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

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Basic information

Entry
Database: PDB / ID: 9czs
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: 3.17 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
DepositionAug 5, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 13, 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)43,6222
Polymers43,6222
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2430 Å2
ΔGint-6 kcal/mol
Surface area19240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.196, 147.634, 42.994
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and resid 27 through 192)
d_2ens_1(chain "B" and (resid 27 through 110 or resid 114 through 192))

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11GLNGLNTHRTHRAA27 - 1926 - 171
d_21GLNGLNSERSERBB27 - 1106 - 89
d_22SERSERTHRTHRBB114 - 19293 - 171

NCS oper: (Code: givenMatrix: (-0.448927358585, -0.893561318656, -0.00352086858454), (-0.893555821073, 0.44893841324, -0.00350652875051), (0.00471395160978, 0.00157191592918, -0.999987653794)Vector: ...NCS oper: (Code: given
Matrix: (-0.448927358585, -0.893561318656, -0.00352086858454), (-0.893555821073, 0.44893841324, -0.00350652875051), (0.00471395160978, 0.00157191592918, -0.999987653794)
Vector: 44.2633071452, 27.2823421904, 19.101443229)

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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: 21810.844 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
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: 2.23 Å3/Da / Density % sol: 44.75 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: Ammonium sulfate, HEPES, PEG 8000, MPD / PH range: 7.5-7.8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95374 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 6, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95374 Å / Relative weight: 1
ReflectionResolution: 3.17→49.21 Å / Num. obs: 12703 / % possible obs: 99.7 % / Redundancy: 1.8 % / Biso Wilson estimate: 59.77 Å2 / CC1/2: 0.976 / Net I/σ(I): 4.9
Reflection shellResolution: 3.17→3.2 Å / Num. unique obs: 2289 / CC1/2: 0.724

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.17→47.11 Å / SU ML: 0.4783 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 29.4456
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2923 1249 9.89 %
Rwork0.2097 11386 -
obs0.2178 12635 99.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 62 Å2
Refinement stepCycle: LAST / Resolution: 3.17→47.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2738 0 0 0 2738
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01082803
X-RAY DIFFRACTIONf_angle_d1.29963793
X-RAY DIFFRACTIONf_chiral_restr0.0654415
X-RAY DIFFRACTIONf_plane_restr0.0154483
X-RAY DIFFRACTIONf_dihedral_angle_d5.9879365
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.900071887984 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.17-3.30.35431350.31841221X-RAY DIFFRACTION94.3
3.3-3.450.36651410.28871227X-RAY DIFFRACTION100
3.45-3.630.33981410.24981312X-RAY DIFFRACTION100
3.63-3.860.34471380.25851266X-RAY DIFFRACTION99.72
3.86-4.160.22251400.211260X-RAY DIFFRACTION100
4.16-4.580.25371430.17871275X-RAY DIFFRACTION100
4.58-5.240.25051380.161270X-RAY DIFFRACTION100
5.24-6.60.36011360.19261278X-RAY DIFFRACTION100
6.61-47.110.25011370.17161277X-RAY DIFFRACTION99.79
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)
13.182684167440.4207123397770.7885919410052.943899567610.4103675995991.65564266886-0.07198826109890.1692393710460.1467455643150.1604281325370.156983884203-0.204808732062-0.1464003157320.223594857727-0.0391280927370.48206130779-0.0590092220638-0.05719162368560.3718535791160.003117105496850.42561497433629.702465394827.577372086715.3576487449
20.8092747540820.0607277392838-0.08143093868481.49581335070.631031868182.986960567070.09526394761790.03486115069730.003993098057640.471636708739-0.3321273777720.0902324939202-0.362889553772-0.4164763244210.1609959701120.546829803142-0.0553313241866-0.05241315887110.4123196601760.02452994091330.4443960511523.578673088822.50442818519.3562615677
31.527618232310.591132293123-2.388796196331.09846886258-1.035369383642.67370138465-0.6881661157080.5004784424450.102718997657-0.259493523650.679128365034-0.795973528691-0.0473707491674-0.283722885281-0.1343755656640.3806083855170.04159052902270.01093452321580.421397615263-0.1905812725330.63389290215138.4844044417-0.936102996333-3.83481603198
45.705275440241.42670685045-1.95797090036.057584606-2.657364915937.13796353774-0.154423877612-1.171214993960.4090662591030.969432135405-0.482522397718-0.321162975679-2.413308352260.9496803083180.4173317385270.6561953656380.00433241954299-0.01530687709140.689735839298-0.1332661080290.5758149242978.9616724013423.01743976119.08611571914
52.585193958150.592721129003-0.2761745430461.713117531690.5617653632762.857382103670.0213636511294-0.460623153929-0.098572427074-0.107888620365-0.0268700252470.116720474364-0.28957419208-0.497618488871-0.02448574222230.3914098632330.133897072497-0.07132109841380.552268351005-0.01325582740070.5192755745035.5253034341510.55321658892.65533665998
61.86697763816-2.00093668451.263632401253.88129118461-2.735689518763.472709363620.4249030400470.1522233292020.0363966580716-0.353702468535-0.4467018581690.303537471699-0.2545450687050.301803894078-0.1774408433720.616516227503-0.1122339634390.007955244343530.505542588383-0.1222598310780.48899716886914.811827236217.08646504420.318789873357
70.847620048291-0.2279956533440.8236247605780.414001592923-0.5060520402171.520970592360.0501312301616-0.06131533451750.06209833268130.0101470239693-0.01688984935160.07162824645150.00123208952042-0.210049903491-0.1172038300990.3975028922420.03395323967680.0460409045430.498387271961-0.05928213689090.4524409958318.16278014477.55133468527.96207183713
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 27 through 105 )AA27 - 1051 - 79
22chain 'A' and (resid 106 through 168 )AA106 - 16880 - 139
33chain 'A' and (resid 169 through 194 )AA169 - 194140 - 165
44chain 'B' and (resid 27 through 41 )BB27 - 411 - 15
55chain 'B' and (resid 42 through 105 )BB42 - 10516 - 79
66chain 'B' and (resid 106 through 135 )BB106 - 13580 - 109
77chain 'B' and (resid 136 through 192 )BB136 - 192110 - 166

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