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- PDB-2dfy: Crystal structure of a cyclized protein fusion of LMO4 LIM domain... -

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Basic information

Entry
Database: PDB / ID: 2dfy
TitleCrystal structure of a cyclized protein fusion of LMO4 LIM domains 1 and 2 with the LIM interacting domain of LDB1
Componentsfusion protein of LIM domain transcription factor LMO4 and LIM domain-binding protein 1
KeywordsTRANSCRIPTION / ZINC finger / LIM only protein / LIM domain / circular protein
Function / homology
Function and homology information


regulation of cell activation / ventral spinal cord interneuron differentiation / spinal cord motor neuron cell fate specification / spinal cord association neuron differentiation / spinal cord motor neuron differentiation / regulation of cell fate specification / positive regulation of kinase activity / motor neuron axon guidance / ventricular septum development / cell leading edge ...regulation of cell activation / ventral spinal cord interneuron differentiation / spinal cord motor neuron cell fate specification / spinal cord association neuron differentiation / spinal cord motor neuron differentiation / regulation of cell fate specification / positive regulation of kinase activity / motor neuron axon guidance / ventricular septum development / cell leading edge / negative regulation of protein-containing complex assembly / regulation of cell migration / thymus development / neural tube closure / transcription corepressor activity / RNA polymerase II transcription regulator complex / DNA-binding transcription factor binding / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / metal ion binding / nucleus
Similarity search - Function
Cysteine Rich Protein / Cysteine Rich Protein / LIM zinc-binding domain signature. / LIM domain / Zinc-binding domain present in Lin-11, Isl-1, Mec-3. / Zinc finger, LIM-type / LIM domain profile. / Ribbon / Mainly Beta
Similarity search - Domain/homology
LIM domain transcription factor LMO4
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsJeffries, C.M.J. / Graham, S.C. / Collyer, C.A. / Guss, J.M. / Matthews, J.M.
CitationJournal: Protein Sci. / Year: 2006
Title: Stabilization of a binary protein complex by intein-mediated cyclization
Authors: Jeffries, C.M.J. / Graham, S.C. / Stokes, P.H. / Collyer, C.A. / Guss, J.M. / Matthews, J.M.
History
DepositionMar 6, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 31, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / 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 / 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
Revision 1.5Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
X: fusion protein of LIM domain transcription factor LMO4 and LIM domain-binding protein 1
C: fusion protein of LIM domain transcription factor LMO4 and LIM domain-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,82712
Polymers42,1192
Non-polymers70710
Water4,396244
1
X: fusion protein of LIM domain transcription factor LMO4 and LIM domain-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,4136
Polymers21,0601
Non-polymers3545
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: fusion protein of LIM domain transcription factor LMO4 and LIM domain-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,4136
Polymers21,0601
Non-polymers3545
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.333, 61.333, 93.019
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number143
Space group name H-MP3
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11C
21X

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: ASN / End label comp-ID: ASN / Refine code: 3 / Auth seq-ID: 19 - 327 / Label seq-ID: 2 - 174

Dom-IDAuth asym-IDLabel asym-ID
1CB
2XA
DetailsTHIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT THAT CONSISTS OF 2 CHAINS. BIOLOGICAL ASSEMBLY CONSISTS OF ONE PROTEIN CHAIN, ONE HALF OF THE ASYMETRIC UNIT.

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Components

#1: Protein fusion protein of LIM domain transcription factor LMO4 and LIM domain-binding protein 1 / / CZ-FLINC4


Mass: 21059.574 Da / Num. of mol.: 2 / Fragment: LMO4 / Mutation: C52S/C64S
Source method: isolated from a genetically manipulated source
Details: Cyclised fusion of LMO4 residues 18-152 to LDB1 LID residues 300-339 via two flexible linkers with sequence GGSGGSGGSGG and TRESGSIEF
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: PNW1120, PCY76 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) RECA / References: UniProt: P61969
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 244 / 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: 2.4 Å3/Da / Density % sol: 48.7 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 1M AMMONIUM SULPHATE, 0.1M TRIS, 15% GLYCEROL, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 296K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 15, 2005 / Details: OSMIC MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. all: 46870 / Num. obs: 44295 / % possible obs: 99.4 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.034 / Net I/σ(I): 36.3
Reflection shellResolution: 1.65→1.69 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 2.2 / % possible all: 99

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0005refinement
PDB_EXTRACT1.701data extraction
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1RUT WITH MULTIPLE CONFORMERS, SOLVENT AND ZINC ATOMS REMOVED
Resolution: 1.65→10 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.959 / SU B: 2.97 / SU ML: 0.046 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.103 / ESU R Free: 0.081 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.194 2368 5.1 %RANDOM
Rwork0.167 ---
all0.168 46663 --
obs0.168 44295 99.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 42.98 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.65→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2420 0 20 244 2684
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0212503
X-RAY DIFFRACTIONr_bond_other_d0.0010.022229
X-RAY DIFFRACTIONr_angle_refined_deg1.3981.9533360
X-RAY DIFFRACTIONr_angle_other_deg0.79435172
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9775316
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.08722.414116
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.39615428
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1051526
X-RAY DIFFRACTIONr_chiral_restr0.0920.2352
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022827
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02555
X-RAY DIFFRACTIONr_nbd_refined0.1930.2476
X-RAY DIFFRACTIONr_nbd_other0.1910.22248
X-RAY DIFFRACTIONr_nbtor_refined0.1750.21241
X-RAY DIFFRACTIONr_nbtor_other0.0810.21521
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1460.2206
X-RAY DIFFRACTIONr_metal_ion_refined0.0130.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2070.216
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1590.281
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1470.223
X-RAY DIFFRACTIONr_mcbond_it1.7551.51998
X-RAY DIFFRACTIONr_mcbond_other0.6271.5667
X-RAY DIFFRACTIONr_mcangle_it1.98922475
X-RAY DIFFRACTIONr_scbond_it2.83131101
X-RAY DIFFRACTIONr_scangle_it3.7694.5884
X-RAY DIFFRACTIONr_rigid_bond_restr2.20435731
X-RAY DIFFRACTIONr_sphericity_free9.0393252
X-RAY DIFFRACTIONr_sphericity_bonded3.59434688
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: C / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
923TIGHT POSITIONAL0.010.05
1403LOOSE POSITIONAL0.085
923TIGHT THERMAL0.090.5
1403LOOSE THERMAL0.6510
LS refinement shellResolution: 1.65→1.692 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.277 189 -
Rwork0.215 3207 -
obs-3396 99.1 %

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