[English] 日本語
Yorodumi
- PDB-6vup: Reverse Transcriptase Diabody with R83T/E85C Mutations -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6vup
TitleReverse Transcriptase Diabody with R83T/E85C Mutations
ComponentsSingle-chain Fv
KeywordsPROTEIN BINDING / Antibody fragment
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
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
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Single-chain Fv
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,93410
Polymers26,3751
Non-polymers5599
Water3,603200
1
A: Single-chain Fv
hetero molecules

A: Single-chain Fv
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,86820
Polymers52,7502
Non-polymers1,11718
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area7450 Å2
ΔGint22 kcal/mol
Surface area19550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.942, 86.686, 37.078
Angle α, β, γ (deg.)90.000, 116.228, 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 on special symmetry positions
IDModelComponents
11A-499-

HOH

21A-519-

HOH

31A-563-

HOH

41A-583-

HOH

-
Components

#1: Antibody Single-chain Fv


Mass: 26375.184 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: scFv / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 200 / 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: 2.13 Å3/Da / Density % sol: 42.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 5.4
Details: 6 % v/v 2-Propanol, 0.1 M Sodium Acetate trihydrate pH 4.5, 26% PEG 550 MME

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 18, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.4→50 Å / Num. obs: 39530 / % possible obs: 97.4 % / Redundancy: 3.3 % / Biso Wilson estimate: 12.65 Å2 / Rmerge(I) obs: 0.041 / Rrim(I) all: 0.049 / Net I/σ(I): 24.7
Reflection shellResolution: 1.4→1.42 Å / Rmerge(I) obs: 0.049 / Num. unique obs: 1905 / Rrim(I) all: 0.301

-
Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6VRP

6vrp


Resolution: 1.4→43.34 Å / SU ML: 0.1165 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 16.5343 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1706 1892 5.01 %
Rwork0.1312 35910 -
obs0.1332 37802 93.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.31 Å2
Refinement stepCycle: LAST / Resolution: 1.4→43.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1710 0 36 200 1946
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00681886
X-RAY DIFFRACTIONf_angle_d0.92672568
X-RAY DIFFRACTIONf_chiral_restr0.0796279
X-RAY DIFFRACTIONf_plane_restr0.0047330
X-RAY DIFFRACTIONf_dihedral_angle_d2.98671324
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.440.20331050.1261863X-RAY DIFFRACTION68.12
1.44-1.470.1861040.12942107X-RAY DIFFRACTION76.8
1.47-1.520.23071220.12512401X-RAY DIFFRACTION86.85
1.52-1.570.18121430.12012545X-RAY DIFFRACTION93.4
1.57-1.620.16571420.11732701X-RAY DIFFRACTION97.36
1.62-1.690.19871410.11512705X-RAY DIFFRACTION98.75
1.69-1.760.1711430.1122710X-RAY DIFFRACTION97.84
1.76-1.860.16481350.10912632X-RAY DIFFRACTION96.55
1.86-1.970.15631430.11262680X-RAY DIFFRACTION97.95
1.97-2.130.15571350.11412711X-RAY DIFFRACTION98.82
2.13-2.340.15281480.12112719X-RAY DIFFRACTION97.52
2.34-2.680.17721430.13772685X-RAY DIFFRACTION98.02
2.68-3.380.19241420.14742724X-RAY DIFFRACTION97.98
3.38-43.340.15791460.14992727X-RAY DIFFRACTION97.56

+
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