[English] 日本語
Yorodumi
- PDB-5cow: C. remanei PGL-1 Dimerization Domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5cow
TitleC. remanei PGL-1 Dimerization Domain
ComponentsPutative uncharacterized protein
KeywordsHYDROLASE / guanosine endonuclease / dimer / P-granule
Function / homologyribonuclease T1 activity / ribonuclease T1 / oogenesis / RNA endonuclease activity / lyase activity / RNA binding / identical protein binding / Guanyl-specific ribonuclease pgl-1
Function and homology information
Biological speciesCaenorhabditis remanei (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.6 Å
AuthorsAoki, S.T. / Bingman, C.A. / Wickens, M. / Kimble, J.E.
Funding support United States, 2items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD)5F32HD071692 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2016
Title: PGL germ granule assembly protein is a base-specific, single-stranded RNase.
Authors: Aoki, S.T. / Kershner, A.M. / Bingman, C.A. / Wickens, M. / Kimble, J.
History
DepositionJul 20, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 3, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 10, 2016Group: Database references
Revision 1.2Sep 6, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 1, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.4Nov 20, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6295
Polymers28,3131
Non-polymers3164
Water3,855214
1
A: Putative uncharacterized protein
hetero molecules

A: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,25810
Polymers56,6252
Non-polymers6338
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_675x-y+1,-y+2,-z+2/31
Buried area2480 Å2
ΔGint-7 kcal/mol
Surface area20930 Å2
MethodPISA
2
A: Putative uncharacterized protein
hetero molecules

A: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,25810
Polymers56,6252
Non-polymers6338
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
Buried area1810 Å2
ΔGint-7 kcal/mol
Surface area21600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.610, 89.610, 51.460
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-776-

HOH

21A-793-

HOH

31A-812-

HOH

DetailsDimer confirmed by gel filtration, chemical crosslinking

-
Components

#1: Protein Putative uncharacterized protein


Mass: 28312.645 Da / Num. of mol.: 1 / Fragment: UNP Residues 203-464 / Mutation: deletion, residues 321-335
Source method: isolated from a genetically manipulated source
Details: codon optimized gene for E. coli expression / Source: (gene. exp.) Caenorhabditis remanei (invertebrata) / Gene: CRE_08178 / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta-2 / References: UniProt: E3M3V1
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 214 / 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: 2.22 Å3/Da / Density % sol: 44.61 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 100 mM PIPES pH 6.0, 24-27% PEG 4K, 200 mM LiSO4

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Dec 8, 2013
RadiationMonochromator: DIAMOND (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.6→38.81 Å / Num. obs: 31737 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 10.9 % / Biso Wilson estimate: 22.95 Å2 / Rmerge F obs: 0.999 / Rmerge(I) obs: 0.079 / Rrim(I) all: 0.083 / Χ2: 1.023 / Net I/σ(I): 17.54 / Num. measured all: 347288
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.6-1.620.5831.921.4212169114311432.018100
1.62-1.670.6571.6321.7429168263226311.711100
1.67-1.720.8171.1522.4725992234723461.209100
1.72-1.770.8810.9283.1622923206620660.973100
1.77-1.830.9070.7184.124382219921990.753100
1.83-1.90.9560.5025.8925073226022600.526100
1.9-1.970.980.3518.1121523193619360.368100
1.97-2.060.9890.22711.9723371211921190.239100
2.06-2.150.9940.15716.2819714178717870.164100
2.15-2.260.9960.11920.1419748179517950.124100
2.26-2.390.9970.09324.3919169174217420.098100
2.39-2.540.9980.0827.3817290157215720.084100
2.54-2.730.9980.0731.0617275157615760.074100
2.73-2.970.9990.05935.215654143014300.062100
2.97-3.280.9990.05339.8213848128712870.056100
3.28-3.710.9990.04843.0212397117011700.05100
3.71-4.370.9990.04246.0210637100810080.044100
4.37-5.610.9990.03846.0889588598590.04100
5.61-910.03346.8562065995990.034100
9-38.810.9990.03142.1317912142120.03399.1

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
PHENIXrefinement
XSCALEdata scaling
PHASERphasing
PDB_EXTRACT3.15data extraction
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5CV3

5cv3


Resolution: 1.6→38.802 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1874 2013 6.35 %
Rwork0.1647 29694 -
obs0.1662 31707 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 100.44 Å2 / Biso mean: 30.3225 Å2 / Biso min: 14.59 Å2
Refinement stepCycle: final / Resolution: 1.6→38.802 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1898 0 18 214 2130
Biso mean--64.12 38.56 -
Num. residues----234
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072023
X-RAY DIFFRACTIONf_angle_d0.9932752
X-RAY DIFFRACTIONf_chiral_restr0.043317
X-RAY DIFFRACTIONf_plane_restr0.005348
X-RAY DIFFRACTIONf_dihedral_angle_d13.138759
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.6-1.640.30951420.26620802222
1.64-1.68440.30561410.248321142255
1.6844-1.73390.25111440.229820892233
1.7339-1.78990.23441420.215620942236
1.7899-1.85390.25571400.192520962236
1.8539-1.92810.21831410.174421102251
1.9281-2.01580.20021440.16520992243
2.0158-2.12210.20051460.16221172263
2.1221-2.25510.17971410.151221222263
2.2551-2.42910.18191450.161721192264
2.4291-2.67350.18861420.172421282270
2.6735-3.06030.22021460.170421402286
3.0603-3.85510.17611480.152321532301
3.8551-38.81370.14131510.144122332384

+
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