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- PDB-6s9s: Dimerization domain of Xenopus laevis LDB1 in complex with darpin 10 -

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Basic information

Entry
Database: PDB / ID: 6s9s
TitleDimerization domain of Xenopus laevis LDB1 in complex with darpin 10
Components
  • Darpin 10
  • LIM domain-binding protein 1
KeywordsGENE REGULATION / WNT signalling / wnt enhanceosome
Function / homology
Function and homology information


LIM domain binding / transcription coregulator binding / nervous system development / DNA-binding transcription factor binding / transcription regulator complex / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / identical protein binding / nucleus
Similarity search - Function
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 speciessynthetic construct (others)
Xenopus laevis (African clawed frog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 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
Revision 1.2Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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
F: Darpin 10
A: LIM domain-binding protein 1


Theoretical massNumber of molelcules
Total (without water)43,2362
Polymers43,2362
Non-polymers00
Water1086
1
F: Darpin 10
A: LIM domain-binding protein 1

F: Darpin 10
A: LIM domain-binding protein 1


Theoretical massNumber of molelcules
Total (without water)86,4724
Polymers86,4724
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area7340 Å2
ΔGint-33 kcal/mol
Surface area29310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.509, 117.117, 93.971
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Darpin 10


Mass: 21438.074 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)
#2: Protein LIM domain-binding protein 1 / xLdb1


Mass: 21797.818 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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.95 Å3/Da / Density % sol: 58.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.1 M TRIS, pH 8.5 20% PEG 8K 0.2 M Li2SO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.98004 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 11, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98004 Å / Relative weight: 1
ReflectionResolution: 2.2→49.75 Å / Num. obs: 22606 / % possible obs: 99.14 % / Redundancy: 13.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.027 / Rrim(I) all: 0.098 / Net I/σ(I): 15.6
Reflection shellResolution: 2.2→2.28 Å / Num. unique obs: 223

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
XSCALEdata scaling
PHENIXphasing
SHELXCDphasing
RefinementMethod to determine structure: SAD / Resolution: 2.2→49.75 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.939 / SU B: 29.332 / SU ML: 0.294 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.252 / ESU R Free: 0.218 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2801 1147 5.1 %RANDOM
Rwork0.2325 ---
obs0.235 21528 99.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 252.91 Å2 / Biso mean: 72.364 Å2 / Biso min: 47.42 Å2
Baniso -1Baniso -2Baniso -3
1-0.65 Å20 Å20 Å2
2---4.09 Å20 Å2
3---3.43 Å2
Refinement stepCycle: final / Resolution: 2.2→49.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2604 0 0 6 2610
Biso mean---55.71 -
Num. residues----325
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0132663
X-RAY DIFFRACTIONr_bond_other_d0.0020.0172433
X-RAY DIFFRACTIONr_angle_refined_deg1.6321.6363608
X-RAY DIFFRACTIONr_angle_other_deg1.2691.5795635
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.45323
X-RAY DIFFRACTIONr_dihedral_angle_2_deg3622.848151
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.07115457
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4651516
X-RAY DIFFRACTIONr_chiral_restr0.0720.2342
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022986
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02566
LS refinement shellResolution: 2.198→2.255 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.508 70 -
Rwork0.491 1575 -
all-1645 -
obs--99.1 %
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)
14.74343.47155.82519.39698.392910.3835-0.17650.37370.1618-0.2809-0.1402-0.1378-0.38720.35240.31670.66250.0384-0.03170.45310.0180.6093-8.2107-7.36411.8463
20.9997-0.3320.41183.0726-0.55540.33990.0807-0.0958-0.23260.03460.06480.2391-0.07040.1595-0.14550.6907-0.0241-0.02220.43410.04430.6158-12.8285-14.161111.4659
33.0697-1.45592.55063.0572-2.17465.19730.2209-0.2428-0.16890.1997-0.04910.5073-0.1991-0.0772-0.17170.6354-0.0147-0.01380.43040.0270.6506-17.6888-15.087713.0185
44.5064-0.64450.42040.18160.29131.74870.2576-0.48210.2334-0.015-0.0473-0.0839-0.1494-0.2835-0.21020.7635-0.10350.04730.3054-0.03770.7057-6.37131.583512.1823
56.15891.99624.15513.89510.99762.97420.21950.009-0.2198-0.05520.03550.0998-0.1348-0.0616-0.2550.71140.03070.08620.46030.01240.6186-21.7749-3.86895.513
612.5339-2.09830.01173.8293-0.25330.30670.3148-0.14760.51020.1691-0.1308-0.1752-0.10520.0809-0.18410.6719-0.03370.00510.5148-0.01060.4873-9.9907-3.569114.5466
71.96941.38751.34373.3504-0.08942.34720.203-0.1968-0.0392-0.0218-0.46140.44340.01410.09110.25840.6415-0.00990.05060.2294-0.00590.829-39.7743-5.01142.0088
8178.1637-78.855820.402535.8938-8.72232.4416-0.4709-0.44164.1153-0.37550.0925-1.6982-0.2299-0.10810.37841.7212-1.0218-0.52630.91970.64651.8315.1471-34.4563-0.4863
91.5262-1.64510.144.44832.87023.7690.2478-0.2775-0.1851-0.5110.0451-0.2405-0.3313-0.0738-0.29290.70660.0189-0.0030.30160.06730.7923-2.0519-35.89763.5495
101.9572-0.4729-0.78793.6490.57391.12920.05740.1028-0.15750.1997-0.17830.12330.2255-0.09670.12090.6843-0.0087-0.05150.30490.04860.7253-9.6505-34.791712.5852
117.3807-8.11097.861316.0297-9.46378.47590.3672-0.3418-0.4280.23840.0307-0.1230.3659-0.3765-0.3980.7591-0.18040.04720.5970.11150.6534-11.6285-40.602119.4081
121.1576-1.294-1.27271.90211.1641.6831-0.0661-0.1451-0.00410.30270.07970.1198-0.0398-0.0248-0.01360.7223-0.07930.00120.46960.07680.6647-13.9215-26.030522.3649
136.53693.5064-8.07581.933-3.68720.2335-0.08770.17280.23130.00870.01640.20460.1718-0.68230.07130.6585-0.17010.12440.45180.0910.8656-22.9627-34.519722.4315
144.0782-3.0815-1.36894.93750.39320.7697-0.1997-0.6394-0.12620.51560.26030.4507-0.0317-0.0333-0.06050.666-0.08050.12810.75850.1120.4964-20.927-23.559927.6405
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A30 - 46
2X-RAY DIFFRACTION2A47 - 77
3X-RAY DIFFRACTION3A78 - 102
4X-RAY DIFFRACTION4A103 - 119
5X-RAY DIFFRACTION5A120 - 142
6X-RAY DIFFRACTION6A143 - 169
7X-RAY DIFFRACTION7A170 - 197
8X-RAY DIFFRACTION8F38 - 43
9X-RAY DIFFRACTION9F44 - 78
10X-RAY DIFFRACTION10F79 - 123
11X-RAY DIFFRACTION11F124 - 131
12X-RAY DIFFRACTION12F132 - 151
13X-RAY DIFFRACTION13F152 - 160
14X-RAY DIFFRACTION14F161 - 193

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