[English] 日本語
Yorodumi
- PDB-1hru: THE STRUCTURE OF THE YRDC GENE PRODUCT FROM E.COLI -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1hru
TitleTHE STRUCTURE OF THE YRDC GENE PRODUCT FROM E.COLI
ComponentsYRDC GENE PRODUCT
KeywordsUNKNOWN FUNCTION / protein folding / structural genomics / RNA / Sua5 / YrdC / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


L-threonylcarbamoyladenylate synthase / L-threonylcarbamoyladenylate synthase / tRNA threonylcarbamoyladenosine modification / regulation of translational fidelity / nucleotidyltransferase activity / rRNA processing / double-stranded RNA binding / tRNA binding / ATP binding / cytosol / cytoplasm
Similarity search - Function
Threonylcarbamoyl-AMP synthase / : / Threonylcarbamoyl-AMP synthase-like domain / Telomere recombination / YrdC-like domain profile. / DHBP synthase / DHBP synthase RibB-like alpha/beta domain superfamily / DHBP synthase / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Threonylcarbamoyl-AMP synthase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsTeplova, M. / Tereshko, V. / Sanishvili, R. / Joachimiak, A. / Bushueva, T. / Anderson, W.F. / Egli, M. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: Protein Sci. / Year: 2000
Title: The structure of the yrdC gene product from Escherichia coli reveals a new fold and suggests a role in RNA binding.
Authors: Teplova, M. / Tereshko, V. / Sanishvili, R. / Joachimiak, A. / Bushueva, T. / Anderson, W.F. / Egli, M.
History
DepositionDec 21, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 31, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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: YRDC GENE PRODUCT
B: YRDC GENE PRODUCT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,5804
Polymers41,3912
Non-polymers1902
Water6,954386
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.500, 71.650, 55.280
Angle α, β, γ (deg.)90.00, 103.25, 90.00
Int Tables number4
Cell settingmonoclinic
Space group name H-MP1211

-
Components

#1: Protein YRDC GENE PRODUCT / 20.8 KDA PROTEIN IN AROE-SMG INTERGENIC REGION


Mass: 20695.273 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: YRDC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21[DE3] / References: UniProt: P45748
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 386 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.82 Å3/Da / Density % sol: 56.31 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: sodium potassium phosphate, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 295.0K
Crystal grow
*PLUS
Details: used seeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15 mg/mlprotein1drop
20.6 Msodium potassium phosphate1reservoir
31

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9795, 0.9794, 0.9465
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Apr 26, 1999
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97951
20.97941
30.94651
ReflectionResolution: 1.96→30 Å / Num. all: 62780 / Num. obs: 62780 / % possible obs: 96.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.68 % / Biso Wilson estimate: 5.6 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 17.6
Reflection shellResolution: 1.96→2.03 Å / Redundancy: 3.65 % / Rmerge(I) obs: 0.486 / Mean I/σ(I) obs: 2.6 / Num. unique all: 23642 / % possible all: 99.8
Reflection
*PLUS
Num. measured all: 230966
Reflection shell
*PLUS
% possible obs: 99.8 %

-
Processing

Software
NameClassification
CNSrefinement
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 2→22.75 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 345209.17 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.214 5212 10.2 %RANDOM
Rwork0.202 ---
obs0.202 51213 83.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 54.84 Å2 / ksol: 0.354 e/Å3
Displacement parametersBiso mean: 25.8 Å2
Baniso -1Baniso -2Baniso -3
1-0.78 Å20 Å27.08 Å2
2---5.13 Å20 Å2
3---4.35 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.21 Å0.21 Å
Refinement stepCycle: LAST / Resolution: 2→22.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2845 0 10 386 3241
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d1.012
X-RAY DIFFRACTIONc_angle_deg2.4
X-RAY DIFFRACTIONc_dihedral_angle_d23.6
X-RAY DIFFRACTIONc_improper_angle_d1.06
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.236 780 10.3 %
Rwork0.217 6806 -
obs--74.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PAPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAWATER.TOP
X-RAY DIFFRACTION3PARION.TOP
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refinement
*PLUS
σ(F): 2 / % reflection Rfree: 10.2 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 25.8 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.06
LS refinement shell
*PLUS
Rfactor Rfree: 0.236 / % reflection Rfree: 10.3 % / Rfactor Rwork: 0.217

+
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