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- PDB-1rut: Complex of LMO4 LIM domains 1 and 2 with the ldb1 LID domain -

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Basic information

Entry
Database: PDB / ID: 1rut
TitleComplex of LMO4 LIM domains 1 and 2 with the ldb1 LID domain
ComponentsFusion protein of Lmo4 protein and LIM domain-binding protein 1
KeywordsPROTEIN BINDING / b-tandem zipper / LIM domain / fusion protein
Function / homology
Function and homology information


regulation of kinase activity / cellular component assembly / negative regulation of erythrocyte differentiation / positive regulation of hemoglobin biosynthetic process / cerebellar Purkinje cell differentiation / head development / epithelial structure maintenance / primitive erythrocyte differentiation / transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery / beta-catenin-TCF complex ...regulation of kinase activity / cellular component assembly / negative regulation of erythrocyte differentiation / positive regulation of hemoglobin biosynthetic process / cerebellar Purkinje cell differentiation / head development / epithelial structure maintenance / primitive erythrocyte differentiation / transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery / beta-catenin-TCF complex / RUNX1 regulates transcription of genes involved in differentiation of HSCs / LIM domain binding / gastrulation with mouth forming second / anterior/posterior axis specification / regulation of focal adhesion assembly / cell leading edge / somatic stem cell population maintenance / positive regulation of cell adhesion / hair follicle development / regulation of cell migration / cerebellum development / positive regulation of transcription elongation by RNA polymerase II / neuron differentiation / Wnt signaling pathway / RNA polymerase II transcription regulator complex / : / nervous system development / DNA-binding transcription factor binding / transcription regulator complex / RNA polymerase II-specific DNA-binding transcription factor binding / transcription by RNA polymerase II / transcription coactivator activity / cell adhesion / negative regulation of DNA-templated transcription / chromatin binding / chromatin / negative regulation of transcription by RNA polymerase II / enzyme binding / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / protein-containing complex / nucleoplasm / 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. / Cysteine Rich Protein / Cysteine Rich Protein / Ribbon / Mainly Beta
Similarity search - Domain/homology
: / LIM domain-binding protein 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.3 Å
AuthorsDeane, J.E. / Ryan, D.P. / Maher, M.J. / Kwan, A.H.Y. / Bacca, M. / Mackay, J.P. / Guss, J.M. / Visvader, J.E. / Matthews, J.M.
Citation
Journal: Embo J. / Year: 2004
Title: Tandem LIM domains provide synergistic binding in the LMO4:Ldb1 complex
Authors: Deane, J.E. / Ryan, D.P. / Sunde, M. / Maher, M.J. / Guss, J.M. / Visvader, J.E. / Matthews, J.M.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2003
Title: Crystallization of FLINC4, an intramolecular LMO4-ldb1 complex
Authors: Deane, J.E. / Maher, M.J. / Langley, D.B. / Graham, S.C. / Visvader, J.E. / Guss, J.M. / Matthews, J.M.
History
DepositionDec 11, 2003Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 12, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 2017Group: Source and taxonomy / Category: entity_src_gen
Revision 1.4Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
X: Fusion protein of Lmo4 protein and LIM domain-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,4575
Polymers20,1961
Non-polymers2624
Water3,495194
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.344, 61.344, 93.159
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number149
Space group name H-MP312
Components on special symmetry positions
IDModelComponents
11X-623-

HOH

21X-687-

HOH

31X-737-

HOH

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Components

#1: Protein Fusion protein of Lmo4 protein and LIM domain-binding protein 1 / / FLINC4


Mass: 20195.641 Da / Num. of mol.: 1 / Mutation: C52S, C64S
Source method: isolated from a genetically manipulated source
Details: Fusion of LMO4 residues 16-152 to ldb1 LID residues 300-339 via a flexible linker with sequence GGSGGSGGSGG
Source: (gene. exp.) Mus musculus (house mouse) / Gene: lmo4, ldb1 / Plasmid: pGEX-2T / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: GenBank: 13097522, UniProt: P70662
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 194 / 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: 2.5 Å3/Da / Density % sol: 50.34 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.7
Details: 1.0M ammonium sulfate, 0.1M MES, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08, 1.282, 1.170, 1.283
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 24, 2003 / Details: mirrors
RadiationMonochromator: Si (111) asymmetric cut, horizontal focus / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.081
21.2821
31.171
41.2831
ReflectionResolution: 1.3→50 Å / Num. all: 45526 / Num. obs: 45441 / % possible obs: 91.3 % / Observed criterion σ(I): -3 / Redundancy: 2.6 % / Biso Wilson estimate: 16.442 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 18
Reflection shellResolution: 1.3→1.35 Å / Redundancy: 2 % / Rmerge(I) obs: 0.291 / Mean I/σ(I) obs: 2.4 / Num. unique all: 3907 / % possible all: 79.2

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.3→46.13 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.944 / SU B: 0.536 / SU ML: 0.023 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.045 / ESU R Free: 0.047 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19316 2291 5 %RANDOM
Rwork0.15499 ---
all0.1568 45437 --
obs0.15686 43146 95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 19.986 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.3→46.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1250 0 4 194 1448
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0211275
X-RAY DIFFRACTIONr_bond_other_d0.0020.021112
X-RAY DIFFRACTIONr_angle_refined_deg1.2421.9451718
X-RAY DIFFRACTIONr_angle_other_deg0.7832594
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2345161
X-RAY DIFFRACTIONr_chiral_restr0.0820.2181
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021453
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02273
X-RAY DIFFRACTIONr_nbd_refined0.1950.2221
X-RAY DIFFRACTIONr_nbd_other0.250.21285
X-RAY DIFFRACTIONr_nbtor_other0.080.2798
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1010.2128
X-RAY DIFFRACTIONr_metal_ion_refined0.0290.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1380.212
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2720.265
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.070.218
X-RAY DIFFRACTIONr_mcbond_it3.8242791
X-RAY DIFFRACTIONr_mcangle_it4.95931266
X-RAY DIFFRACTIONr_scbond_it5.1812484
X-RAY DIFFRACTIONr_scangle_it6.553452
X-RAY DIFFRACTIONr_rigid_bond_restr1.38211275
X-RAY DIFFRACTIONr_sphericity_free10.4478198
X-RAY DIFFRACTIONr_sphericity_bonded8.01981250
LS refinement shellResolution: 1.302→1.336 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.273 142
Rwork0.249 2880
obs-3022

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