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- PDB-2ckk: High resolution crystal structure of the human kin17 C-terminal d... -

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Basic information

Entry
Database: PDB / ID: 2ckk
TitleHigh resolution crystal structure of the human kin17 C-terminal domain containing a kow motif
ComponentsKIN17
KeywordsNUCLEAR PROTEIN / BETA BARREL / RIBOSOMAL PROTEIN / RIBONUCLEOPROTEIN
Function / homology
Function and homology information


Protein methylation / nuclear matrix / mRNA processing / double-stranded DNA binding / DNA recombination / DNA replication / intracellular membrane-bounded organelle / DNA repair / DNA damage response / protein-containing complex ...Protein methylation / nuclear matrix / mRNA processing / double-stranded DNA binding / DNA recombination / DNA replication / intracellular membrane-bounded organelle / DNA repair / DNA damage response / protein-containing complex / DNA binding / RNA binding / nucleoplasm / nucleus / metal ion binding / cytoplasm
Similarity search - Function
DNA/RNA-binding protein Kin17, WH-like domain / KIN17-like protein / DNA/RNA-binding protein KIN17, WH-like domain superfamily / KN17, SH3-like C-terminal domain / Kin17, KOW domain / Domain of Kin17 curved DNA-binding protein / KN17 SH3-like C-terminal domain / Domain of Kin17 curved DNA-binding protein / SH3 type barrels. - #30 / SH3 type barrels. - #140 ...DNA/RNA-binding protein Kin17, WH-like domain / KIN17-like protein / DNA/RNA-binding protein KIN17, WH-like domain superfamily / KN17, SH3-like C-terminal domain / Kin17, KOW domain / Domain of Kin17 curved DNA-binding protein / KN17 SH3-like C-terminal domain / Domain of Kin17 curved DNA-binding protein / SH3 type barrels. - #30 / SH3 type barrels. - #140 / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. / SH3 type barrels. / Ribosomal protein L2, domain 2 / Roll / Mainly Beta
Similarity search - Domain/homology
ACETATE ION / IODIDE ION / DNA/RNA-binding protein KIN17
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.45 Å
Authorsle Maire, A. / Schiltz, M. / Pinon-Lataillade, G. / Stura, E. / Couprie, J. / Gondry, M. / Angulo-Mora, J. / Zinn-Justin, S.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: A Tandem of SH3-Like Domains Participates in RNA Binding in Kin17, a Human Protein Activated in Response to Genotoxics.
Authors: Le Maire, A. / Schiltz, M. / Stura, E.A. / Pinon-Lataillade, G. / Couprie, J. / Moutiez, M. / Gondry, M. / Angulo, J.F. / Zinn-Justin, S.
History
DepositionApr 20, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 4, 2006Provider: repository / Type: Initial release
Revision 1.1Jan 30, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.method
Revision 1.2Feb 6, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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
A: KIN17
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,93114
Polymers14,3491
Non-polymers1,58213
Water3,801211
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)45.752, 46.309, 60.798
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 KIN17 / HSKIN17 PROTEIN / KIN / ANTIGENIC DETERMINANT OF RECA PROTEIN HOMOLOG


Mass: 14348.669 Da / Num. of mol.: 1 / Fragment: C-TERMINAL DOMAIN, RESIDUES 268-393
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: O60870
#2: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: I
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 211 / 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: 2.3 Å3/Da / Density % sol: 45 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.3
Details: VAPOR DIFFUSION, SITTING DROP 10% ETHYLENE GLYCOL, 27% PEG 6000, 500 MM LICL, 100 MM SODIUM ACETATE PH 6.3 290 K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 1.13
DetectorType: MARRESEARCH / Detector: CCD / Date: Aug 27, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.13 Å / Relative weight: 1
ReflectionResolution: 1.81→99 Å / Num. obs: 21818 / % possible obs: 95 % / Observed criterion σ(I): 2 / Redundancy: 7 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 23.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALEPACKdata scaling
SHARPphasing
RefinementMethod to determine structure: SIRAS / Resolution: 1.45→32.62 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.958 / SU B: 2.035 / SU ML: 0.036 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.064 / ESU R Free: 0.06 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.175 1204 5.1 %RANDOM
Rwork0.137 ---
obs0.139 22249 98.9 %-
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: 15.31 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å20 Å2
2---0.05 Å20 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.45→32.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms949 0 16 211 1176
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.022970
X-RAY DIFFRACTIONr_bond_other_d0.0020.02938
X-RAY DIFFRACTIONr_angle_refined_deg1.5191.9981304
X-RAY DIFFRACTIONr_angle_other_deg1.96732199
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7045119
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.74724.86537
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.08215200
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.011155
X-RAY DIFFRACTIONr_chiral_restr0.0910.2153
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021031
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02169
X-RAY DIFFRACTIONr_nbd_refined0.2050.2160
X-RAY DIFFRACTIONr_nbd_other0.1910.2999
X-RAY DIFFRACTIONr_nbtor_refined0.1720.2469
X-RAY DIFFRACTIONr_nbtor_other0.0890.2641
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1460.2134
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.070.23
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2460.229
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1790.217
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2351.5597
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.8942971
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.9093396
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.5294.5333
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.45→1.48 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.358 62
Rwork0.225 1391

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