[English] 日本語
Yorodumi
- PDB-6sa6: DARPin-Armadillo fusion A5 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6sa6
TitleDARPin-Armadillo fusion A5
ComponentsDARPin-Armadillo fusion A5
KeywordsDE NOVO PROTEIN / protein fusion / DARPin / Armadillo / shared helix / crystallization chaperone
Function / homologyAnkyrin repeat-containing domain / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Mainly Alpha
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsErnst, P. / Honegger, A. / van der Valk, F. / Ewald, C. / Mittl, P.R.E. / Pluckthun, A.
CitationJournal: Sci Rep / Year: 2019
Title: Rigid fusions of designed helical repeat binding proteins efficiently protect a binding surface from crystal contacts.
Authors: Ernst, P. / Honegger, A. / van der Valk, F. / Ewald, C. / Mittl, P.R.E. / Pluckthun, A.
History
DepositionJul 16, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 20, 2019Provider: repository / Type: Initial release
Revision 1.1May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DARPin-Armadillo fusion A5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,44410
Polymers41,9391
Non-polymers5059
Water6,197344
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1410 Å2
ΔGint-7 kcal/mol
Surface area18300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.080, 51.560, 67.720
Angle α, β, γ (deg.)90.000, 95.240, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein DARPin-Armadillo fusion A5


Mass: 41939.000 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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 344 / 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: 2.37 Å3/Da / Density % sol: 48.21 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / Details: 18.6 % PEG 6,000 200 mM MgCl2 0.1M Tris HCl pH 8.1

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Apr 10, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→45.56 Å / Num. obs: 49693 / % possible obs: 95.7 % / Redundancy: 3.203 % / Biso Wilson estimate: 25.96 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.049 / Rrim(I) all: 0.059 / Χ2: 0.992 / Net I/σ(I): 13.01 / Num. measured all: 159188 / Scaling rejects: 144
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
1.6-1.642.9951.0531.1710279380234320.5061.27790.3
1.64-1.693.3120.9211.5111739372835440.6061.09995.1
1.69-1.743.2640.7271.9711383365834870.6770.87195.3
1.74-1.793.1840.5832.4310616350233340.7860.70395.2
1.79-1.853.0130.4593.079694339832170.8350.55894.7
1.85-1.913.0830.3474.219562327631020.9040.4294.7
1.91-1.983.340.2437.2110320321330900.950.28996.2
1.98-2.073.3670.16110.269989306429670.9740.19196.8
2.07-2.163.2650.12612.179299293028480.9830.1597.2
2.16-2.263.1610.09214.478714283527570.9890.11297.2
2.26-2.393.330.06718.388605265925840.9940.0897.2
2.39-2.533.3780.05620.518327252624650.9950.06697.6
2.53-2.73.2930.04822.587781240923630.9950.05898.1
2.7-2.923.0410.0423.356572222421610.9960.04997.2
2.92-3.23.2250.03626.826480207020090.9970.04397.1
3.2-3.583.1490.03229.485621185117850.9970.03996.4
3.58-4.133.0130.02832.44763163715810.9960.03596.6
4.13-5.063.1990.02637.214315141013490.9980.03195.7
5.06-7.163.190.02737.43334110710450.9970.03394.4
7.16-45.563.1330.02940.4217956205730.9960.03492.4

-
Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.13_2998refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→45.56 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.23
RfactorNum. reflection% reflection
Rfree0.2013 2484 5 %
Rwork0.1823 --
obs0.1832 49683 95.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 143.07 Å2 / Biso mean: 37.8961 Å2 / Biso min: 15.67 Å2
Refinement stepCycle: final / Resolution: 1.6→45.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2944 0 72 344 3360
Biso mean--77.61 40.83 -
Num. residues----395
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.6-1.63080.36861260.3436240689
1.6308-1.66410.30831350.3168257295
1.6641-1.70030.32061380.314261796
1.7003-1.73990.31931370.3037261095
1.7399-1.78340.36221360.3414258295
1.7834-1.83160.29721360.3386257495
1.8316-1.88550.29671350.2806256595
1.8855-1.94630.28211360.2284258395
1.9463-2.01590.2291400.2016266297
2.0159-2.09660.21381380.1928262297
2.0966-2.1920.21581410.1845268197
2.192-2.30760.2031400.1679265498
2.3076-2.45220.18211400.1639267297
2.4522-2.64150.16931410.1622268098
2.6415-2.90730.19111420.1683268198
2.9073-3.32780.18061400.1674267997
3.3278-4.19230.18141410.1474266996
4.19-45.560.16841420.1613269095
Refinement TLS params.Method: refined / Origin x: 2.0482 Å / Origin y: 1.4501 Å / Origin z: -18.7235 Å
111213212223313233
T0.198 Å20.0092 Å20.0097 Å2-0.2167 Å20.0105 Å2--0.1975 Å2
L0.2293 °2-0.2516 °20.2824 °2-0.4319 °2-0.3239 °2--0.3444 °2
S0.0341 Å °-0.0217 Å °0.0055 Å °-0.0318 Å °-0.0178 Å °-0.0142 Å °0.0526 Å °0.021 Å °-0.0005 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA3 - 397
2X-RAY DIFFRACTION1allD2 - 3
3X-RAY DIFFRACTION1allE1 - 7
4X-RAY DIFFRACTION1allS1 - 344

+
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