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- PDB-4zg0: Crystal structure of Mouse Syndesmos protein -

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Basic information

Entry
Database: PDB / ID: 4zg0
TitleCrystal structure of Mouse Syndesmos protein
ComponentsProtein syndesmos
KeywordsHYDROLASE / Nudix hydrolase / cytoplasmic protein / syndecan-4 cytoplasmic domain interactor
Function / homology
Function and homology information


negative regulation of double-strand break repair via nonhomologous end joining / snoRNA binding / nucleus
Similarity search - Function
: / U8 snoRNA-decapping enzyme-like / Nucleoside Triphosphate Pyrophosphohydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / NUDIX hydrolase-like domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Tudor-interacting repair regulator protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.006 Å
AuthorsLee, I. / Kim, H. / Yoo, J. / Cho, H. / Lee, W.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2015
Title: Crystal structure of syndesmos and its interaction with Syndecan-4 proteoglycan
Authors: Kim, H. / Yoo, J. / Lee, I. / Kang, Y.J. / Cho, H.S. / Lee, W.
History
DepositionApr 22, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 20, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 1, 2016Group: Database references
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein syndesmos
B: Protein syndesmos


Theoretical massNumber of molelcules
Total (without water)47,0052
Polymers47,0052
Non-polymers00
Water4,666259
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3040 Å2
ΔGint-21 kcal/mol
Surface area18600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.318, 68.701, 66.191
Angle α, β, γ (deg.)90.000, 103.930, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Protein syndesmos / NUDT16-like protein 1


Mass: 23502.262 Da / Num. of mol.: 2 / Fragment: UNP residues 8-204
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Nudt16l1, Sdos / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q8VHN8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 259 / 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: 2.27 Å3/Da / Density % sol: 45.88 %
Crystal growTemperature: 290 K / Method: batch mode / pH: 5.5 / Details: 0.2M Li sulfate, 0.1M Bis-Tris, 25%(m/w) PEG3350

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 5, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 26347 / % possible obs: 96.5 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 34.79
Reflection shellResolution: 2→2.07 Å / Redundancy: 3 % / Rmerge(I) obs: 0.155 / % possible all: 89.3

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
PDB_EXTRACT3.15data extraction
HKL-2000data processing
Cootmodel building
MOLREPphasing
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3COU

3cou


Resolution: 2.006→37.044 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.52 / Phase error: 22.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2254 1999 7.86 %random selection
Rwork0.1778 23425 --
obs0.1815 25424 96.01 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 86.24 Å2 / Biso mean: 30.1055 Å2 / Biso min: 14.03 Å2
Refinement stepCycle: final / Resolution: 2.006→37.044 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3047 0 0 259 3306
Biso mean---32.08 -
Num. residues----386
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083112
X-RAY DIFFRACTIONf_angle_d1.0874193
X-RAY DIFFRACTIONf_chiral_restr0.042459
X-RAY DIFFRACTIONf_plane_restr0.005539
X-RAY DIFFRACTIONf_dihedral_angle_d13.7961153
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0061-2.05630.22211180.1851385150381
2.0563-2.11190.25711380.19531613175194
2.1119-2.1740.25051450.19171692183797
2.174-2.24420.23511350.18991586172192
2.2442-2.32440.28071360.21241589172592
2.3244-2.41740.25941460.19551711185798
2.4174-2.52740.27781470.19691722186999
2.5274-2.66060.24961460.19091714186098
2.6606-2.82730.26951470.19751725187299
2.8273-3.04550.24981470.19481721186899
3.0455-3.35180.21831480.17917211869100
3.3518-3.83640.21091460.1691728187498
3.8364-4.83170.17721480.1391738188699
4.8317-37.05010.20031520.17281780193299

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