[English] 日本語
Yorodumi
- PDB-6vgv: Crystal structure of VidaL intein -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6vgv
TitleCrystal structure of VidaL intein
ComponentsVidaL
KeywordsSPLICING / Intein / split intein / atypical intein / protein splicing
Function / homologyEndonuclease - Pi-scei; Chain A, domain 1 / Hedgehog/Intein (Hint) domain / Beta Complex / Mainly Beta
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsBurton, A.J. / Haugbro, M. / Parisi, E. / Muir, T.W.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R37-GM086868 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: Live-cell protein engineering with an ultra-short split intein.
Authors: Burton, A.J. / Haugbro, M. / Parisi, E. / Muir, T.W.
History
DepositionJan 9, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 27, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 3, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jun 17, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Mar 6, 2024Group: Advisory / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: VidaL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,7327
Polymers16,1791
Non-polymers5536
Water2,054114
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)100.122, 40.827, 36.188
Angle α, β, γ (deg.)90.000, 103.452, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

-
Components

#1: Protein VidaL


Mass: 16179.247 Da / Num. of mol.: 1 / Mutation: C4A, N142A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 114 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.22 Å3/Da / Density % sol: 44.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.1 M sodium acetate (pH 4.6) with 2 M ammonium sulfate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Aug 30, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.65→26.95 Å / Num. obs: 17134 / % possible obs: 98.9 % / Redundancy: 5.9 % / Biso Wilson estimate: 16.62 Å2 / CC1/2: 0.995 / Rpim(I) all: 0.023 / Rrim(I) all: 0.063 / Net I/σ(I): 4
Reflection shellResolution: 1.65→1.75 Å / Mean I/σ(I) obs: 3.5 / Num. unique obs: 2567 / Rpim(I) all: 0.185 / Rrim(I) all: 0.323 / % possible all: 94.6

-
Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
DENZOdata reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: VidaL SeMet structure

Resolution: 1.65→26.95 Å / SU ML: 0.1386 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.6494 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.2086 844 4.93 %
Rwork0.1633 16283 -
obs0.1656 17127 98.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.75 Å2
Refinement stepCycle: LAST / Resolution: 1.65→26.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1132 0 36 114 1282
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00551215
X-RAY DIFFRACTIONf_angle_d0.7961643
X-RAY DIFFRACTIONf_chiral_restr0.058183
X-RAY DIFFRACTIONf_plane_restr0.0048208
X-RAY DIFFRACTIONf_dihedral_angle_d8.7991983
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.750.26771360.19572567X-RAY DIFFRACTION94.64
1.75-1.890.21871390.17972708X-RAY DIFFRACTION99.41
1.89-2.080.25341260.17022741X-RAY DIFFRACTION99.79
2.08-2.380.20391430.16232741X-RAY DIFFRACTION99.9
2.38-2.990.21721530.17382733X-RAY DIFFRACTION100
2.99-26.950.18451470.14822793X-RAY DIFFRACTION99.22
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.03522598440.0276904663311-2.291415227823.501814907120.4996167927375.380805656370.0340731558833-0.3392492017670.0170861635339-0.136019437958-0.0293905095778-0.246077118459-0.02088286429980.361997823791-0.003934044118630.08330654048910.0227852255035-0.01524107008380.1717076086720.01673844467230.14105763065324.3245340768-10.82924123765.6177069165
21.471557016310.395035312493-1.137876028330.6492221376510.02968378014172.734266340550.000154172910948-0.078565465708-0.03205871913660.0177309539267-0.04872642146530.0290070006723-0.0309601813080.07096914531020.05864017561020.08485501418380.0235357503663-0.02104799289620.07949390950820.009061990152390.1186846400648.87541121129-11.574695591311.5469785736
35.422580153161.899776225210.358877993851.68823961199-0.820578758466.54188847735-0.1141740471020.06240507432770.537601052137-0.02831605682810.09071231040260.34488808726-0.568502100434-0.165764550401-0.01688618159370.1592170453090.03932893489970.006665308079240.1031061380290.01806230143120.1664729959889.60182105234-11.42005807778.59840777664
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 43 )
2X-RAY DIFFRACTION2chain 'A' and (resid 44 through 134 )
3X-RAY DIFFRACTION3chain 'A' and (resid 135 through 143 )

+
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