[English] 日本語
Yorodumi
- PDB-7rii: [I11L]hyen D crystal structure -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7rii
Title[I11L]hyen D crystal structure
ComponentsCyclotide hyen-D
KeywordsPLANT PROTEIN / Cytotoxicity / cyclotides / quasi-racemic crystallography
Function / homology
Function and homology information


hemolysis in another organism / cytolysis in another organism / defense response
Similarity search - Function
Cyclotide, bracelet, conserved site / Cyclotides bracelet subfamily signature. / Cyclotides profile. / Cyclotide / Cyclotide superfamily / Cyclotide family
Similarity search - Domain/homology
PHOSPHATE ION / Cyclotide hyen-D
Similarity search - Component
Biological speciesHybanthus enneaspermus (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.22 Å
AuthorsDu, Q. / Huang, Y.H. / Craik, D.J. / Wang, C.K.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC)CE200100012 Australia
CitationJournal: Molecules / Year: 2021
Title: Enabling efficient folding and high-resolution crystallographic analysis of bracelet cyclotides
Authors: Craik, D.J. / Huang, Y.H. / Wang, C.K. / Du, Q. / King, G.
History
DepositionJul 20, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 29, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cyclotide hyen-D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,2782
Polymers3,1831
Non-polymers951
Water57632
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)18.755, 21.153, 26.296
Angle α, β, γ (deg.)87.250, 82.940, 89.130
Int Tables number2
Space group name H-MP-1

-
Components

#1: Protein/peptide Cyclotide hyen-D


Mass: 3182.778 Da / Num. of mol.: 1 / Mutation: I11L / Source method: obtained synthetically / Source: (synth.) Hybanthus enneaspermus (plant) / References: UniProt: C0HLN8
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 32 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.62 Å3/Da / Density % sol: 24.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 20% PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95372 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 7, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
ReflectionResolution: 1.22→21.13 Å / Num. obs: 11130 / % possible obs: 93.26 % / Redundancy: 3.4 % / CC1/2: 0.989 / Rmerge(I) obs: 0.1293 / Net I/σ(I): 5.09
Reflection shellResolution: 1.22→1.264 Å / Num. unique obs: 1091 / CC1/2: 0.889

-
Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2KNM

2knm


Resolution: 1.22→21.13 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 16.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2233 1111 9.99 %
Rwork0.2047 10013 -
obs0.2065 11124 93.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 34.99 Å2 / Biso mean: 9.7245 Å2 / Biso min: 5.7 Å2
Refinement stepCycle: final / Resolution: 1.22→21.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms217 0 5 32 254
Biso mean--11.63 17.13 -
Num. residues----30
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.22-1.280.36111320.32111216134891
1.28-1.340.39891430.30121227137091
1.34-1.430.28761340.25481241137593
1.43-1.540.25281360.21791244138093
1.54-1.690.2071450.19911253139894
1.69-1.940.16921370.17621272140994
1.94-2.440.19351430.17571277142096
2.44-21.130.19731410.18461283142495
Refinement TLS params.Method: refined / Origin x: 7.2404 Å / Origin y: 3.5327 Å / Origin z: 5.8203 Å
111213212223313233
T0.0702 Å2-0.0059 Å2-0.0014 Å2-0.0877 Å2-0.0081 Å2--0.0585 Å2
L0.6598 °2-0.0073 °20.2318 °2-1.6521 °2-1.1163 °2--1.231 °2
S0.0315 Å °0.0403 Å °0.01 Å °-0.0152 Å °-0.0148 Å °0.0403 Å °0.0095 Å °0.014 Å °-0.0196 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 30
2X-RAY DIFFRACTION1allA101
3X-RAY DIFFRACTION1allS1 - 36

+
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