[English] 日本語
Yorodumi
- PDB-1mj0: SANK E3_5: an artificial Ankyrin repeat protein -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1mj0
TitleSANK E3_5: an artificial Ankyrin repeat protein
ComponentsSANK E3_5 Protein
KeywordsDE NOVO PROTEIN / Ankyrin repeat / protein engineering / consensus
Function / homologyAnkyrin repeat-containing domain / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Mainly Alpha / :
Function and homology information
Biological speciesDesigned synthetic gene (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.031 Å
AuthorsKohl, A. / Binz, H.K. / Forrer, P. / Stumpp, M.T. / Plueckthun, A. / Gruetter, M.G.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2003
Title: Designed to be stable: Crystal structure of a consensus ankyrin repeat protein
Authors: Kohl, A. / Binz, H.K. / Forrer, P. / Stumpp, M.T. / Plueckthun, A. / Gruetter, M.G.
History
DepositionAug 26, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 21, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: SANK E3_5 Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,0534
Polymers17,7391
Non-polymers3143
Water3,207178
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.864, 47.360, 47.003
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-323-

HOH

-
Components

#1: Protein SANK E3_5 Protein


Mass: 17738.664 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Designed synthetic gene (others) / Plasmid: pQE30 derivative / Production host: Escherichia coli (E. coli) / Strain (production host): XL1 blue / References: GenBank: 28274847
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 178 / 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: 2.32 Å3/Da / Density % sol: 46.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.8
Details: PEG 4000, Li2SO4, NH4OAc, pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
150 mMTris-HCl1droppH8.0
2150 mM1dropNaCl
39 mg/mlprotein1drop
416-22 %PEG40001reservoir
50.2 M1reservoirLi2SO4
60.1 M1reservoirpH4.6-5.0NH4OAc

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: OTHER / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 25, 2001
RadiationMonochromator: Mirror, Biophysics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.02→20 Å / Num. all: 11291 / Num. obs: 11091 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 15.4 % / Biso Wilson estimate: 25.2 Å2 / Rsym value: 0.1 / Net I/σ(I): 20.3
Reflection shellResolution: 2.02→2.09 Å / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 48.8 / Num. unique all: 917 / Rsym value: 0.33 / % possible all: 83.8
Reflection
*PLUS
Highest resolution: 2.03 Å / Num. obs: 11291 / % possible obs: 98.4 % / Num. measured all: 173985 / Rmerge(I) obs: 0.1
Reflection shell
*PLUS
% possible obs: 83.8 % / Rmerge(I) obs: 0.33

-
Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMAC5refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1AWC

1awc


Resolution: 2.031→20 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.916 / SU B: 7.445 / SU ML: 0.211 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 2 / ESU R: 0.209 / ESU R Free: 0.18 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.22971 1140 10.3 %RANDOM
Rwork0.17917 ---
obs0.18432 9924 99.45 %-
all-11091 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 17.984 Å2
Baniso -1Baniso -2Baniso -3
1-1.3 Å20 Å20 Å2
2---0.51 Å20 Å2
3----0.79 Å2
Refinement stepCycle: LAST / Resolution: 2.031→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1194 0 18 178 1390
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0211200
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9261.9691639
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.0973162
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.95915189
X-RAY DIFFRACTIONr_chiral_restr0.1310.2189
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02906
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2710.3668
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1850.5121
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2770.343
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1550.512
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it1.2431.5783
X-RAY DIFFRACTIONr_mcangle_it2.04721245
X-RAY DIFFRACTIONr_scbond_it3.5653417
X-RAY DIFFRACTIONr_scangle_it5.3724.5394
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.031→2.083 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.294 54
Rwork0.197 685
Refinement
*PLUS
Highest resolution: 2.03 Å / Lowest resolution: 20 Å / Rfactor Rfree: 0.23 / Rfactor Rwork: 0.184
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.022
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.926

+
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://pdbjlvh1.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