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- PDB-6brt: F-box protein CTH with hydrolase -

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Open data


ID or keywords:

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Basic information

Entry
Database: PDB / ID: 6brt
TitleF-box protein CTH with hydrolase
ComponentsD3-CTH-D14-D-ring
KeywordsLIGASE / Ubiquitin ligase / F-box
Function / homology
Function and homology information


cellular response to strigolactone / strigolactone biosynthetic process / secondary shoot formation / hydrolase activity
Similarity search - Function
Strigolactone esterase D14 family / Alpha/beta hydrolase family / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
(5R)-5-hydroxy-3-methylfuran-2(5H)-one / AB hydrolase-1 domain-containing protein / AB hydrolase-1 domain-containing protein
Similarity search - Component
Biological speciesOryza glumipatula (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.393 Å
AuthorsShabek, N. / Zheng, N. / Mao, H. / Hinds, T.R. / Ticchiarelli, F. / Leyser, O.
CitationJournal: Nature / Year: 2018
Title: Structural plasticity of D3-D14 ubiquitin ligase in strigolactone signalling.
Authors: Shabek, N. / Ticchiarelli, F. / Mao, H. / Hinds, T.R. / Leyser, O. / Zheng, N.
History
DepositionDec 1, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 21, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 5, 2018Group: Data collection / Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Dec 12, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: D3-CTH-D14-D-ring
B: D3-CTH-D14-D-ring
C: D3-CTH-D14-D-ring
D: D3-CTH-D14-D-ring
E: D3-CTH-D14-D-ring
F: D3-CTH-D14-D-ring
G: D3-CTH-D14-D-ring
H: D3-CTH-D14-D-ring
hetero molecules


Theoretical massNumber of molelcules
Total (without water)250,2569
Polymers250,1428
Non-polymers1141
Water9,872548
1
A: D3-CTH-D14-D-ring
E: D3-CTH-D14-D-ring
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,6503
Polymers62,5362
Non-polymers1141
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: D3-CTH-D14-D-ring
G: D3-CTH-D14-D-ring


Theoretical massNumber of molelcules
Total (without water)62,5362
Polymers62,5362
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: D3-CTH-D14-D-ring
D: D3-CTH-D14-D-ring


Theoretical massNumber of molelcules
Total (without water)62,5362
Polymers62,5362
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
F: D3-CTH-D14-D-ring
H: D3-CTH-D14-D-ring


Theoretical massNumber of molelcules
Total (without water)62,5362
Polymers62,5362
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)183.843, 183.843, 153.662
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65

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Components

#1: Protein
D3-CTH-D14-D-ring


Mass: 31267.793 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza glumipatula (plant) / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): k-12 / References: UniProt: A0A0D9Z3L0, UniProt: A0A0D9Z3K8*PLUS
#2: Chemical ChemComp-H3M / (5R)-5-hydroxy-3-methylfuran-2(5H)-one


Mass: 114.099 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H6O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 548 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 3.01 Å3/Da / Density % sol: 59.15 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 0.02 M amino acid mixture (Glu, Ala, Gly, Lys, and Ser); imidazole; 0.1 M MES monohydrate, pH 6.5, 40% glycerol, 20% PEG4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 22, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.393→44.158 Å / Num. obs: 115751 / % possible obs: 100 % / Redundancy: 11.7 % / Biso Wilson estimate: 26.31 Å2 / Rsym value: 0.172 / Net I/σ(I): 60.1
Reflection shellResolution: 2.393→2.479 Å / Rsym value: 0.699

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
HKL-2000data scaling
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
MOLREPphasing
RefinementResolution: 2.393→44.158 Å / FOM work R set: 0.7001 / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 35.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.306 1990 1.72 %
Rwork0.2473 113562 -
obs0.2483 115552 99.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 157.76 Å2 / Biso mean: 32.1 Å2 / Biso min: 0 Å2
Refinement stepCycle: final / Resolution: 2.393→44.158 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16607 0 8 551 17166
Biso mean--38.63 24.12 -
Num. residues----2161
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00916981
X-RAY DIFFRACTIONf_angle_d1.08923146
X-RAY DIFFRACTIONf_chiral_restr0.0452690
X-RAY DIFFRACTIONf_plane_restr0.0043000
X-RAY DIFFRACTIONf_dihedral_angle_d14.3546013
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3926-2.45250.35541390.29717948808798
2.4525-2.51880.3161460.279181378283100
2.5188-2.59290.3671380.278280398177100
2.5929-2.67660.34541430.272481028245100
2.6766-2.77220.35621440.277680948238100
2.7722-2.88320.31391410.273481298270100
2.8832-3.01440.34551430.268680958238100
3.0144-3.17320.32021420.266281108252100
3.1732-3.3720.3461440.258881288272100
3.372-3.63220.33031420.245481128254100
3.6322-3.99750.28261450.242581428287100
3.9975-4.57550.24241420.213581288270100
4.5755-5.76260.30181410.221781868327100
5.7626-44.16520.23761400.21278212835299
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.9488-0.66950.05470.42570.20180.4687-0.19490.4034-0.090.11130.0654-0.9842-0.58550.93730.13370.1986-0.1009-0.07480.58130.02620.6027146.3471167.140424.1303
21.33190.3878-0.22292.2519-0.73692.56340.01260.0658-0.1310.0903-0.11070.01710.02910.28480.07710.12620.0409-0.00860.0595-0.00930.1077128.6079160.312726.5176
31.7507-0.70160.44441.7561-0.21971.2294-0.14430.63880.2283-0.4278-0.032-0.4762-0.14420.74180.05530.04050.07670.14550.24090.11640.1803134.7537165.347812.928
41.1682-0.8868-0.56931.5143-0.35180.5774-0.13060.1804-0.123-0.09920.04930.03970.0571-0.14870.07730.138-0.00710.03030.1292-0.02010.084119.5416158.562911.6177
51.5723-0.228-0.84940.65410.78311.8047-0.06710.3399-0.3306-0.0747-0.11330.06910.188-0.09750.06080.26850.02010.06050.10330.02090.169122.1827146.400920.3989
63.2244-4.02050.51085.3049-0.95360.3143-0.35860.0870.92950.21130.2286-0.0316-0.6273-0.26580.00190.8160.03150.06730.4002-0.050.6459116.1529133.785213.6104
70.47230.7958-0.52161.91540.26352.0104-0.15040.1015-0.0361-0.16710.15020.0158-0.0212-0.3095-0.01690.36610.016-0.04720.2154-0.02640.2784120.2937111.57369.5153
83.06531.14731.43931.86320.30653.2254-0.10750.12120.33570.15790.02640.1762-0.222-0.1544-0.01340.3840.11150.0550.23830.05790.3048121.6144114.088911.153
93.4861-1.21830.71041.228-0.84471.2464-0.2092-0.0735-0.01520.31580.09050.1015-0.3170.08670.10660.38080.05940.00120.2463-0.07840.3679121.8904119.384423.9879
102.4842-0.29290.51332.2218-0.42712.3235-0.0929-0.109-0.12410.2733-0.09980.11250.2471-0.01260.13530.43750.08080.07820.2522-0.05110.3484113.989105.800325.3537
111.5921-0.01350.21970.74241.12571.57030.0196-0.365-0.00620.55540.20020.06590.66870.2319-0.07320.54070.1647-0.09260.3253-0.0260.3172134.193597.110627.5707
121.86510.20760.04110.0740.38710.8929-0.139-0.101-0.23630.33910.1507-0.0460.27460.179-0.05750.40410.0451-0.01630.26040.00110.3445127.247103.740823.3738
131.64710.4246-1.09780.8141.15132.4825-0.19580.0182-0.26370.2848-0.00330.00820.4592-0.26680.20140.4641-0.06320.03720.3139-0.01890.3677111.592299.206916.3288
141.03090.4965-0.22412.08960.15532.33040.02190.09560.0617-0.0926-0.06840.2049-0.1982-0.53740.04930.252-0.0226-0.01350.4635-0.07640.3074167.3494193.457210.5126
151.74480.3150.16250.621-0.30491.41060.0438-0.39930.49330.1996-0.21480.19810.0127-0.16270.15480.30180.0356-0.01180.6107-0.13010.4531165.9199195.708719.8785
162.3163-0.14540.82260.31850.61371.1745-0.0307-0.0038-0.16180.1381-0.02490.1-0.0019-0.28380.01950.308-0.04680.01030.445-0.05120.354172.7594181.094425.0351
170.87420.8420.04091.22620.26171.86450.0503-0.1241-0.14660.0055-0.06760.37350.0479-0.3044-0.04490.2486-0.05720.00710.6337-0.05850.3947157.6275179.836118.379
181.1199-0.73250.14171.7214-0.0321.63560.06680.10440.2956-0.0534-0.12650.0485-0.2109-0.07230.08190.311-0.01690.03330.37870.01960.3579175.7661197.7315-4.0962
192.14660.55810.30381.51950.49870.72880.1160.0384-0.2039-0.2401-0.1266-0.2128-0.21020.1068-0.03680.3287-0.0178-0.0010.36640.03090.2835182.1412187.5689-11.4035
201.5480.0275-0.95381.1357-0.61461.5584-0.10550.12830.0397-0.2652-0.0536-0.2468-0.00070.24280.14850.3143-0.01270.01330.41920.07110.3284190.5726190.7907-8.6738
211.7658-0.45010.03851.5112-0.112.4890.12650.03560.14270.0168-0.08090.0112-0.11470.28130.00220.0455-0.0170.03490.09450.00830.1032127.9528172.453135.8607
221.3449-0.4332-0.30242.3838-0.41521.44640.0062-0.4290.05490.1521-0.0748-0.0262-0.11330.23380.03460.0824-0.0641-0.0620.11-0.05020.1503126.0774176.922549.7214
231.3267-0.69570.75652.1597-1.8041.78280.0576-0.0210.1149-0.17790.01440.0750.0450.0669-0.06740.1034-0.0182-0.01610.0801-0.01410.1223113.2888162.218548.7951
240.81270.22740.70251.00430.4022.93660.1397-0.06740.247-0.0209-0.09350.078-0.0972-0.21280.02920.0983-0.01460.01510.0884-0.0440.1878115.1876183.615543.6614
252.51530.24241.14621.7532-0.34383.16850.13260.3444-0.2350.12340.09660.35950.1259-0.0019-0.12890.27320.05670.0470.3023-0.06260.356997.604383.5882-13.4403
262.6476-0.323-0.68043.71911.80864.78250.2425-0.09790.0794-0.1940.12970.18230.2015-0.2659-0.25030.32290.0659-0.03240.27350.00790.3356100.953578.1669-19.7106
271.86430.68680.54821.2480.01070.9208-0.0201-0.2670.12150.4496-0.06590.4805-0.2066-0.40650.09960.4505-0.0280.15940.3956-0.08940.485796.629886.7046-2.5746
282.89420.09850.61922.0371-0.21661.9487-0.2329-0.2187-0.16770.2565-0.26710.0036-0.10720.21380.26720.4105-0.03730.070.52510.02780.3699102.776672.1111-0.3201
291.13270.7891-0.23852.16660.35822.73460.1198-0.3294-0.01880.3682-0.07050.1678-0.00050.3534-0.0820.38960.00420.00180.4066-0.08150.3242120.948684.14210.189
301.27350.8968-0.29572.6971-0.32281.0320.1114-0.1662-0.09250.31960.1276-0.1271-0.25270.1091-0.14450.3393-0.0273-0.0150.416-0.02140.3235110.38582.9886-1.2312
311.37570.264-1.62881.8357-0.77272.790.2001-0.3291-0.34010.285-0.09320.09490.20950.3607-0.11450.36690.01790.00260.38140.01460.4037107.365466.7793-9.351
324.5677-0.65560.8811.713-0.63664.2757-0.1890.14790.87860.1383-0.1834-0.1266-0.33370.08910.22910.43810.0254-0.02040.2360.00450.3373129.9929122.23321.2582
331.4364-0.45330.14411.77670.12971.9314-0.02450.07830.2537-0.1361-0.0371-0.0408-0.3283-0.06760.05040.45130.00440.03810.28340.01740.3165133.0814118.8197-6.4077
342.63840.58620.47681.8818-0.216-0.0590.0490.2715-0.2954-0.1754-0.0712-0.2038-0.05170.1283-0.04590.37060.04170.03050.3266-0.02170.3065134.4188102.7199-14.9475
350.8679-0.2739-0.42621.1741-0.35091.9774-0.0813-0.07920.0052-0.2843-0.0344-0.51860.03120.35220.07070.38750.02380.00950.33480.03620.4149147.9811111.0352-4.6401
362.09380.5241-0.24141.50570.01542.02830.01790.0870.1944-0.0911-0.04350.15630.1451-0.13330.0580.32450.09280.00420.30770.00710.3301100.352391.872-29.634
371.4741-0.15340.17212.65680.29210.6665-0.07790.11620.12880.00440.0128-0.2358-0.20090.01720.03320.34730.0808-0.01330.3164-0.00370.2873112.484392.7403-36.9733
380.4599-0.06380.12021.483-0.60140.8535-0.01280.03660.162-0.1595-0.0907-0.1407-0.16970.12760.06750.3330.0221-0.01730.2883-0.01540.3309113.6485100.4824-34.2815
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid -16 through 16 )A-16 - 16
2X-RAY DIFFRACTION2chain 'A' and (resid 17 through 60 )A17 - 60
3X-RAY DIFFRACTION3chain 'A' and (resid 61 through 90 )A61 - 90
4X-RAY DIFFRACTION4chain 'A' and (resid 91 through 205 )A91 - 205
5X-RAY DIFFRACTION5chain 'A' and (resid 206 through 268 )A206 - 268
6X-RAY DIFFRACTION6chain 'B' and (resid -16 through 9 )B-16 - 9
7X-RAY DIFFRACTION7chain 'B' and (resid 10 through 41 )B10 - 41
8X-RAY DIFFRACTION8chain 'B' and (resid 42 through 60 )B42 - 60
9X-RAY DIFFRACTION9chain 'B' and (resid 61 through 90 )B61 - 90
10X-RAY DIFFRACTION10chain 'B' and (resid 91 through 137 )B91 - 137
11X-RAY DIFFRACTION11chain 'B' and (resid 138 through 164 )B138 - 164
12X-RAY DIFFRACTION12chain 'B' and (resid 165 through 205 )B165 - 205
13X-RAY DIFFRACTION13chain 'B' and (resid 206 through 268 )B206 - 268
14X-RAY DIFFRACTION14chain 'C' and (resid 4 through 41 )C4 - 41
15X-RAY DIFFRACTION15chain 'C' and (resid 42 through 109 )C42 - 109
16X-RAY DIFFRACTION16chain 'C' and (resid 110 through 196 )C110 - 196
17X-RAY DIFFRACTION17chain 'C' and (resid 197 through 268 )C197 - 268
18X-RAY DIFFRACTION18chain 'D' and (resid 4 through 85 )D4 - 85
19X-RAY DIFFRACTION19chain 'D' and (resid 86 through 183 )D86 - 183
20X-RAY DIFFRACTION20chain 'D' and (resid 184 through 268 )D184 - 268
21X-RAY DIFFRACTION21chain 'E' and (resid 3 through 60 )E3 - 60
22X-RAY DIFFRACTION22chain 'E' and (resid 61 through 137 )E61 - 137
23X-RAY DIFFRACTION23chain 'E' and (resid 138 through 195 )E138 - 195
24X-RAY DIFFRACTION24chain 'E' and (resid 196 through 268 )E196 - 268
25X-RAY DIFFRACTION25chain 'F' and (resid 4 through 31 )F4 - 31
26X-RAY DIFFRACTION26chain 'F' and (resid 32 through 51 )F32 - 51
27X-RAY DIFFRACTION27chain 'F' and (resid 52 through 90 )F52 - 90
28X-RAY DIFFRACTION28chain 'F' and (resid 91 through 137 )F91 - 137
29X-RAY DIFFRACTION29chain 'F' and (resid 138 through 168 )F138 - 168
30X-RAY DIFFRACTION30chain 'F' and (resid 169 through 205 )F169 - 205
31X-RAY DIFFRACTION31chain 'F' and (resid 206 through 268 )F206 - 268
32X-RAY DIFFRACTION32chain 'G' and (resid 4 through 25 )G4 - 25
33X-RAY DIFFRACTION33chain 'G' and (resid 26 through 120 )G26 - 120
34X-RAY DIFFRACTION34chain 'G' and (resid 121 through 205 )G121 - 205
35X-RAY DIFFRACTION35chain 'G' and (resid 206 through 268 )G206 - 268
36X-RAY DIFFRACTION36chain 'H' and (resid 4 through 85 )H4 - 85
37X-RAY DIFFRACTION37chain 'H' and (resid 86 through 181 )H86 - 181
38X-RAY DIFFRACTION38chain 'H' and (resid 182 through 268 )H182 - 268

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Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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