[English] 日本語
Yorodumi
- PDB-6fsq: Structure of A3_bGFPD, an artificial bi-domain protein based on t... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6fsq
TitleStructure of A3_bGFPD, an artificial bi-domain protein based on two different alphaRep domains : A3 and a GFP binding domain (bGFPD)
ComponentsalphaRep A3_bGFPD
KeywordsBIOSYNTHETIC PROTEIN / alphaRep / artificial protein / chimera / bidomain
Function / homologyMALONATE ION
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.79 Å
AuthorsLi de la Sierra-Gallay, I. / Leger, C.
Citation
#1: Journal: To Be Published
Title: Bi-domain artificial protein alphaRep display inducible cooperativity
Authors: Leger, C. / Gallay, I.
History
DepositionFeb 20, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 8, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 27, 2019Group: Data collection / Database references / Other
Category: citation / citation_author ...citation / citation_author / database_PDB_rev / pdbx_database_proc / pdbx_database_status
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_PDB_rev.date / _database_PDB_rev.mod_type / _database_PDB_rev.num / _database_PDB_rev.replaces / _pdbx_database_status.author_approval_type / _pdbx_database_status.date_author_approval / _pdbx_database_status.date_of_NDB_release / _pdbx_database_status.date_of_PDB_release / _pdbx_database_status.date_of_sf_release / _pdbx_database_status.status_code / _pdbx_database_status.status_code_sf
Revision 1.2Jan 17, 2024Group: 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: alphaRep A3_bGFPD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,5853
Polymers44,4601
Non-polymers1252
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area340 Å2
ΔGint-9 kcal/mol
Surface area18130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.940, 89.030, 143.610
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

-
Components

#1: Protein alphaRep A3_bGFPD


Mass: 44460.203 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H2O4
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.41 Å3/Da / Density % sol: 48.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 1.6M Tri-sodium citrate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 11, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.79→47.869 Å / Num. obs: 10938 / % possible obs: 99.6 % / Redundancy: 12.759 % / Biso Wilson estimate: 48.68 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.206 / Rrim(I) all: 0.214 / Χ2: 0.898 / Net I/σ(I): 12.95 / Num. measured all: 139553
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.79-2.9612.5211.2312.0821035171516800.8971.28398
2.96-3.1613.6480.8273.4322356163816380.9610.859100
3.16-3.4212.9730.3856.9819862153115310.9920.401100
3.42-3.7412.5330.24311.6717897142814280.9950.254100
3.74-4.1813.0020.17617.1616591127612760.9970.183100
4.18-4.8212.1390.13720.813935114811480.9970.143100
4.82-5.8812.840.1420.51125459779770.9970.146100
5.88-8.2512.3830.10926.6897337887860.9990.11499.7
8.25-47.86911.8120.06838.855994774740.9990.07199.4

-
Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XSCALEdata scaling
PDB_EXTRACT3.22data extraction
MOLREPphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LTJ

3ltj


Resolution: 2.79→44.51 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.889 / SU B: 20.923 / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.401 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2698 547 5 %RANDOM
Rwork0.2056 ---
obs0.2088 10389 99.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 129.75 Å2 / Biso mean: 61.873 Å2 / Biso min: 31.89 Å2
Baniso -1Baniso -2Baniso -3
1--7.41 Å2-0 Å20 Å2
2---0.06 Å2-0 Å2
3---7.47 Å2
Refinement stepCycle: final / Resolution: 2.79→44.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2829 0 8 0 2837
Biso mean--61.5 --
Num. residues----368
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0192872
X-RAY DIFFRACTIONr_bond_other_d0.0060.022810
X-RAY DIFFRACTIONr_angle_refined_deg1.3391.983868
X-RAY DIFFRACTIONr_angle_other_deg0.96136480
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7145366
X-RAY DIFFRACTIONr_dihedral_angle_2_deg44.01224.211133
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.70515522
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7111527
X-RAY DIFFRACTIONr_chiral_restr0.0750.2427
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023234
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02569
LS refinement shellResolution: 2.792→2.865 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.371 36 -
Rwork0.466 698 -
all-734 -
obs--95.45 %

+
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