[English] 日本語
Yorodumi
- PDB-8pf0: Diubiquitin-derived artificial binding protein (Affilin) variant ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8pf0
TitleDiubiquitin-derived artificial binding protein (Affilin) variant Af1 specific to oncofetal fibronectin
ComponentsAffilin variant Af1 (77405)
KeywordsDE NOVO PROTEIN / extra domain B / EDB / oncofetal fibronectin / ubiquitin / diubiqutin / Affilin / beta strand register shift / strand slippage / scaffold / artificial binding protein / plasticity / directed evolution
Function / homologyCOPPER (II) ION / IMIDAZOLE
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsParthier, C. / Katzschmann, A. / Fiedler, E. / Haupts, U. / Reimann, A.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Commun Biol / Year: 2024
Title: Ubiquitin-derived artificial binding proteins targeting oncofetal fibronectin reveal scaffold plasticity by beta-strand slippage.
Authors: Katzschmann, A. / Haupts, U. / Reimann, A. / Settele, F. / Gloser-Braunig, M. / Fiedler, E. / Parthier, C.
History
DepositionJun 15, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 26, 2024Provider: repository / Type: Initial release
Revision 1.1Aug 14, 2024Group: Database references / Category: citation / citation_author
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 / _citation_author.identifier_ORCID / _citation_author.name

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Affilin variant Af1 (77405)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,9217
Polymers17,5291
Non-polymers3926
Water1,40578
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area780 Å2
ΔGint-23 kcal/mol
Surface area9740 Å2
Unit cell
Length a, b, c (Å)62.767, 62.767, 67.841
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

-
Components

#1: Protein Affilin variant Af1 (77405)


Mass: 17529.107 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#2: Chemical
ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: Cu
#3: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H5N2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 78 / 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: 3.81 Å3/Da / Density % sol: 67.73 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 100 mM Imidazol/MES, 60 mM calcium/magnesium chloride, 30% PEG 8000/ethylene glycol (w/v), 10 mM copper(II)chloride dehydrate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 28, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. obs: 26176 / % possible obs: 99.5 % / Redundancy: 3.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.031 / Rrim(I) all: 0.036 / Net I/σ(I): 22.88
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
2.2-2.30.38731890.910.4511
2.3-2.40.33527170.9170.3891
2.4-2.50.21523940.9550.251
2.5-2.60.15120050.9770.1751
2.6-30.06755320.9960.0781
3-3.40.03132510.9990.0361
3.4-3.80.02319960.9990.0271
3.8-4.20.0213550.9990.0241
4.2-4.60.0218800.9990.0251
4.6-100.0226170.9990.0231
10-200.0332400.9970.0381

-
Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
XSCALEdata scaling
XDSdata reduction
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 2.2→19.05 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.17 / Phase error: 29.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2261 1285 5.04 %
Rwork0.1932 --
obs0.195 25510 97.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→19.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1223 0 14 78 1315
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071255
X-RAY DIFFRACTIONf_angle_d1.0891698
X-RAY DIFFRACTIONf_dihedral_angle_d13.094479
X-RAY DIFFRACTIONf_chiral_restr0.067195
X-RAY DIFFRACTIONf_plane_restr0.004218
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2001-2.2880.50971150.51022161X-RAY DIFFRACTION79
2.288-2.39190.37821420.29552667X-RAY DIFFRACTION97
2.3919-2.51780.27111510.22492806X-RAY DIFFRACTION100
2.5178-2.67510.23551430.20152747X-RAY DIFFRACTION100
2.6751-2.8810.22391470.18562773X-RAY DIFFRACTION100
2.881-3.16980.20561490.18912795X-RAY DIFFRACTION100
3.1698-3.62570.25121450.18342737X-RAY DIFFRACTION100
3.6257-4.55770.20431470.1622778X-RAY DIFFRACTION100
4.5577-19.050.19061460.18022761X-RAY DIFFRACTION100
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)
18.98010.7012-1.35967.3581-2.86256.6371-0.02210.28320.3321-0.02180.011-0.3335-0.35340.05160.01670.331-0.0264-0.01850.230.00130.260318.242427.927340.3691
22.39892.78261.48233.3611.74910.92210.75940.9491-0.7426-1.2430.0369-1.15090.6560.4723-0.77381.45760.3271-0.33840.8691-0.02821.727119.482511.05227.2187
38.87280.4333-0.7167.98763.28825.98150.0442-0.34690.27140.0526-0.01020.3484-0.2079-0.0601-0.05810.30180.0302-0.00010.2369-0.00480.226613.0742-3.725935.3309
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 73 )
2X-RAY DIFFRACTION2chain 'A' and (resid 74 through 80 )
3X-RAY DIFFRACTION3chain 'A' and (resid 81 through 152 )

+
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