[English] 日本語
Yorodumi
- PDB-2qrx: Crystal structure of Drosophila melanogaster Translin protein -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2qrx
TitleCrystal structure of Drosophila melanogaster Translin protein
ComponentsGM27569p
KeywordsDNA BINDING PROTEIN / D. Melanogaster / Translin / Crystal structur
Function / homology
Function and homology information


negative regulation of circadian sleep/wake cycle, sleep / behavioral response to starvation / Small interfering RNA (siRNA) biogenesis / RNA metabolic process / regulatory ncRNA-mediated post-transcriptional gene silencing / single-stranded DNA binding / sequence-specific DNA binding / protein stabilization / protein homodimerization activity / RNA binding ...negative regulation of circadian sleep/wake cycle, sleep / behavioral response to starvation / Small interfering RNA (siRNA) biogenesis / RNA metabolic process / regulatory ncRNA-mediated post-transcriptional gene silencing / single-stranded DNA binding / sequence-specific DNA binding / protein stabilization / protein homodimerization activity / RNA binding / membrane / identical protein binding / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Translin; domain 1 / Translin, N-terminal / Translin, C-terminal / Translin / Translin family / Translin superfamily / Translin family / Immunoglobulin FC, subunit C / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces ...Translin; domain 1 / Translin, N-terminal / Translin, C-terminal / Translin / Translin family / Translin superfamily / Translin family / Immunoglobulin FC, subunit C / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.6 Å
AuthorsGupta, G.D. / Makde, R.D. / Kumar, V.
CitationJournal: Febs J. / Year: 2008
Title: Crystal structures of Drosophila mutant translin and characterization of translin variants reveal the structural plasticity of translin proteins.
Authors: Gupta, G.D. / Makde, R.D. / Rao, B.J. / Kumar, V.
History
DepositionJul 30, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 5, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Nov 10, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: GM27569p


Theoretical massNumber of molelcules
Total (without water)27,0481
Polymers27,0481
Non-polymers00
Water0
1
A: GM27569p

A: GM27569p

A: GM27569p

A: GM27569p


Theoretical massNumber of molelcules
Total (without water)108,1914
Polymers108,1914
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_565-x,-y+1,z1
crystal symmetry operation9_555-x,-x+y,-z+1/31
crystal symmetry operation12_565x,x-y+1,-z+1/31
Buried area9290 Å2
ΔGint-67 kcal/mol
Surface area35320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)152.778, 152.778, 94.007
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222

-
Components

#1: Protein GM27569p / translin protein / CG11761-PA


Mass: 27047.820 Da / Num. of mol.: 1 / Mutation: P168S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: translin / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q7JVK6

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 5.9 Å3/Da / Density % sol: 78.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 2.0M ammonium sulfate, 2% MPD, 5% glycerol, 100mM MES buffer, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Sep 19, 2004 / Details: OSMIC mirror
RadiationMonochromator: Ni filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.6→20 Å / Num. all: 7311 / Num. obs: 7311 / % possible obs: 93.7 % / Observed criterion σ(I): 0 / Redundancy: 2.8 % / Biso Wilson estimate: 51 Å2 / Rmerge(I) obs: 0.106 / Net I/σ(I): 13.3
Reflection shellResolution: 3.6→3.79 Å / Redundancy: 3 % / Rmerge(I) obs: 0.412 / Mean I/σ(I) obs: 2.8 / Num. unique all: 1012 / % possible all: 91.4

-
Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1J1J

1j1j


Resolution: 3.6→20 Å / Cor.coef. Fo:Fc: 0.912 / Cor.coef. Fo:Fc free: 0.898 / SU B: 17.33 / SU ML: 0.27 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1 / ESU R Free: 0.43 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.249 335 4.5 %RANDOM
Rwork0.215 ---
obs0.217 7308 100 %-
all-7311 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 65.4 Å2
Baniso -1Baniso -2Baniso -3
1--4.16 Å2-2.08 Å20 Å2
2---4.16 Å20 Å2
3---6.24 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.432 Å1 Å
Refinement stepCycle: LAST / Resolution: 3.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1502 0 0 0 1502
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0221527
X-RAY DIFFRACTIONr_angle_refined_deg1.8041.9552063
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3375184
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.07924.35978
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.14615278
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.6321510
X-RAY DIFFRACTIONr_chiral_restr0.1170.2237
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021141
X-RAY DIFFRACTIONr_nbd_refined0.2780.2735
X-RAY DIFFRACTIONr_nbtor_refined0.3380.21085
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1850.257
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2190.230
X-RAY DIFFRACTIONr_mcbond_it0.781.5932
X-RAY DIFFRACTIONr_mcangle_it1.51221477
X-RAY DIFFRACTIONr_scbond_it2.0683661
X-RAY DIFFRACTIONr_scangle_it3.7574.5586
LS refinement shellResolution: 3.601→3.691 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.238 25 -
Rwork0.239 462 -
obs-462 90.02 %

+
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