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- PDB-4h7w: Crystal Structure of Human C16orf57 -

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Basic information

Entry
Database: PDB / ID: 4h7w
TitleCrystal Structure of Human C16orf57
ComponentsUPF0406 protein C16orf57
KeywordsUNKNOWN FUNCTION / 2H Phosphoesterase
Function / homology
Function and homology information


poly(U)-specific exoribonuclease activity, producing 3' uridine cyclic phosphate ends / U6 snRNA 3'-end processing / snRNA 3'-end processing / intercellular bridge / RNA splicing / Lyases; Phosphorus-oxygen lyases / 3'-5'-RNA exonuclease activity / lyase activity / nucleoplasm / nucleus
Similarity search - Function
U6 snRNA phosphodiesterase 1 / Uncharacterised conserved protein / Cyclic Phosphodiesterase; Chain: A, / Cyclic phosphodiesterase / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
U6 snRNA phosphodiesterase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.1 Å
AuthorsHilcenko, C. / Simpson, P.J. / Warren, A.J.
CitationJournal: Blood / Year: 2013
Title: Aberrant 3' oligoadenylation of spliceosomal U6 small nuclear RNA in poikiloderma with neutropenia.
Authors: Hilcenko, C. / Simpson, P.J. / Finch, A.J. / Bowler, F.R. / Churcher, M.J. / Jin, L. / Packman, L.C. / Shlien, A. / Campbell, P. / Kirwan, M. / Dokal, I. / Warren, A.J.
History
DepositionSep 21, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 6, 2013Provider: repository / Type: Initial release
Revision 1.1May 22, 2013Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: UPF0406 protein C16orf57
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6863
Polymers22,5591
Non-polymers1282
Water3,657203
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.247, 51.070, 48.013
Angle α, β, γ (deg.)90.00, 107.44, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein UPF0406 protein C16orf57


Mass: 22558.875 Da / Num. of mol.: 1 / Fragment: UNP residues 73-265
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: C16orf57 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): C41 (DE3) / References: UniProt: Q9BQ65
#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.: 203 / 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: 2.24 Å3/Da / Density % sol: 45.15 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 25% PEG 4000, 0.2 M ammonium sulphate, 0.1 M Na citrate pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å
DetectorType: ADSC / Detector: CCD / Date: May 13, 2011
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.1→45.81 Å / Num. obs: 79339 / % possible obs: 99 % / Redundancy: 5.2 % / Biso Wilson estimate: 7.53 Å2 / Rmerge(I) obs: 0.076 / Rsym value: 0.076 / Net I/σ(I): 12
Reflection shellResolution: 1.1→1.16 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.324 / Mean I/σ(I) obs: 2.3 / Num. unique all: 11429 / Rsym value: 0.324 / % possible all: 99

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Processing

Software
NameVersionClassification
SHARPphasing
REFMAC5.6.0117refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SAD / Resolution: 1.1→45.81 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.97 / SU B: 0.664 / SU ML: 0.015 / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / ESU R: 0.026 / ESU R Free: 0.027 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.15434 3982 5 %RANDOM
Rwork0.13163 ---
obs0.13276 75335 98.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.759 Å2
Baniso -1Baniso -2Baniso -3
1-0.22 Å20 Å20.09 Å2
2---0.05 Å20 Å2
3----0.12 Å2
Refinement stepCycle: LAST / Resolution: 1.1→45.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1538 0 7 203 1748
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.021700
X-RAY DIFFRACTIONr_bond_other_d0.0030.021149
X-RAY DIFFRACTIONr_angle_refined_deg2.2251.9392330
X-RAY DIFFRACTIONr_angle_other_deg1.74432809
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3675220
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.11323.37286
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.89415298
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.541511
X-RAY DIFFRACTIONr_chiral_restr0.1350.2261
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.021909
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02382
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr8.41432849
X-RAY DIFFRACTIONr_sphericity_free40.743555
X-RAY DIFFRACTIONr_sphericity_bonded12.55652939
LS refinement shellResolution: 1.103→1.132 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 291 -
Rwork0.265 5419 -
obs--97.17 %
Refinement TLS params.Method: refined / Origin x: -5.989 Å / Origin y: 13.484 Å / Origin z: 36.871 Å
111213212223313233
T0.0047 Å2-0 Å2-0.0006 Å2-0.0019 Å2-0 Å2--0.0046 Å2
L0.0028 °20.0039 °20.0004 °2-0.0089 °2-0.0005 °2--0.0004 °2
S-0.0004 Å °0.0003 Å °-0.0003 Å °-0.0015 Å °0.0004 Å °-0.0001 Å °0.0002 Å °0.0002 Å °-0 Å °

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