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- PDB-4hm9: Crystal structure of full-length human catenin-beta-like 1 -

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Basic information

Entry
Database: PDB / ID: 4hm9
TitleCrystal structure of full-length human catenin-beta-like 1
ComponentsBeta-catenin-like protein 1
KeywordsPROTEIN TRANSPORT / all alpha-helical / armadillo repeats
Function / homology
Function and homology information


somatic diversification of immunoglobulins / Prp19 complex / mRNA Splicing - Major Pathway / spliceosomal complex / mRNA splicing, via spliceosome / adaptive immune response / positive regulation of apoptotic process / centrosome / enzyme binding / nucleoplasm ...somatic diversification of immunoglobulins / Prp19 complex / mRNA Splicing - Major Pathway / spliceosomal complex / mRNA splicing, via spliceosome / adaptive immune response / positive regulation of apoptotic process / centrosome / enzyme binding / nucleoplasm / membrane / nucleus / cytosol
Similarity search - Function
Beta-catenin-like protein 1, N-terminal / Beta-catenin-like protein 1 / Catenin-beta-like, Arm-motif containing nuclear / Eukaryotic domain of unknown function (DUF1716) / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / Armadillo-like helical / Alpha Horseshoe / Armadillo-type fold / Mainly Alpha
Similarity search - Domain/homology
Beta-catenin-like protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.1001 Å
AuthorsDu, Z. / Huang, X. / Wang, G. / Wu, Y.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2013
Title: The structure of full-length human CTNNBL1 reveals a distinct member of the armadillo-repeat protein family.
Authors: Huang, X. / Wang, G. / Wu, Y. / Du, Z.
History
DepositionOct 18, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 31, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 21, 2013Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-catenin-like protein 1


Theoretical massNumber of molelcules
Total (without water)65,6901
Polymers65,6901
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.990, 116.360, 137.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Beta-catenin-like protein 1 / Nuclear-associated protein / NAP / Testis development protein NYD-SP19


Mass: 65689.781 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: C20orf33, CTNNBL1, PP8304 / Plasmid: pET48B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8WYA6

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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: 2.98 Å3/Da / Density % sol: 58.74 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG 2000, Tris 8.0, KBr, vapor diffusion, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-E / Wavelength: 0.97872 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 15, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.399→46.145 Å / Num. all: 31661 / Num. obs: 31661 / % possible obs: 100 % / Redundancy: 6.7 % / Rsym value: 0.238 / Net I/σ(I): 6.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsRsym valueDiffraction-ID% possible all
2.399-2.535.50.0350.23.466199.9
2.53-2.686.60.0350.32.5181100
2.68-2.876.90.0350.41.61100
2.87-3.170.0350.80.9021100
3.1-3.397.10.0351.70.4441100
3.39-3.797.20.0353.30.2221100
3.79-4.387.20.0355.40.1291100
4.38-5.367.10.0356.20.1041100
5.36-7.596.90.0356.70.0981100
7.59-46.1456.30.0359.90.057199.6

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.8 Å34.35 Å
Translation2.8 Å34.35 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.20data scaling
PHASERphasing
PHENIX1.8_1069refinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.1001→42.618 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.3 / σ(F): 0 / Phase error: 20.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2253 876 5.97 %
Rwork0.1742 --
obs0.1772 14669 98.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 60.2381 Å2
Refinement stepCycle: LAST / Resolution: 3.1001→42.618 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4117 0 0 0 4117
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024168
X-RAY DIFFRACTIONf_angle_d0.5975600
X-RAY DIFFRACTIONf_dihedral_angle_d14.2341635
X-RAY DIFFRACTIONf_chiral_restr0.045635
X-RAY DIFFRACTIONf_plane_restr0.003737
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1001-3.29420.30621350.22592176X-RAY DIFFRACTION96
3.2942-3.54850.29751440.19882244X-RAY DIFFRACTION98
3.5485-3.90530.22871470.17962258X-RAY DIFFRACTION99
3.9053-4.46990.22571460.16092322X-RAY DIFFRACTION99
4.4699-5.62960.19131490.16532332X-RAY DIFFRACTION100
5.6296-42.62160.1941550.16162461X-RAY DIFFRACTION100

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