[English] 日本語
Yorodumi
- PDB-6vun: Reverse Transcriptase Diabody with R83C Mutation -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6vun
TitleReverse Transcriptase Diabody with R83C Mutation
ComponentsSingle-chain Fv
KeywordsPROTEIN BINDING / Antibody fragment
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / CITRATE ANION
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsChesterman, C. / Arnold, E.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R37 AI027690 United States
CitationJournal: Structure / Year: 2021
Title: Co-crystallization with diabodies: A case study for the introduction of synthetic symmetry.
Authors: Chesterman, C. / Arnold, E.
History
DepositionFeb 16, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 17, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 10, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Jun 16, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.3Oct 11, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Single-chain Fv
B: Single-chain Fv
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,60812
Polymers50,8602
Non-polymers74810
Water9,296516
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5770 Å2
ΔGint-15 kcal/mol
Surface area20570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.089, 56.632, 161.888
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

-
Components

#1: Antibody Single-chain Fv


Mass: 25430.182 Da / Num. of mol.: 2 / Mutation: R83C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C6H5O7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 516 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 50.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 14% v/v Propanol, 0.1 M Sodium citrate dibasic dehydrate pH 5.0, 10% w/v PEG 10,000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9794 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 5, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.4→50 Å / Num. obs: 170553 / % possible obs: 99.6 % / Redundancy: 8.9 % / Biso Wilson estimate: 12.48 Å2 / Rmerge(I) obs: 0.051 / Rrim(I) all: 0.055 / Net I/σ(I): 44
Reflection shellResolution: 1.4→1.42 Å / Rmerge(I) obs: 0.617 / Num. unique obs: 4903 / Rrim(I) all: 0.661 / % possible all: 98.9

-
Processing

Software
NameVersionClassification
PHENIX(1.14_3260)refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6VRP

6vrp


Resolution: 1.4→45.542 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 15.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1671 3502 2.05 %
Rwork0.1379 --
obs0.1385 170553 88.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.4→45.542 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3482 0 49 516 4047
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063893
X-RAY DIFFRACTIONf_angle_d0.9495344
X-RAY DIFFRACTIONf_dihedral_angle_d17.4421366
X-RAY DIFFRACTIONf_chiral_restr0.077584
X-RAY DIFFRACTIONf_plane_restr0.005699
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.41880.2281600.1872965X-RAY DIFFRACTION39
1.4188-1.43910.2227820.16673638X-RAY DIFFRACTION48
1.4391-1.46050.2053920.15714223X-RAY DIFFRACTION56
1.4605-1.48340.1832980.14884770X-RAY DIFFRACTION63
1.4834-1.50770.18751090.1455322X-RAY DIFFRACTION71
1.5077-1.53370.19721300.13755998X-RAY DIFFRACTION79
1.5337-1.56160.18421420.12986184X-RAY DIFFRACTION83
1.5616-1.59160.16961310.12256568X-RAY DIFFRACTION87
1.5916-1.62410.15551570.12247078X-RAY DIFFRACTION94
1.6241-1.65940.16081560.12567370X-RAY DIFFRACTION97
1.6594-1.6980.18411460.12517498X-RAY DIFFRACTION99
1.698-1.74050.12811630.1237508X-RAY DIFFRACTION99
1.7405-1.78750.19261520.12257508X-RAY DIFFRACTION100
1.7875-1.84010.14381660.12687554X-RAY DIFFRACTION99
1.8401-1.89950.1821440.1277505X-RAY DIFFRACTION100
1.8995-1.96740.15681650.12427590X-RAY DIFFRACTION100
1.9674-2.04620.14441650.12337477X-RAY DIFFRACTION100
2.0462-2.13930.16211580.12147550X-RAY DIFFRACTION100
2.1393-2.25210.1541560.12397581X-RAY DIFFRACTION100
2.2521-2.39320.13911610.12787440X-RAY DIFFRACTION99
2.3932-2.5780.16481570.13037553X-RAY DIFFRACTION100
2.578-2.83740.16941620.13787555X-RAY DIFFRACTION100
2.8374-3.24780.14951500.14727536X-RAY DIFFRACTION100
3.2478-4.09150.19121570.15137541X-RAY DIFFRACTION100
4.0915-45.5420.18161430.16417539X-RAY DIFFRACTION100

+
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