain 'D' and (resseq 1:76)
8X-RAY DIFFRACTION8chain 'E' and (resseq 1:76)
9X-RAY DIFFRACTION9chain 'F' and (resseq 1:76)
10X-RAY DIFFRACTION10chain 'G' and (resseq 1:76)
11X-RAY DIFFRACTION11chain 'H' and (resseq 1:76)
12X-RAY DIFFRACTION12chain 'I' and (resseq 1:76)
13X-RAY DIFFRACTION13chain 'J' and (resseq -1:147)
14X-RAY DIFFRACTION14chain 'K' and (resseq -1:147)
15X-RAY DIFFRACTION15chain 'J' and (resseq 1025:1271)
16X-RAY DIFFRACTION16chain 'K' and (resseq 1025:1271)
17X-RAY DIFFRACTION17chain 'L' and (resseq -1:147)
18X-RAY DIFFRACTION18chain 'L' and (resseq 1025:1271)
19X-RAY DIFFRACTION19chain 'M' and (resseq 1:76)
20X-RAY DIFFRACTION20chain 'N' and (resseq 1:76)
21X-RAY DIFFRACTION21chain 'O' and (resseq 1:76)
22X-RAY DIFFRACTION22chain 'P' and (resseq 1:76)
23X-RAY DIFFRACTION23chain 'Q' and (resseq 1:76)
24X-RAY DIFFRACTION24chain 'R' and (resseq 1:76)

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