[English] 日本語
Yorodumi
- PDB-4zv6: Crystal structure of the artificial alpharep-7 octarellinV.1 complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4zv6
TitleCrystal structure of the artificial alpharep-7 octarellinV.1 complex
Components
  • AlphaRep-7
  • Octarellin V.1
KeywordsDE NOVO PROTEIN / synthetic gene / artificial protein / Rossmann-like
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.22 Å
AuthorsFigueroa, M. / Sleutel, M. / Urvoas, A. / Valerio-Lepiniec, M. / Minard, P. / Martial, J.A. / van de Weerdt, C.
Funding support Belgium, 1items
OrganizationGrant numberCountry
European Space AgencyESA AO-2004-070 Belgium
CitationJournal: J.Struct.Biol. / Year: 2016
Title: The unexpected structure of the designed protein Octarellin V.1 forms a challenge for protein structure prediction tools.
Authors: Figueroa, M. / Sleutel, M. / Vandevenne, M. / Parvizi, G. / Attout, S. / Jacquin, O. / Vandenameele, J. / Fischer, A.W. / Damblon, C. / Goormaghtigh, E. / Valerio-Lepiniec, M. / Urvoas, A. / ...Authors: Figueroa, M. / Sleutel, M. / Vandevenne, M. / Parvizi, G. / Attout, S. / Jacquin, O. / Vandenameele, J. / Fischer, A.W. / Damblon, C. / Goormaghtigh, E. / Valerio-Lepiniec, M. / Urvoas, A. / Durand, D. / Pardon, E. / Steyaert, J. / Minard, P. / Maes, D. / Meiler, J. / Matagne, A. / Martial, J.A. / Van de Weerdt, C.
History
DepositionMay 18, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0May 25, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 8, 2016Group: Database references
Revision 1.2May 8, 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: AlphaRep-7
B: Octarellin V.1


Theoretical massNumber of molelcules
Total (without water)57,2302
Polymers57,2302
Non-polymers00
Water181
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2960 Å2
ΔGint-6 kcal/mol
Surface area20930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.133, 42.021, 85.186
Angle α, β, γ (deg.)90.00, 106.35, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein AlphaRep-7


Mass: 32362.977 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Plasmid: pQE81 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
#2: Protein Octarellin V.1


Mass: 24867.068 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Plasmid: pJB122 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.19 Å3/Da / Density % sol: 43.95 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 21% (w/v) PEG400, 100mM MgCl2, 100mM Hepes pH 7.5, 20mg/ml octarellin-alpha rep complex

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97934 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 10, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.22→47.1 Å / Num. obs: 24372 / % possible obs: 98.8 % / Redundancy: 3.7 % / Net I/σ(I): 16.15

-
Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
XDSdata reduction
XDSdata scaling
RefinementResolution: 2.22→47.097 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 35.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2868 1254 5.08 %
Rwork0.2325 --
obs0.2354 24708 98.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.22→47.097 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3403 0 0 1 3404
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093444
X-RAY DIFFRACTIONf_angle_d1.2264616
X-RAY DIFFRACTIONf_dihedral_angle_d16.8941317
X-RAY DIFFRACTIONf_chiral_restr0.083510
X-RAY DIFFRACTIONf_plane_restr0.006605
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.22-2.30890.36311290.31432494X-RAY DIFFRACTION97
2.3089-2.4140.3821240.29782572X-RAY DIFFRACTION99
2.414-2.54130.32341190.27122615X-RAY DIFFRACTION99
2.5413-2.70050.35111410.26452570X-RAY DIFFRACTION99
2.7005-2.90890.31831660.26622578X-RAY DIFFRACTION99
2.9089-3.20160.39671470.27322606X-RAY DIFFRACTION99
3.2016-3.66480.31871260.24162648X-RAY DIFFRACTION99
3.6648-4.61660.24311370.21382658X-RAY DIFFRACTION100
4.6166-47.10740.26141650.21142713X-RAY DIFFRACTION100

+
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