[English] 日本語
Yorodumi
- PDB-3da5: Crystal Structure of Piwi/Argonaute/Zwille(PAZ) domain from Therm... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3da5
TitleCrystal Structure of Piwi/Argonaute/Zwille(PAZ) domain from Thermococcus thioreducens
ComponentsArgonaute
KeywordsRNA BINDING PROTEIN / PAZ domain / RNA binding / SH3-like barrel
Function / homology
Function and homology information


Cathepsin B; Chain A - #180 / Argonaute PAZ domain, archaea / PAZ domain / PAZ domain superfamily / PAZ domain profile. / PAZ domain / Cathepsin B; Chain A / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Biological speciesThermococcus thioreducens (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.94 Å
AuthorsHughes, R.C. / Ng, J.D.
CitationJournal: to be published
Title: Crystal Structure of Piwi/Argonaute/Zwille(PAZ) domain from Thermococcus thioreducens
Authors: Hughes, R.C. / Ng, J.D.
History
DepositionMay 28, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 29, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Aug 30, 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: Argonaute
B: Argonaute


Theoretical massNumber of molelcules
Total (without water)30,8712
Polymers30,8712
Non-polymers00
Water37821
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.392, 60.896, 66.447
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Argonaute


Mass: 15435.667 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus thioreducens (archaea) / Strain: OGL-20 / Gene: Ago-PAZ / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: D0VWU1*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / 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: 1.88 Å3/Da / Density % sol: 34.47 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 8.5
Details: Dioxane, PEG8000, pH 8.5, vapor diffusion, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 1, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.94→44.9 Å / Num. obs: 14536 / % possible obs: 81.1 % / Observed criterion σ(F): 1.7 / Observed criterion σ(I): 3 / Redundancy: 4.9 % / Biso Wilson estimate: 32.7 Å2 / Rmerge(I) obs: 0.046 / Rsym value: 0.046 / Net I/σ(I): 30.7
Reflection shellResolution: 1.94→2.01 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 3.23 / Num. unique all: 1048 / Rsym value: 0.32 / % possible all: 59.4

-
Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.22 Å44.9 Å
Translation2.22 Å44.9 Å

-
Processing

Software
NameVersionClassificationNB
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1U04

1u04


Resolution: 1.94→44.9 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.936 / SU B: 5.393 / SU ML: 0.158 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.274 / ESU R Free: 0.217 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.267 730 5 %RANDOM
Rwork0.216 ---
obs0.218 14511 81.13 %-
all-17886 --
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: 34.363 Å2
Baniso -1Baniso -2Baniso -3
1-0.32 Å20 Å20 Å2
2--0.7 Å20 Å2
3----1.03 Å2
Refinement stepCycle: LAST / Resolution: 1.94→44.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2016 0 0 21 2037
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0222073
X-RAY DIFFRACTIONr_bond_other_d0.0010.021420
X-RAY DIFFRACTIONr_angle_refined_deg1.7721.952817
X-RAY DIFFRACTIONr_angle_other_deg0.99133447
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.1835240
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.24823.981108
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.915344
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.261513
X-RAY DIFFRACTIONr_chiral_restr0.1150.2295
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022286
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02430
X-RAY DIFFRACTIONr_nbd_refined0.2380.2382
X-RAY DIFFRACTIONr_nbd_other0.1990.21396
X-RAY DIFFRACTIONr_nbtor_refined0.1880.21000
X-RAY DIFFRACTIONr_nbtor_other0.090.21045
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1220.247
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0090.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.240.226
X-RAY DIFFRACTIONr_symmetry_vdw_other0.250.257
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2730.25
X-RAY DIFFRACTIONr_mcbond_it1.4591.51261
X-RAY DIFFRACTIONr_mcbond_other0.3181.5476
X-RAY DIFFRACTIONr_mcangle_it2.27621964
X-RAY DIFFRACTIONr_scbond_it2.9443965
X-RAY DIFFRACTIONr_scangle_it4.4194.5853
LS refinement shellResolution: 1.94→1.988 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.278 47 -
Rwork0.262 704 -
all-751 -
obs--57.28 %

+
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