[English] 日本語
Yorodumi
- PDB-4tya: An Ligand-observed Mass Spectrometry-based Approach Integrated in... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4tya
TitleAn Ligand-observed Mass Spectrometry-based Approach Integrated into the Fragment Based Lead Discovery Pipeline
ComponentsPolyprotein
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / Inhibitor / NS5B / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


serine-type peptidase activity / helicase activity / RNA-directed RNA polymerase / viral RNA genome replication / nucleotide binding / RNA-directed RNA polymerase activity / ATP hydrolysis activity / RNA binding / membrane
Similarity search - Function
RNA dependent RNA polymerase, hepatitis C virus / Viral RNA dependent RNA polymerase / Reverse transcriptase/Diguanylate cyclase domain / Reverse transcriptase/Diguanylate cyclase domain / Alpha-Beta Plaits / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / DNA/RNA polymerase superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
4-(trifluoromethyl)benzoic acid / RNA-directed RNA polymerase
Similarity search - Component
Biological speciesHepatitis C virus
MethodX-RAY DIFFRACTION / Resolution: 2.94 Å
AuthorsShui, W. / Yang, C. / Lin, J. / Chen, X. / Qin, S. / Chen, S.
CitationJournal: Sci Rep / Year: 2015
Title: A ligand-observed mass spectrometry approach integrated into the fragment based lead discovery pipeline
Authors: Chen, X. / Qin, S. / Chen, S. / Li, J. / Li, L. / Wang, Z. / Wang, Q. / Lin, J. / Yang, C. / Shui, W.
History
DepositionJul 8, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 6, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 2, 2015Group: Data collection
Revision 1.2Sep 27, 2017Group: Data collection / Derived calculations / Category: diffrn_detector / pdbx_struct_oper_list
Item: _diffrn_detector.detector / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Polyprotein
B: Polyprotein
C: Polyprotein
D: Polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)251,9288
Polymers251,1684
Non-polymers7604
Water00
1
A: Polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,9822
Polymers62,7921
Non-polymers1901
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,9822
Polymers62,7921
Non-polymers1901
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,9822
Polymers62,7921
Non-polymers1901
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,9822
Polymers62,7921
Non-polymers1901
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)102.178, 102.156, 251.981
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein
Polyprotein


Mass: 62791.984 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hepatitis C virus / Production host: Escherichia coli (E. coli) / References: UniProt: D0PY27, RNA-directed RNA polymerase
#2: Chemical
ChemComp-3AE / 4-(trifluoromethyl)benzoic acid


Mass: 190.119 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H5F3O2

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.6 Å3/Da / Density % sol: 52.72 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: PEG4000, Dithiothreitol, 2-(N-morpholino)ethanesulfonic acid, Glycerin
PH range: 5.5-6.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5415 Å
DetectorType: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: May 23, 2012
RadiationMonochromator: Cu filter / Protocol: LAUE / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5415 Å / Relative weight: 1
ReflectionResolution: 2.94→50 Å / Num. obs: 56755 / % possible obs: 99 % / Redundancy: 4.5 % / Net I/σ(I): 16.9

-
Processing

Software
NameVersionClassification
HKL-3000data collection
HKL-3000data extraction
HKL-3000data processing
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
REFMAC5.8.0049refinement
REFMAC5.8.0049refinement
RefinementResolution: 2.94→47.34 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.858 / SU B: 18.555 / SU ML: 0.34 / Cross valid method: THROUGHOUT / ESU R Free: 0.46 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27032 2832 5.1 %RANDOM
Rwork0.20091 ---
obs0.20446 53023 98.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.763 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20 Å2-0 Å2
2---0.01 Å2-0 Å2
3----0.04 Å2
Refinement stepCycle: 1 / Resolution: 2.94→47.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16888 0 52 0 16940
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01917304
X-RAY DIFFRACTIONr_bond_other_d0.0010.0216444
X-RAY DIFFRACTIONr_angle_refined_deg1.4891.96423484
X-RAY DIFFRACTIONr_angle_other_deg0.834337812
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.37452160
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.63722.784704
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.676152912
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.04615136
X-RAY DIFFRACTIONr_chiral_restr0.0760.22656
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02119356
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023956
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.6363.2158688
X-RAY DIFFRACTIONr_mcbond_other1.6363.2148687
X-RAY DIFFRACTIONr_mcangle_it2.7654.81410832
X-RAY DIFFRACTIONr_mcangle_other2.7654.81410833
X-RAY DIFFRACTIONr_scbond_it1.6213.3948616
X-RAY DIFFRACTIONr_scbond_other1.623.3948616
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.7755.02212650
X-RAY DIFFRACTIONr_long_range_B_refined4.22425.12719397
X-RAY DIFFRACTIONr_long_range_B_other4.22325.12319395
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.943→3.02 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.339 184 -
Rwork0.288 3515 -
obs--89.26 %

+
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