[English] 日本語
Yorodumi
- PDB-3h38: The structure of CCA-adding enzyme apo form II -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3h38
TitleThe structure of CCA-adding enzyme apo form II
ComponentsTRNA nucleotidyl transferase-related protein
KeywordsTRANSFERASE / TRANSFERASE/RNA / Nucleotide-binding / Nucleotidyltransferase / RNA-binding
Function / homology
Function and homology information


RNA processing / nucleotidyltransferase activity / tRNA binding / ATP binding / metal ion binding
Similarity search - Function
: / cca-adding enzyme, domain 2 / cca-adding enzyme, domain 2 / tRNA nucleotidyltransferase/poly(A) polymerase, RNA and SrmB- binding domain / Probable RNA and SrmB- binding site of polymerase A / Poly A polymerase, head domain / Poly A polymerase head domain / DDH domain / DHH family / DHH phosphoesterase superfamily ...: / cca-adding enzyme, domain 2 / cca-adding enzyme, domain 2 / tRNA nucleotidyltransferase/poly(A) polymerase, RNA and SrmB- binding domain / Probable RNA and SrmB- binding site of polymerase A / Poly A polymerase, head domain / Poly A polymerase head domain / DDH domain / DHH family / DHH phosphoesterase superfamily / DHHA1 domain / DHHA1 domain / Domain in cystathionine beta-synthase and other proteins. / CBS domain superfamily / CBS domain / CBS domain / CBS domain profile. / Beta Polymerase, domain 2 / Beta Polymerase; domain 2 / Nucleotidyltransferase superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
tRNA nucleotidyl transferase-related protein
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.37 Å
AuthorsToh, Y. / Tomita, K.
CitationJournal: Embo J. / Year: 2009
Title: Mechanism for the definition of elongation and termination by the class II CCA-adding enzyme
Authors: Toh, Y. / Takeshita, D. / Numata, T. / Fukai, S. / Nureki, O. / Tomita, K.
History
DepositionApr 16, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 13, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 5, 2014Group: Database references
Revision 1.3Nov 1, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: TRNA nucleotidyl transferase-related protein


Theoretical massNumber of molelcules
Total (without water)51,5311
Polymers51,5311
Non-polymers00
Water1,49583
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)173.348, 50.455, 69.871
Angle α, β, γ (deg.)90.00, 91.00, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein TRNA nucleotidyl transferase-related protein / tRNA nucleotidyltransferase / tRNA adenyl-/cytidyl-transferase / tRNA CCA-pyrophosphorylase / tRNA-NT


Mass: 51530.617 Da / Num. of mol.: 1 / Fragment: UNP residues 437-863
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Plasmid: pET-22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9WZH4, EC: 2.7.7.25
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 83 / 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: 2.96 Å3/Da / Density % sol: 58.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.1
Details: 10% PEG 4000, 0.2M KCl, 5mM magnesium chloride, 0.05M HEPES pH8.1 , VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 27, 2005
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.37→50 Å / Num. obs: 23735 / % possible obs: 95.5 % / Redundancy: 2.8 % / Biso Wilson estimate: 35.85 Å2 / Rsym value: 0.082 / Net I/σ(I): 17.1
Reflection shellResolution: 2.37→2.45 Å / Redundancy: 2 % / Mean I/σ(I) obs: 2.6 / Num. unique all: 2187 / Rsym value: 0.286 / % possible all: 88.5

-
Processing

Software
NameVersionClassification
ADSCQuantumdata collection
AMoREphasing
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3H37

3h37


Resolution: 2.37→43.33 Å / SU ML: 0.79 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2662 1200 5.06 %RANDOM
Rwork0.2113 ---
obs0.2142 23733 95.31 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 37.796 Å2 / ksol: 0.325 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-13.436 Å2-0 Å21.378 Å2
2---5.158 Å20 Å2
3----10 Å2
Refinement stepCycle: LAST / Resolution: 2.37→43.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3493 0 0 83 3576
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0153560
X-RAY DIFFRACTIONf_angle_d1.7044788
X-RAY DIFFRACTIONf_chiral_restr0.118531
X-RAY DIFFRACTIONf_plane_restr0.009611
X-RAY DIFFRACTIONf_dihedral_angle_d21.1791367
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3697-2.46460.34081230.26622281X-RAY DIFFRACTION87
2.4646-2.57670.30481210.25462370X-RAY DIFFRACTION91
2.5767-2.71260.30461300.24042438X-RAY DIFFRACTION94
2.7126-2.88250.27761470.23072450X-RAY DIFFRACTION94
2.8825-3.1050.27871170.23042552X-RAY DIFFRACTION97
3.105-3.41730.26891380.22782538X-RAY DIFFRACTION98
3.4173-3.91160.26321370.19822612X-RAY DIFFRACTION99
3.9116-4.92710.22651450.17072595X-RAY DIFFRACTION99
4.9271-43.33760.24471420.1952697X-RAY DIFFRACTION99

+
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