[English] 日本語
Yorodumi
- PDB-5mfb: Designed armadillo repeat protein YIII(Dq)4CqI -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5mfb
TitleDesigned armadillo repeat protein YIII(Dq)4CqI
ComponentsYIII(Dq)4CqI
KeywordsDE NOVO PROTEIN / Designed armadillo repeat protein / peptide binding
Function / homologyLeucine-rich Repeat Variant / Leucine-rich Repeat Variant / Alpha Horseshoe / Mainly Alpha
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsHansen, S. / Ernst, P. / Reichen, C. / Ewald, C. / Mittl, P. / Plueckthun, A.
CitationJournal: J. Struct. Biol. / Year: 2018
Title: Curvature of designed armadillo repeat proteins allows modular peptide binding.
Authors: Hansen, S. / Ernst, P. / Konig, S.L.B. / Reichen, C. / Ewald, C. / Nettels, D. / Mittl, P.R.E. / Schuler, B. / Pluckthun, A.
History
DepositionNov 18, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 13, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 21, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 2.0May 8, 2024Group: Atomic model / Data collection / Database references
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2
Item: _atom_site.occupancy / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: YIII(Dq)4CqI
B: YIII(Dq)4CqI


Theoretical massNumber of molelcules
Total (without water)50,4092
Polymers50,4092
Non-polymers00
Water1,24369
1
A: YIII(Dq)4CqI


Theoretical massNumber of molelcules
Total (without water)25,2041
Polymers25,2041
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: YIII(Dq)4CqI


Theoretical massNumber of molelcules
Total (without water)25,2041
Polymers25,2041
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)139.230, 46.560, 90.810
Angle α, β, γ (deg.)90.00, 128.55, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-307-

HOH

-
Components

#1: Protein YIII(Dq)4CqI


Mass: 25204.289 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli K-12 (bacteria)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 69 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.28 Å3/Da / Density % sol: 46.13 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.3 M Na-Acetate, 0.1 M Na-Cacodylate pH 6.5, 25 % PEG 2K MME

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Apr 28, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→42.81 Å / Num. obs: 20111 / % possible obs: 97.3 % / Redundancy: 3.8 % / Biso Wilson estimate: 57.99 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.081 / Net I/σ(I): 10.31
Reflection shellResolution: 2.3→2.36 Å / Redundancy: 4 % / Rmerge(I) obs: 1.85 / Mean I/σ(I) obs: 0.76 / CC1/2: 0.298 / % possible all: 97.1

-
Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→42.81 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.94 / SU R Cruickshank DPI: 0.331 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.319 / SU Rfree Blow DPI: 0.229 / SU Rfree Cruickshank DPI: 0.235
RfactorNum. reflection% reflectionSelection details
Rfree0.241 975 4.85 %RANDOM
Rwork0.184 ---
obs0.187 20111 97.9 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.8611 Å20 Å26.5212 Å2
2---4.7727 Å20 Å2
3---2.9117 Å2
Refine analyzeLuzzati coordinate error obs: 0.33 Å
Refinement stepCycle: 1 / Resolution: 2.3→42.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3486 0 0 69 3555
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013500HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.294746HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1280SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes152HARMONIC2
X-RAY DIFFRACTIONt_gen_planes477HARMONIC5
X-RAY DIFFRACTIONt_it3500HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.4
X-RAY DIFFRACTIONt_other_torsion21.55
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion498SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4244SEMIHARMONIC4
LS refinement shellResolution: 2.3→2.42 Å / Rfactor Rfree error: 0 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.249 133 4.6 %
Rwork0.228 2761 -
all0.229 2894 -
obs--97.27 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.8591-1.5817-1.3981.8888-0.04913.9954-0.3698-0.22520.20130.0313-0.0416-0.0203-0.22020.32450.4115-0.12090.0687-0.0798-0.2072-0.0616-0.2793-52.797212.070283.5144
22.38010.221-0.29273.7681-1.91484.49480.32970.2647-0.43590.3532-0.4031-0.52460.175-0.20590.0735-0.2655-0.047-0.0356-0.17130.0583-0.1895-28.741630.464198.3572
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }

+
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