[English] 日本語
Yorodumi
- PDB-3bgy: Triclinic structure of Mimivirus Capping Enzyme Triphosphatase at... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3bgy
TitleTriclinic structure of Mimivirus Capping Enzyme Triphosphatase at 1.65 A
ComponentsPolynucleotide 5'-triphosphatase
KeywordsHYDROLASE / VIRAL PROTEIN / RNA capping / Tunnel Triphsophatase / Metalloenzyme / Beta Barrel / mRNA capping / mRNA processing / Multifunctional enzyme / Nucleotidyltransferase / S-adenosyl-L-methionine / Transferase / Virion
Function / homology
Function and homology information


mRNA 5'-triphosphate monophosphatase activity / mRNA 5'-phosphatase / polynucleotide 5'-phosphatase activity / virion component / mRNA guanylyltransferase activity / mRNA guanylyltransferase / mRNA (guanine-N7)-methyltransferase / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / GTP binding / RNA binding
Similarity search - Function
mRNA triphosphatase Cet1-like / mRNA triphosphatase Cet1-like / mRNA triphosphatase Cet1-like superfamily / mRNA Triphosphatase Cet1; Chain A / mRNA (guanine-N(7))-methyltransferase domain / mRNA cap guanine-N7 methyltransferase / mRNA (guanine-N(7))-methyltransferase domain / mRNA (guanine-N(7)-)-methyltransferase (EC 2.1.1.56) domain profile. / CYTH-like domain superfamily / S-adenosyl-L-methionine-dependent methyltransferase superfamily ...mRNA triphosphatase Cet1-like / mRNA triphosphatase Cet1-like / mRNA triphosphatase Cet1-like superfamily / mRNA Triphosphatase Cet1; Chain A / mRNA (guanine-N(7))-methyltransferase domain / mRNA cap guanine-N7 methyltransferase / mRNA (guanine-N(7))-methyltransferase domain / mRNA (guanine-N(7)-)-methyltransferase (EC 2.1.1.56) domain profile. / CYTH-like domain superfamily / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Nucleic acid-binding, OB-fold / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Probable mRNA-capping enzyme
Similarity search - Component
Biological speciesAcanthamoeba polyphaga mimivirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.65 Å
AuthorsSmith, P. / Bennaroch, D. / Shuman, S.
CitationJournal: To be Published
Title: Triclinic structure of Mimivirus Capping Enzyme Triphosphatase at 1.65 A
Authors: Benarroch, D. / Smith, P. / Shuman, S.
History
DepositionNov 27, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 1, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Polynucleotide 5'-triphosphatase
B: Polynucleotide 5'-triphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,4167
Polymers55,1212
Non-polymers2955
Water10,449580
1
A: Polynucleotide 5'-triphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7374
Polymers27,5601
Non-polymers1773
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Polynucleotide 5'-triphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,6783
Polymers27,5601
Non-polymers1182
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)39.640, 48.460, 69.700
Angle α, β, γ (deg.)74.62, 86.48, 76.36
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein Polynucleotide 5'-triphosphatase


Mass: 27560.297 Da / Num. of mol.: 2 / Fragment: Residues 1-237
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acanthamoeba polyphaga mimivirus / Genus: Mimivirus / Gene: YP_142736 / Plasmid: Pet28a-smt3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Codon Plus / References: UniProt: Q5UQX1, polynucleotide 5'-phosphatase
#2: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 580 / 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: 2.28 Å3/Da / Density % sol: 45.96 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 6 / Details: pH 6.0, VAPOR DIFFUSION, HANGING DROP

-
Data collection

DiffractionMean temperature: 130 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.601, 1.21
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 27, 2007
RadiationMonochromator: Si111, small gap ID / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.6011
21.211
ReflectionResolution: 1.65→40 Å / Num. obs: 51783 / % possible obs: 85.1 % / Observed criterion σ(I): -1 / Redundancy: 57.88 % / Biso Wilson estimate: 22 Å2 / Rsym value: 0.048
Reflection shellResolution: 1.65→1.68 Å / Redundancy: 1.2 % / Rmerge(I) obs: 0.193 / Mean I/σ(I) obs: 3.65 / Num. unique all: 2896 / Rsym value: 0.41 / % possible all: 66.6

-
Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data collection
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: SAD / Resolution: 1.65→33.83 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 8412397.67 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.212 2620 5.1 %RANDOM
Rwork0.184 ---
obs0.184 51783 88.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 34.3456 Å2 / ksol: 0.33 e/Å3
Displacement parametersBiso mean: 28.6 Å2
Baniso -1Baniso -2Baniso -3
1-1.23 Å2-2.44 Å2-0.93 Å2
2--0.57 Å21.53 Å2
3----1.8 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.18 Å
Luzzati d res low-6 Å
Luzzati sigma a0.18 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 1.65→33.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3914 0 20 580 4514
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.014
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.72
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it3.294.5
X-RAY DIFFRACTIONc_mcangle_it4.346
X-RAY DIFFRACTIONc_scbond_it5.196
X-RAY DIFFRACTIONc_scangle_it7.347.5
LS refinement shellResolution: 1.65→1.68 Å / Rfactor Rfree error: 0.031 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 102 4.6 %
Rwork0.294 2121 -
obs--76.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramsolven.top
X-RAY DIFFRACTION3solvent.paramwater.top

+
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://pdbjlvh1.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