[English] 日本語
Yorodumi
- PDB-7osv: DeNovoTIM6-SB, a de novo designed TIM barrel with a salt-bridge c... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7osv
TitleDeNovoTIM6-SB, a de novo designed TIM barrel with a salt-bridge cluster (crystal form 1)
ComponentsDeNovoTIM6-SB
KeywordsDE NOVO PROTEIN / TIM barrel / salt bridge cluster
Function / homologyACETATE ION / DI(HYDROXYETHYL)ETHER
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.66 Å
AuthorsKordes, S. / Romero-Romero, S. / Hocker, B.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research Foundation (DFG)HO4022/2-3 Germany
European Research Council (ERC)ERC Consolidator grant 647548 Protein Lego Germany
CitationJournal: Protein Sci. / Year: 2022
Title: A newly introduced salt bridge cluster improves structural and biophysical properties of de novo TIM barrels.
Authors: Kordes, S. / Romero-Romero, S. / Lutz, L. / Hocker, B.
History
DepositionJun 9, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 15, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 16, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DeNovoTIM6-SB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,9905
Polymers22,6701
Non-polymers3204
Water2,072115
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area640 Å2
ΔGint0 kcal/mol
Surface area8610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)29.370, 65.630, 44.610
Angle α, β, γ (deg.)90.000, 95.738, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

-
Components

#1: Protein DeNovoTIM6-SB


Mass: 22669.711 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: M (N-terminal) and GLEHHHHHH (C-terminal) come from the expresion vector.
Source: (gene. exp.) synthetic construct (others) / Plasmid: pET21b(+) / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 115 / 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: 1.96 Å3/Da / Density % sol: 37.3 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.2 M Ammonium sulfate, 0.2 M sodium acetate pH 4.6, 28% PEG 4000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 16, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.66→32.81 Å / Num. obs: 19751 / % possible obs: 98.89 % / Redundancy: 6.9 % / Biso Wilson estimate: 27.41 Å2 / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.1385 / Rpim(I) all: 0.057 / Rrim(I) all: 0.1501 / Net I/σ(I): 7.77
Reflection shellResolution: 1.66→1.72 Å / Redundancy: 7 % / Rmerge(I) obs: 1.77 / Mean I/σ(I) obs: 0.96 / Num. unique obs: 1947 / CC1/2: 0.339 / CC star: 0.712 / Rpim(I) all: 1.114 / Rrim(I) all: 2.99 / % possible all: 97.45

-
Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PHENIX1.19.2_4158refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5BVL

5bvl


Resolution: 1.66→32.81 Å / SU ML: 0.2675 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 29.6892
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2373 988 5 %
Rwork0.2088 18763 -
obs0.2102 19751 98.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.7 Å2
Refinement stepCycle: LAST / Resolution: 1.66→32.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1354 0 20 116 1490
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00571390
X-RAY DIFFRACTIONf_angle_d0.59151876
X-RAY DIFFRACTIONf_chiral_restr0.0492212
X-RAY DIFFRACTIONf_plane_restr0.0049244
X-RAY DIFFRACTIONf_dihedral_angle_d6.9304196
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.66-1.750.37131370.37672596X-RAY DIFFRACTION96.47
1.75-1.850.31511410.2992685X-RAY DIFFRACTION99.37
1.85-20.30671400.25212672X-RAY DIFFRACTION98.77
2-2.20.22041400.19732664X-RAY DIFFRACTION98.08
2.2-2.520.23951430.19272700X-RAY DIFFRACTION99.61
2.52-3.170.23661430.21282727X-RAY DIFFRACTION99.86
3.17-32.810.21311440.18652719X-RAY DIFFRACTION98.55
Refinement TLS params.Method: refined / Origin x: 17.9931368244 Å / Origin y: 23.1375605104 Å / Origin z: 32.2013283573 Å
111213212223313233
T0.212796659671 Å20.00521804960816 Å2-0.0202153947368 Å2-0.216594015614 Å2-0.00283005543353 Å2--0.239535023311 Å2
L1.30125327439 °2-0.250492565247 °2-0.325710612097 °2-2.21671224645 °20.0699320893767 °2--0.530300339686 °2
S0.0310699388861 Å °0.0229723508743 Å °0.0207181176714 Å °0.0718513497851 Å °-0.0372212397213 Å °-0.00679287723548 Å °-0.0257536964751 Å °-0.0434031719452 Å °0.019597622216 Å °
Refinement TLS groupSelection details: all

+
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