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- PDB-3kvh: Crystal structure of human protein syndesmos (NUDT16-like protein) -

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Basic information

Entry
Database: PDB / ID: 3kvh
TitleCrystal structure of human protein syndesmos (NUDT16-like protein)
ComponentsProtein syndesmos
KeywordsRNA BINDING PROTEIN / NUDT16-LIKE / NUDT16L1 / SYNDESMOS / NUDIX / RNA REGULATION / RNA-BINDING / STRUCTURAL GENOMICS CONSORTIUM / SGC / RNA DEGRADATION
Function / homology
Function and homology information


negative regulation of double-strand break repair via nonhomologous end joining / snoRNA binding / RNA 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 speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsTresaugues, L. / Siponen, M.I. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. ...Tresaugues, L. / Siponen, M.I. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Johansson, A. / Johansson, I. / Kallas, A. / Karlberg, T. / Kotenyova, T. / Kotzsch, A. / Kraulis, P. / Moche, M. / Nielsen, T.K. / Nyman, T. / Persson, C. / Roos, A.K. / Schuler, H. / Schutz, P. / Thorsell, A.G. / Van Den Berg, S. / Weigelt, J. / Welin, M. / Wisniewska, M. / Nordlund, P. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Crystal structure of human protein syndesmos (NUDT16L1)
Authors: Tresaugues, L. / Siponen, M.I. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Johansson, A. / ...Authors: Tresaugues, L. / Siponen, M.I. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Johansson, A. / Johansson, I. / Kallas, A. / Karlberg, T. / Kotenyova, T. / Kotzsch, A. / Kraulis, P. / Moche, M. / Nielsen, T.K. / Nyman, T. / Persson, C. / Roos, A.K. / Schuler, H. / Schutz, P. / Thorsell, A.G. / Van Den Berg, S. / Weigelt, J. / Welin, M. / Wisniewska, M. / Nordlund, P.
History
DepositionNov 30, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 19, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Sep 6, 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 / database_2 / pdbx_initial_refinement_model / pdbx_struct_special_symmetry / 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 / _struct_ref_seq_dif.details / _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: Protein syndesmos
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,0663
Polymers23,9391
Non-polymers1282
Water3,099172
1
A: Protein syndesmos
hetero molecules

A: Protein syndesmos
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,1336
Polymers47,8782
Non-polymers2554
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area4020 Å2
ΔGint-50 kcal/mol
Surface area18210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.811, 60.278, 60.483
Angle α, β, γ (deg.)90.00, 118.64, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-233-

HOH

21A-242-

HOH

31A-304-

HOH

41A-325-

HOH

51A-385-

HOH

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Components

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


Mass: 23938.902 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NUDT16L1, SDOS / Plasmid: pNIC-CH2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9BRJ7
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 172 / 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: 46.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M hepes pH 7.5, 20%w/v jeffamine M-600, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 1, 2009 / Details: mirrors
RadiationMonochromator: Si 111 double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→28.829 Å / Num. all: 23962 / Num. obs: 23914 / % possible obs: 99.8 % / Observed criterion σ(F): -3 / Redundancy: 3.6 % / Rmerge(I) obs: 0.069 / Rsym value: 0.058 / Net I/σ(I): 8.8
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.777 / Mean I/σ(I) obs: 1.9 / Rsym value: 0.649 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.5.0102refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3COU

3cou


Resolution: 1.7→27.01 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.95 / SU B: 4.875 / SU ML: 0.072 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.104 / ESU R Free: 0.103 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2169 1193 5 %RANDOM
Rwork0.18359 ---
obs0.18522 22718 99.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.166 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å20 Å20.12 Å2
2--1.13 Å20 Å2
3----0.93 Å2
Refinement stepCycle: LAST / Resolution: 1.7→27.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1506 0 7 172 1685
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0221575
X-RAY DIFFRACTIONr_bond_other_d0.0010.021098
X-RAY DIFFRACTIONr_angle_refined_deg1.0251.9752133
X-RAY DIFFRACTIONr_angle_other_deg0.8232665
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9965202
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.87722.20668
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.9615279
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0451515
X-RAY DIFFRACTIONr_chiral_restr0.0610.2243
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021738
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02339
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4771.5970
X-RAY DIFFRACTIONr_mcbond_other0.1011.5398
X-RAY DIFFRACTIONr_mcangle_it0.921553
X-RAY DIFFRACTIONr_scbond_it1.4213605
X-RAY DIFFRACTIONr_scangle_it2.214.5573
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.338 94 -
Rwork0.328 1643 -
obs--99.14 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.58360.1861-1.60290.9709-0.14383.1939-0.04950.0137-0.00190.0949-0.07840.06960.0113-0.17980.12790.0807-0.0238-0.00890.0501-0.00960.0714-11.045334.184213.5679
21.78120.2976-0.35712.36450.03692.6422-0.04-0.16440.02280.111-0.0428-0.03430.00580.12390.08270.01090.00150.00780.0557-0.00210.03111.53838.69788.6912
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A9 - 114
2X-RAY DIFFRACTION2A115 - 207

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