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- PDB-9ozv: Structure of the self-association domain of LDB2 -

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Basic information

Entry
Database: PDB / ID: 9ozv
TitleStructure of the self-association domain of LDB2
ComponentsLIM domain-binding protein 2
KeywordsSTRUCTURAL PROTEIN / lim domain binding / transcriptional factors
Function / homology
Function and homology information


positive regulation of cellular component biogenesis / regulation of kinase activity / epithelial structure maintenance / LIM domain binding / cell leading edge / somatic stem cell population maintenance / hair follicle development / regulation of cell migration / transcription regulator complex / nucleolus ...positive regulation of cellular component biogenesis / regulation of kinase activity / epithelial structure maintenance / LIM domain binding / cell leading edge / somatic stem cell population maintenance / hair follicle development / regulation of cell migration / transcription regulator complex / nucleolus / enzyme binding / positive regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / plasma membrane
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.
Similarity search - Domain/homology
LIM domain-binding protein 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.59 Å
AuthorsVu, T.H. / Patel, K. / Smith, N.C. / Matthews, J.M.
Funding support Australia, 2items
OrganizationGrant numberCountry
Australian Research Council (ARC)DP220101489 Australia
Australian Research Council (ARC)DP190102543 Australia
CitationJournal: To Be Published
Title: Structure of the self-association domain of LDB2
Authors: Vu, T.H. / Patel, K. / Smith, N.C. / Matthews, J.M.
History
DepositionJun 5, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 30, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: LIM domain-binding protein 2
B: LIM domain-binding protein 2


Theoretical massNumber of molelcules
Total (without water)43,6522
Polymers43,6522
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis, light scattering, cross-linking
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3200 Å2
ΔGint-4 kcal/mol
Surface area17030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.628, 95.876, 49.129
Angle α, β, γ (deg.)90.000, 108.020, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and ((resid 27 and (name N or name...
d_2ens_1(chain "B" and ((resid 27 and (name N or name...

NCS domain segments:

Component-ID: 1 / Ens-ID: ens_1 / Beg auth comp-ID: GLN / Beg label comp-ID: GLN / End auth comp-ID: LEU / End label comp-ID: LEU / Auth seq-ID: 27 - 204 / Label seq-ID: 6 - 183

Dom-IDAuth asym-IDLabel asym-ID
d_1AA
d_2BB

NCS oper: (Code: givenMatrix: (-0.998539171787, -0.0132953054593, 0.0523713400513), (0.0230757231977, -0.981349418886, 0.190842419424), (0.0488572758648, 0.19177213798, 0.980222634757)Vector: 19. ...NCS oper: (Code: given
Matrix: (-0.998539171787, -0.0132953054593, 0.0523713400513), (0.0230757231977, -0.981349418886, 0.190842419424), (0.0488572758648, 0.19177213798, 0.980222634757)
Vector: 19.7127167894, 39.1468527288, -4.16274790839)

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Components

#1: Protein LIM domain-binding protein 2 / LDB-2 / Carboxyl-terminal LIM domain-binding protein 1 / CLIM-1 / LIM domain-binding factor CLIM1


Mass: 21825.814 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: LDB2 self-association domain, residues 22-205 / Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ldb2, Clim1 / Production host: Escherichia coli (E. coli) / References: UniProt: O55203
Has protein modificationN

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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: 2.08 Å3/Da / Density % sol: 41.17 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: Ammonium sulfate, HEPES, PEG 8000, MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95373 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 8, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95373 Å / Relative weight: 1
ReflectionResolution: 2.59→47.94 Å / Num. obs: 10574 / % possible obs: 99.1 % / Redundancy: 1.9 % / Biso Wilson estimate: 70.55 Å2 / CC1/2: 0.998 / Net I/σ(I): 6.4
Reflection shellResolution: 2.59→2.7 Å / Num. unique obs: 10574 / CC1/2: 0.999

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.59→46.72 Å / SU ML: 0.5316 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 42.7326
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3414 1043 9.99 %
Rwork0.2682 9398 -
obs0.2755 10441 98.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 111.32 Å2
Refinement stepCycle: LAST / Resolution: 2.59→46.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2986 0 0 0 2986
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00373058
X-RAY DIFFRACTIONf_angle_d0.7174138
X-RAY DIFFRACTIONf_chiral_restr0.0463450
X-RAY DIFFRACTIONf_plane_restr0.0071528
X-RAY DIFFRACTIONf_dihedral_angle_d12.78851134
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 1.41571371034 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.59-2.730.42251380.40881258X-RAY DIFFRACTION92.7
2.73-2.90.441490.38971328X-RAY DIFFRACTION99.19
2.9-3.120.41661500.35621363X-RAY DIFFRACTION99.67
3.12-3.440.38491520.28971359X-RAY DIFFRACTION99.67
3.44-3.930.34761490.27151340X-RAY DIFFRACTION99.2
3.93-4.950.29331520.24091375X-RAY DIFFRACTION99.35
4.96-46.720.32311530.22921375X-RAY DIFFRACTION99.09
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)
14.47008104908-1.36758400641-0.004029161300636.3372621499-2.678618980465.472446596050.0849723797185-0.19870174750.2054807503160.542929771152-0.1558242753-0.0126673633319-0.3406486768480.03830927275340.001591672468940.656488091219-0.0635552185330.04446579144040.543601661816-0.03818598456370.87872855549611.052963194632.62430670117.74867862806
23.1566001278-1.355792759660.5814878533855.282038219182.201396297284.47100410192-0.0288803429062-0.1798815377910.1652541658390.4475536450030.05922113259540.1305514568880.009165769500770.1491768617190.0006440299601880.541595280124-0.02867348645010.07270164284580.5717383504150.009088980841880.590074102279.031150772278.8255749287710.1721429752
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11(chain 'B' and resid 25 through 205)BB25 - 2051 - 181
22(chain 'A' and resid 27 through 204)AA27 - 2041 - 178

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