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- PDB-4mfv: Crystal structure of human CTNNBL1(residues 33~563) -

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Basic information

Entry
Database: PDB / ID: 4mfv
TitleCrystal structure of human CTNNBL1(residues 33~563)
ComponentsBeta-catenin-like protein 1
KeywordsGENE REGULATION / ARM 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 / nucleus / membrane / 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: 2.92 Å
AuthorsAhn, J.W. / Kim, S. / Kim, K.J.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Structural insights into the novel ARM-repeat protein CTNNBL1 and its association with the hPrp19-CDC5L complex
Authors: Ahn, J.W. / Kim, S. / Kim, E.J. / Kim, Y.J. / Kim, K.J.
History
DepositionAug 28, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 12, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 23, 2014Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Revision 1.3Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

Downloads & links

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Assembly

Deposited unit
A: Beta-catenin-like protein 1
B: Beta-catenin-like protein 1


Theoretical massNumber of molelcules
Total (without water)123,3612
Polymers123,3612
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)90.037, 90.037, 175.746
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31

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Components

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


Mass: 61680.375 Da / Num. of mol.: 2 / Fragment: UNP residues 33-563
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: C20orf33, CTNNBL1, PP8304 / Plasmid: pPosKJ / Production host: Escherichia coli (E. coli) / Strain (production host): B834 / 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: 3.33 Å3/Da / Density % sol: 63.11 % / Mosaicity: 1.039 °
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 9.5
Details: PEG8000, CAPs, NaCl, pH 9.5, vapor diffusion, hanging drop, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97985 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Feb 25, 2009
RadiationMonochromator: Double Crystal Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97985 Å / Relative weight: 1
ReflectionRedundancy: 7.2 % / Number: 233350 / Rmerge(I) obs: 0.078 / Χ2: 2.83 / D res high: 2.92 Å / D res low: 50 Å / Num. obs: 32475 / % possible obs: 94.1
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
2.923.0277.610.2660.7183.1
3.023.1587.210.2360.7954.1
3.153.2994.810.2010.9915.7
3.293.4696.810.1611.2847.1
3.463.689610.141.4877.4
3.683.9696.310.1132.1418
3.964.3696.510.0883.0958.6
4.364.9997.810.083.8239.1
4.996.2998.910.0824.3698.6
6.295098.910.0525.0828.8
ReflectionResolution: 2.92→46.88 Å / Num. all: 34493 / Num. obs: 32475 / % possible obs: 94.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 7.2 % / Rmerge(I) obs: 0.078 / Rsym value: 0.062 / Net I/σ(I): 30.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allRsym value% possible all
2.92-3.023.10.2662.626930.34277.6
3.02-3.154.10.2363.629740.28587.2
3.15-3.295.70.2015.932800.23394.8
3.29-3.467.10.16110.433790.17696.8
3.46-3.687.40.1413.532410.15296
3.68-3.9680.1132233750.1296.3
3.96-4.368.60.08838.832990.09396.5
4.36-4.999.10.0854.734020.08497.8
4.99-6.298.60.0825534000.08598.9
6.29-508.80.05287.734320.05698.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4MFU

4mfu


Resolution: 2.92→46.84 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.872 / WRfactor Rfree: 0.2808 / WRfactor Rwork: 0.2201 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7769 / SU B: 21.164 / SU ML: 0.386 / SU Rfree: 0.464 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.468 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.3053 1635 5 %RANDOM
Rwork0.2328 ---
obs0.2364 32463 94.12 %-
all-34477 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 178.28 Å2 / Biso mean: 88.826 Å2 / Biso min: 20 Å2
Baniso -1Baniso -2Baniso -3
1--0.77 Å2-0.77 Å2-0 Å2
2---0.77 Å2-0 Å2
3---2.51 Å2
Refinement stepCycle: LAST / Resolution: 2.92→46.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7866 0 0 0 7866
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0197970
X-RAY DIFFRACTIONr_bond_other_d0.0010.027870
X-RAY DIFFRACTIONr_angle_refined_deg1.4811.98210716
X-RAY DIFFRACTIONr_angle_other_deg0.864318130
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5965976
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.9825.149404
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.768151590
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.8651558
X-RAY DIFFRACTIONr_chiral_restr0.0780.21220
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.028952
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021734
X-RAY DIFFRACTIONr_mcbond_it5.7988.9783910
X-RAY DIFFRACTIONr_mcbond_other5.7988.9773909
X-RAY DIFFRACTIONr_mcangle_it9.0413.4594884
LS refinement shellResolution: 2.92→2.999 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.414 99 -
Rwork0.347 1817 -
all-1916 -
obs--74.81 %

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