[English] 日本語
Yorodumi
- PDB-4h7w: Crystal Structure of Human C16orf57 -

+
Open data


ID or keywords:

Loading...

-
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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 °

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more