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- PDB-6s9t: Dimerization domain of Xenopus laevis LDB1 in complex with darpin 3 -

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Basic information

Entry
Database: PDB / ID: 6s9t
TitleDimerization domain of Xenopus laevis LDB1 in complex with darpin 3
Components
  • Darpin 3
  • LIM domain-binding protein 1
KeywordsGENE REGULATION / WNT signalling / wnt enhanceosome
Function / homology
Function and homology information


LIM domain binding / transcription coregulator binding / transcription coregulator activity / DNA-binding transcription factor binding / positive regulation of DNA-templated transcription / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / identical protein binding / nucleus
Similarity search - Function
LIM domain-binding protein 1 / LIM-domain binding protein/SEUSS / LIM interaction domain / LIM-domain binding protein / LIM interaction domain (LID) / LIM interaction domain (LID) domain profile. / Ankyrin repeat-containing domain / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Mainly Alpha
Similarity search - Domain/homology
LIM domain-binding protein 1
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.05 Å
AuthorsRenko, M. / Schaefer, J.V. / Pluckthun, A. / Bienz, M.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom) United Kingdom
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2019
Title: Rotational symmetry of the structured Chip/LDB-SSDP core module of the Wnt enhanceosome.
Authors: Renko, M. / Fiedler, M. / Rutherford, T.J. / Schaefer, J.V. / Pluckthun, A. / Bienz, M.
History
DepositionJul 15, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 9, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: LIM domain-binding protein 1
D: Darpin 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,3354
Polymers39,9472
Non-polymers3882
Water48627
1
A: LIM domain-binding protein 1
D: Darpin 3
hetero molecules

A: LIM domain-binding protein 1
D: Darpin 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,6718
Polymers79,8944
Non-polymers7774
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area7770 Å2
ΔGint-21 kcal/mol
Surface area27780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.217, 70.217, 122.257
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein LIM domain-binding protein 1 / xLdb1


Mass: 22172.979 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: ldb1 / Production host: Escherichia coli (E. coli) / References: UniProt: P70060
#2: Protein Darpin 3 /


Mass: 17773.859 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 27 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.55 Å3/Da / Density % sol: 51.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.1 M TrisHCL, pH 7.0 32% PEG200 0.05 M Li2SO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.97886 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 19, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97886 Å / Relative weight: 1
ReflectionResolution: 2.05→43.15 Å / Num. obs: 22528 / % possible obs: 99.92 % / Redundancy: 39.5 % / CC1/2: 1 / Rmerge(I) obs: 0.127 / Rpim(I) all: 0.021 / Rrim(I) all: 0.129 / Net I/σ(I): 23.5
Reflection shellResolution: 2.05→2.12 Å / Num. unique obs: 2198

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Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
PDB_EXTRACT3.25data extraction
XSCALEdata scaling
SHELXCDphasing
XDSdata reduction
RefinementMethod to determine structure: SAD / Resolution: 2.05→43.15 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.932 / SU B: 15.729 / SU ML: 0.188 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.205 / ESU R Free: 0.195
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2793 1071 4.7 %RANDOM
Rwork0.2179 ---
obs0.2206 21557 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 132.28 Å2 / Biso mean: 57.123 Å2 / Biso min: 40.85 Å2
Baniso -1Baniso -2Baniso -3
1--0.84 Å2-0.42 Å20 Å2
2---0.84 Å20 Å2
3---2.73 Å2
Refinement stepCycle: final / Resolution: 2.05→43.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2369 0 26 27 2422
Biso mean--78.08 52.86 -
Num. residues----295
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0132454
X-RAY DIFFRACTIONr_bond_other_d0.0020.0172259
X-RAY DIFFRACTIONr_angle_refined_deg1.7221.6463310
X-RAY DIFFRACTIONr_angle_other_deg1.3041.5775241
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5315295
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.18422.993137
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.86915397
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.4691514
X-RAY DIFFRACTIONr_chiral_restr0.0740.2314
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022724
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02518
LS refinement shellResolution: 2.05→2.1 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.376 97 -
Rwork0.341 1550 -
obs--99.82 %
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)
12.74980.1111.92731.1334-0.38352.0628-0.06470.21050.242-0.06480.13-0.1001-0.07940.1802-0.06530.21090.08220.02670.5770.01230.449535.330935.23872.6787
22.7249-1.9875-0.16921.5030.1880.0923-0.1066-0.3645-0.60450.07820.26310.28840.04280.062-0.15640.19870.12350.00950.62950.10220.574133.592325.054815.4052
31.23850.17220.10552.6211.72041.13870.0037-0.04520.0323-0.04720.03590.031-0.00370.039-0.03960.29840.1110.01670.49140.00140.485825.60431.93876.2917
43.82561.7376-0.59214.26990.0990.13630.126-0.20310.21890.0391-0.0385-0.1035-0.00420.0068-0.08750.27190.09290.00270.5821-0.00350.413829.651936.909513.2298
53.4942-0.02282.23043.08481.59912.2842-0.05810.142-0.3250.05520.11670.1113-0.0430.1451-0.05860.2810.15880.05690.4192-0.0010.566212.66412.30750.5576
63.57211.53241.3820.94741.393.58690.17860.25660.0452-0.0992-0.1539-0.0802-0.3594-0.2157-0.02480.27670.14690.02380.55940.03120.455861.822728.4403-1.5928
74.1219-0.7786-1.15940.86510.20170.32710.22230.0986-0.16640.0663-0.25980.0759-0.0685-0.00940.03750.2310.0705-0.02920.5951-0.03590.468156.88924.93485.2533
87.5949-3.7996-1.84511.9620.85262.19790.06730.0389-0.23640.0764-0.05140.0525-0.18080.066-0.01590.25580.061-0.01840.5878-0.00190.427157.114923.059112.9701
93.00830.95421.06120.98840.36860.46720.0504-0.2978-0.7363-0.10290.18180.3202-0.0881-0.0626-0.23220.14030.0277-0.09870.47860.13370.751347.588517.675214.0049
100.08780.32840.11783.26330.92680.28990.2067-0.01610.11550.9291-0.44370.95150.4076-0.10370.2371.0761-0.0436-0.01160.1247-0.04660.61745.85377.844617.818
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A30 - 71
2X-RAY DIFFRACTION2A72 - 91
3X-RAY DIFFRACTION3A92 - 142
4X-RAY DIFFRACTION4A143 - 169
5X-RAY DIFFRACTION5A170 - 196
6X-RAY DIFFRACTION6D219 - 242
7X-RAY DIFFRACTION7D243 - 273
8X-RAY DIFFRACTION8D274 - 288
9X-RAY DIFFRACTION9D289 - 332
10X-RAY DIFFRACTION10D333 - 346

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